Ab-initio calculations for the beta-tin diamond transition in Silicon: comparing theories with experiments

We investigate the pressure-induced metal-insulator transition from diamond to beta-tin in bulk Silicon, using quantum Monte Carlo (QMC) and density functional theory (DFT) approaches. We show that it is possible to efficiently describe many-body effects, using a variational wave function with an optimized Jastrow factor and a Slater determinant. Variational results are obtained with a small computational cost and are further improved by performing diffusion Monte Carlo calculations and an explicit optimization of molecular orbitals in the determinant. Finite temperature corrections and zero point motion effects are included by calculating phonon dispersions in both phases at the DFT level. Our results indicate that the theoretical QMC (DFT) transition pressure is significantly larger (smaller) than the accepted experimental value. We discuss the limitation of DFT approaches due to the choice of the exchange and correlation functionals and the difficulty to determine consistent pseudopotentials within the QMC framework, a limitation that may significantly affect the accuracy of the technique.Comment: 13 pages, 9 figures, submitted to the Physical Review B on October 2

The nonlinear anomalous lattice elasticity associated with the high-pressure phase transition in spodumene: A high precission static compression study

The high-pressure behavior of the lattice elasticity of spodumene, LiAlSi2O6, was studied by static compression in a diamond-anvil cell up to 9.3 GPa. Investigations by means of single-crystal XRD and Raman spectroscopy within the hydrostatic limits of the pressure medium focus on the pressure ranges around similar to 3.2 and similar to 7.7 GPa, which have been reported previously to comprise two independent structural phase transitions. While our measurements confirm the well-established first-order C2/c-P2(1)/c transformation at 3.19 GPa (with 1.2% volume discontinuity and a hysteresis between 0.02 and 0.06 GPa), both unit-cell dimensions and the spectral changes observed in high-pressure Raman spectra give no evidence for structural changes related to a second phase transition. Monoclinic lattice parameters and unit-cell volumes at in total 59 different pressure points have been used to re-calculate the lattice-related properties of spontaneous strain, volume strain, and the bulk moduli as a function of pressure across the transition. A modified Landau free energy expansion in terms of a one component order parameter has been developed and tested against these experimentally determined data. The Landau solution provides a much better reproduction of the observed anomalies than any equation-of-state fit to data sets truncated below and above P (tr), thus giving Landau parameters of K (0) = 138.3(2) GPa, K' = 7.46(5), lambda (V) = 33.6(2) GPa, a = 0.486(3), b = -29.4(6) GPa and c = 551(11) GPa

Compressional behaviour of paulingite -A sub-nanosponge?

Introduction Paulingite is a rare zeolite, found in vesicles in basalt flows, with ideal chemical formula: (K,Na,Ca0.5,Ba0.5,)10(Al10Si32O84)\uf0d730H2O (Z = 16). Its crystal structure was solved and refined by Gordon et al. (1966) in the space group Im3m, showing the complex framework topology of this zeolite designated with the IZA-code \u201cPAU\u201d. A structural re-investigation was carried out later by Lengauer et al. (1997). The tetrahedral framework topology of paulingite is characterized by a connecting double 8-ring (D8R), which links alternatively the \uf061-cage (truncated cuboctahedron) and the \uf067-cage (gmelinite-type cage). The D8R, the \uf061-cage and the \uf067-cage represent the building-block units of the PAU framework. The main voids systems of the PAU framework are represented by two parallel (and independent) sets of a three-dimensional channel systems oriented along the principal axes and shifted \ubd, \ubd, \ubd against each other. Along the threefold axis of the PAU framework, a second type of a channel system exists, which is built up by the \uf061-cage and a modified form of the levyne-cage only observed in the paulingite topology (i.e., \uf070-cage) (Lengauer et al. 1997). The PAU framework type is considered as one of the most complex in the mineral world. In all the structure refinements so far reported, the Si/Al-distribution was modelled as completely disordered. A series of extra-framework sites were located. The long \u201cfree diameters\u201d of the channel systems make this zeolite a good candidate to explore the P-induced penetration of external molecular species in response to hydrostatic compression (e.g., Gatta 2008, 2010). Experimental Methods A sample of paulingite from Vina\u159ick\ue1 hora Hill near Kladno (Czech Republic) was used for our experiments. A sample from the same locality was previously used by Lengauer et al. (1997) for their chemical and crystallographic study. Electron microprobe analysis (in wavelength dispersive mode) along with thermo-gravimetric data yielded the following chemical formula: (Ca2.57K2.28Ba1.39Na0.38)(Alll.55Si30.59O84)x 27H2O (Lengauer et al. 1997). A single-crystal of paulingite, free of defects under polarized microscope, was selected for the in-situ diffraction experiment with a diamond anvil cell (DAC). Intensity diffraction data were first collected at room-conditions with a Stoe StadiVari diffractometer with an high-brilliance Incoatec Mo I\ub5s X-ray-source and a Dectris Pilatus 300K pixel detector. The structure refinement was performed in the space group Im3m using the structural model of Lengauer et al. (1997) to a R1 = 0.0802 for 2477 Fo > 4\uf073(Fo) and 255 refined parameters. The same crystal was used for the high-pressure (HP) experiment performed using an ETH-type DAC. The experiment was conducted using a mixture of methanol:ethanol = 4:1 as hydrostatic P-transmitting medium, along with a few ruby chips serving as P-calibrant. Unit-cell parameters were measured between 0.0001 (crystal in the DAC with no pressure medium) and 3.3(1) GPa. Two further in-situ HP synchrotron X-ray powder diffraction experiments were performed at the X7A beamline at the national synchrotron light source (NSLS) at Brookhaven National Laboratory (BNL). A gas-proportional position-sensitive detector was used. The wavelength of the incident beam was 0.60046(1) \uc5 as determined from a CeO2 standard. A modified Merrill\u2013Bassett DAC was used to generate HP-conditions. Two compression experiments with two different P-fluids were performed, i.e., with silicon-oil and a mix of methanol:ethanol:water = 16:3:1. The evolution of the cell parameters with P for all three pressure-transmitting media is shown in Fig. 1. Results and Discussion The evolution of the unit-cell parameters of paulingite with P based on our experiments with different P-media show a dramatic role played by the compression-fluid on the behavior of this zeolite (Figure 1). Due to its polymeric nature, silicon-oil can be unambiguously considered as a \u201cnon-penetrating\u201d P-medium. The compressional pattern obtained with silicon-oil describes the actual elastic behavior of paulingite (i.e., without any interference of the P-fluid). The Birch-Murnaghan equation of state truncated to the second-order was used to fit the experimental P-V data within the P-range investigated (i.e. 0.0001-2.5(1) GPa), giving the following isothermal bulk modulus: K0 = \uf0620-1 = V0(\uf0b6P/\uf0b6V) = 18(1) GPa (\uf0620 = 0.055(3) GPa-1). Paulingite appears to be one of the softest crystalline inorganic materials reported so far. The HP-data obtained using the mix methanol:ethanol = 4:1 and methanol:ethanol:water = 16:3:1 suggest that these molecules act as \u201cpenetrating\u201d media in response to the applied pressure. The P-induced penetration of external molecules through the cavities leads to a lower bulk compressibility of paulingite. The different compressibility of paulingite in methanol:ethanol = 4:1 and methanol:ethanol:water = 16:3:1 mix reflects the different penetrability of the media. Water is clearly the most penetrating molecule in response to the applied pressure, and so in general an hydrous medium tends to decrease significantly the compressional pattern of a porous material (Gatta 2008, 2010). Interestingly, the P-induced penetration of external molecules in paulingite structure does not lead to spectacular expansion (with a drastic discontinuity in the P-V behaviour), as observed for example in natrolite (Lee et al. 2002). The complexity of the paulingite structure did not allow to perform structure refinement at high pressure, hindering a description of the penetration mechanisms at the atomic scale. A series of further experiments are in progress in order to explore: 1) the reversibility of the P-induced penetration of aforementioned molecules and 2) the behavior of this zeolite as a \u201csub-nanosponge\u201d for other small molecules in response to hydrostatic pressure. Acknowledgment GDG acknowledges the Italian Ministry of Education, MIUR-Project: \u201cFuturo in Ricerca 2012 - ImPACT- RBFR12CLQD\u201d. References Gatta, G.D. (2008) Does porous mean soft? On the elastic behaviour and structural evolution of zeolites under pressure. Zeitschrift f\ufcr Kristallographie, 223, 160\u2013170. Gatta, G.D. (2010) Extreme deformation mechanisms in open-framework silicates at high-pressure: Evidence of anomalous inter-tetrahedral angles. Microporous and Mesoporous Materials, 128, 78\u201384. Gordon, E.K., Samson, S. and Kamb, W.B. (1966). Crystal structure of the zeolite paulingite. Science, 154, 1004-1007. Lee, Y., Vogt, T., Hriljac, J.A., Parise, J.B., and Artioli, G. (2002) Pressure-Induced Volume Expansion of Zeolites in the Natrolite Family. Journal of the American Chemical Society, 124, 5466-5475. Lengauer, C.L., Giester, G., and Tillmanns, E. (1997). Mineralogical characterization of paulingite from Vinarick\ue1 Hora, Czech Republic. Mineralogical Magazine, 61, 591-606

Finite strain Landau theory of high pressure phase transformations

The properties of materials near structural phase transitions are often successfully described in the framework of Landau theory. While the focus is usually on phase transitions, which are induced by temperature changes approaching a critical temperature T-c, here we will discuss structural phase transformations driven by high hydrostatic pressure, as they are of major importance for understanding processes in the interior of the earth. Since at very high pressures the deformations of a material are generally very large, one needs to apply a fully nonlinear description taking physical as well as geometrical nonlinearities (finite strains) into account. In particular it is necessary to retune conventional Landau theory to describe such phase transitions. In Troster et al (2002 Phys. Rev. Lett. 88 55503) we constructed a Landau-type free energy based on an order parameter part, an order parameter-(finite) strain coupling and a nonlinear elastic term. This model provides an excellent and efficient framework for the systematic study of phase transformations for a wide range of materials up to ultrahigh pressures

Barx1-Mediated Inhibition of Wnt Signaling in the Mouse Thoracic Foregut Controls Tracheo-Esophageal Septation and Epithelial Differentiation

Mesenchymal cells underlying the definitive endoderm in vertebrate animals play a vital role in digestive and respiratory organogenesis. Although several signaling pathways are implicated in foregut patterning and morphogenesis, and despite the clinical importance of congenital tracheal and esophageal malformations in humans, understanding of molecular mechanisms that allow a single tube to separate correctly into the trachea and esophagus is incomplete. The homoebox gene Barx1 is highly expressed in prospective stomach mesenchyme and required to specify this organ. We observed lower Barx1 expression extending contiguously from the proximal stomach domain, along the dorsal anterior foregut mesenchyme and in mesenchymal cells between the nascent esophagus and trachea. This expression pattern exactly mirrors the decline in Wnt signaling activity in late development of the adjacent dorsal foregut endoderm and medial mainstem bronchi. The hypopharynx in Barx1−/− mouse embryos is abnormally elongated and the point of esophago-tracheal separation shows marked caudal displacement, resulting in a common foregut tube that is similar to human congenital tracheo-esophageal fistula and explains neonatal lethality. Moreover, the Barx1−/− esophagus displays molecular and cytologic features of respiratory endoderm, phenocopying abnormalities observed in mouse embryos with activated ß-catenin. The zone of canonical Wnt signaling is abnormally prolonged and expanded in the proximal Barx1−/− foregut. Thus, as in the developing stomach, but distinct from the spleen, Barx1 control of thoracic foregut specification and tracheo-esophageal septation is tightly associated with down-regulation of adjacent Wnt pathway activity

Systematic Detection of Epistatic Interactions Based on Allele Pair Frequencies

Epistatic genetic interactions are key for understanding the genetic contribution to complex traits. Epistasis is always defined with respect to some trait such as growth rate or fitness. Whereas most existing epistasis screens explicitly test for a trait, it is also possible to implicitly test for fitness traits by searching for the over- or under-representation of allele pairs in a given population. Such analysis of imbalanced allele pair frequencies of distant loci has not been exploited yet on a genome-wide scale, mostly due to statistical difficulties such as the multiple testing problem. We propose a new approach called Imbalanced Allele Pair frequencies (ImAP) for inferring epistatic interactions that is exclusively based on DNA sequence information. Our approach is based on genome-wide SNP data sampled from a population with known family structure. We make use of genotype information of parent-child trios and inspect 3×3 contingency tables for detecting pairs of alleles from different genomic positions that are over- or under-represented in the population. We also developed a simulation setup which mimics the pedigree structure by simultaneously assuming independence of the markers. When applied to mouse SNP data, our method detected 168 imbalanced allele pairs, which is substantially more than in simulations assuming no interactions. We could validate a significant number of the interactions with external data, and we found that interacting loci are enriched for genes involved in developmental processes

Forty-Three Loci Associated with Plasma Lipoprotein Size, Concentration, and Cholesterol Content in Genome-Wide Analysis

While conventional LDL-C, HDL-C, and triglyceride measurements reflect aggregate properties of plasma lipoprotein fractions, NMR-based measurements more accurately reflect lipoprotein particle concentrations according to class (LDL, HDL, and VLDL) and particle size (small, medium, and large). The concentrations of these lipoprotein sub-fractions may be related to risk of cardiovascular disease and related metabolic disorders. We performed a genome-wide association study of 17 lipoprotein measures determined by NMR together with LDL-C, HDL-C, triglycerides, ApoA1, and ApoB in 17,296 women from the Women's Genome Health Study (WGHS). Among 36 loci with genome-wide significance (P<5×10−8) in primary and secondary analysis, ten (PCCB/STAG1 (3q22.3), GMPR/MYLIP (6p22.3), BTNL2 (6p21.32), KLF14 (7q32.2), 8p23.1, JMJD1C (10q21.3), SBF2 (11p15.4), 12q23.2, CCDC92/DNAH10/ZNF664 (12q24.31.B), and WIPI1 (17q24.2)) have not been reported in prior genome-wide association studies for plasma lipid concentration. Associations with mean lipoprotein particle size but not cholesterol content were found for LDL at four loci (7q11.23, LPL (8p21.3), 12q24.31.B, and LIPG (18q21.1)) and for HDL at one locus (GCKR (2p23.3)). In addition, genetic determinants of total IDL and total VLDL concentration were found at many loci, most strongly at LIPC (15q22.1) and APOC-APOE complex (19q13.32), respectively. Associations at seven more loci previously known for effects on conventional plasma lipid measures reveal additional genetic influences on lipoprotein profiles and bring the total number of loci to 43. Thus, genome-wide associations identified novel loci involved with lipoprotein metabolism—including loci that affect the NMR-based measures of concentration or size of LDL, HDL, and VLDL particles—all characteristics of lipoprotein profiles that may impact disease risk but are not available by conventional assay