DFT study of pressure induced phase transitions in LiYF4

An investigation of the pressure induced phase transition from the scheelite phase (I41/a, Z=4) to the fergusonite-like phase (I2/a, Z=4)/LaTaO(P21/c, Z=4) of LiYF4 is presented. Employing density functional theory (DFT) within the generalized gradient approximation, the internal degrees of freedom were relaxed for a pressure range of 0 GPa to 20 Gpa. The influence of pressure on the lattice vibration spectrum of the scheelite phase (I41/a, Z=4) was evaluated using the direct approach, i.e. using force constants calculated from atomic displacements. The transition volume is in good agreement with experiment, while the transition pressure is overestimated of 6 GPa. At 20 GPa, a P21/c structure with apentacoordinated lithium cation is found to be the most stable phase. This structure is compatible with a transition driven by a Bg zone-center soft optic mode linked to a soft-acoustic mode along the [11-1] direction as observed for the proper ferroelastic transition of BiVO4

Landau theory applied to phase transitions in calcium orthotungstate and isostructural compounds

The pressure-driven tetragonal-to-monoclinic phase transition in CaWO4 and related scheelite-structured orthotungstates is analysed in terms of spontaneous strains. Based upon our previous high-pressure x-ray diffraction results and the Landau theory, it is suggested that the scheelite-to-fergusonite transition is of second order in nature.Comment: 14 pages, 3 figure

Structural and vibrational study of pseudocubic CdIn2Se4 under compression

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp5077565We report a comprehensive experimental and theoretical study of the structural and vibrational properties of a-CdIn2Se4 under compression. Angle-dispersive synchrotron X-ray diffraction and Raman spectroscopy evidence that this ordered-vacancy compound with pseudocubic structure undergoes a phase transition (7 GPa) toward a disordered rocksalt structure as observed in many other ordered-vacancy compounds. The equation of state and the pressure dependence of the Raman-active modes of this semiconductor have been determined and compared both to ab initio total energy and lattice dynamics calculations and to related compounds. Interestingly, on decreasing pressure, at similar to 2 GPa, CdIn2Se4 transforms into a spinel structure which, according to calculations, is energetically competitive with the initial pseudocubic phase. The phase behavior of this compound under compression and the structural and compressibility trends in AB(2)Se(4) selenides are discussed.This study was supported by the Spanish government MEC under Grant Nos: MAT2013-46649-C4-3-P, MAT2013-46649-C4-2-P, MAT2010-21270-C04-03/04, and CTQ2009-14596-C02-01, by MALTA Consolider Ingenio 2010 Project (CSD2007-00045) and by Generalitat Valenciana (GVA-ACOMP-2013-1012). A.M. and P.R-H. acknowledge computing time provided by Red Espanola de Supercomputacion (RES) and MALTA-Cluster, and also to S. Munoz-Rodriguez for providing a data-parsing application. J.A.S. acknowledges Juan de la Cierva fellowship program for financial support.Santamaría Pérez, D.; Gomis, O.; Pereira, ALJ.; Vilaplana Cerda, RI.; Popescu, C.; Sans Tresserras, JÁ.; Manjón Herrera, FJ.... (2014). Structural and vibrational study of pseudocubic CdIn2Se4 under compression. Journal of Physical Chemistry C. 118(46):26987-26999. https://doi.org/10.1021/jp5077565S26987269991184

Substrate specificity of the TRAMP nuclear surveillance complexes

During nuclear surveillance in yeast and human cells, the RNA exosome functions together with the TRAMP complexes. Here, the authors defined the protein composition of the TRAMP complexes and identified specific RNA binding sites for the different TRAMP components

Genome-wide search for breast cancer linkage in large Icelandic non-BRCA1/2 families

Abstract Introduction: A significant proportion of high-risk breast cancer families are not explained by mutations in known genes. Recent genome-wide searches (GWS) have not revealed any single major locus reminiscent of BRCA1 and BRCA2, indicating that still unidentified genes may explain relatively few families each or interact in a way obscure to linkage analyses. This has drawn attention to possible benefits of studying populations where genetic heterogeneity might be reduced. We thus performed a GWS for linkage on nine Icelandic multiple-case non-BRCA1/2 families of desirable size for mapping highly penetrant loci. To follow up suggestive loci, an additional 13 families from other Nordic countries were genotyped for selected markers. Methods: GWS was performed using 811 microsatellite markers providing about five centiMorgan (cM) resolution. Multipoint logarithm of odds (LOD) scores were calculated using parametric and nonparametric methods. For selected markers and cases, tumour tissue was compared to normal tissue to look for allelic loss indicative of a tumour suppressor gene. Results: The three highest signals were located at chromosomes 6q, 2p and 14q. One family contributed suggestive LOD scores (LOD 2.63 to 3.03, dominant model) at all these regions, without consistent evidence of a tumour suppressor gene. Haplotypes in nine affected family members mapped the loci to 2p23.2 to p21, 6q14.2 to q23.2 and 14q21.3 to q24.3. No evidence of a highly penetrant locus was found among the remaining families. The heterogeneity LOD (HLOD) at the 6q, 2p and 14q loci in all families was 3.27, 1.66 and 1.24, respectively. The subset of 13 Nordic families showed supportive HLODs at chromosome 6q (ranging from 0.34 to 1.37 by country subset). The 2p and 14q loci overlap with regions indicated by large families in previous GWS studies of breast cancer. Conclusions: Chromosomes 2p, 6q and 14q are candidate sites for genes contributing together to high breast cancer risk. A polygenic model is supported, suggesting the joint effect of genes in contributing to breast cancer risk to be rather common in non-BRCA1/2 families. For genetic counselling it would seem important to resolve the mode of genetic interaction

Structural and elastic properties of defect chalcopyrite HgGa2S4 under high pressure

In this work, we focus on the study of the structural and elastic properties of mercury digallium sulfide (HgGa2S4) at high pressures. This compound belongs to the family of AB(2)X(4) ordered-vacancy compounds and exhibits a tetragonal defect chalcopyrite structure. X-ray diffraction measurements at room temperature have been performed under compression up to 15.1 GPa in a diamond anvil cell. Our measurements have been complemented and compared with ab initio total energy calculations. The axial compressibility and the equation of state of the low-pressure phase of HgGa2S4 have been experimentally and theoretically determined and compared to other related ordered-vacancy compounds. The pressure dependence of the theoretical cation-anion and vacancy-anion distances and compressibilities in HgGa2S4 are reported and discussed in comparison to other related ordered-vacancy compounds. Finally, the pressure dependence of the theoretical elastic constants and elastic moduli of HgGa2S4 has been studied. Our calculations indicate that the low-pressure phase of HgGa2S4 becomes mechanically unstable above 13.8 GPa. (C) 2013 Elsevier B. V. All rights reserved.This study was supported by the Spanish government MEC under Grants No: MAT2010-21270-C04-01/03/04 and CTQ2009-14596-C02-01, by the Comunidad de Madrid and European Social Fund (S2009/PPQ-1551 4161893), by MALTA Consolider Ingenio 2010 Project (CSD2007-00045), by Generalitat Valenciana (GVA-ACOMP-2013-1012), and by the Vicerrectorado de Investigacion y Desarrollo of the Universidad Politecnica de Valencia (UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11). E.P-G., A. M., and P.R-H. acknowledge computing time provided by Red Espa ola de Supercomputacion (RES) and MALTA-Cluster. J.A.S. acknowledges Juan de la Cierva fellowship program for financial support.Gomis Hilario, O.; Santamaría-Pérez, D.; Vilaplana Cerda, RI.; Luna Molina, R.; Sans, JA.; Manjón Herrera, FJ.; Errandonea, D.... (2014). Structural and elastic properties of defect chalcopyrite HgGa2S4 under high pressure. Journal of Alloys and Compounds. 583:70-78. https://doi.org/10.1016/j.jallcom.2013.08.123S707858

Structural and vibrational properties of CdAl2S4 under high pressure: Experimental and theoretical approach

"This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp5037926.”The behavior of defect chalcopyrite CdAl2S4 at high pressures and ambient temperature has been investigated in a joint experimental and theoretical study. High-pressure X-ray diffraction and Raman scattering measurements were complemented with theoretical ab initio calculations. The equation of state and pressure dependences of the structural parameters of CdAl2S4 were determined and compared to those of other AB(2)X(4) ordered-vacancy compounds. The pressure dependence of the Raman-active mode frequencies is reported, as well as the theoretical phonon dispersion curves and phonon density of states at 1 atm. Our measurements suggest that defect chalcopyrite CdAl2S4 undergoes a phase transition above 15 GPa to a disordered-rocksalt structure, whose equation of state was also obtained up to 25 GPa. In a downstroke from 25 GPa to 1 atm, our measurements indicate that CdAl2S4 does not return to the defect chalcopyrite phase; it partially retains the disordered-rocksalt phase and partially transforms into the spinel structure. The nature of the spinel structure was confirmed by the good agreement of our experimental results with our theoretical calculations. All in all, our experimental and theoretical results provide evidence that the spinel and defect chalcopyrite phases of CdAl2S4 are competitive at 1 atm. This result opens the way to the synthesis of spinel-type CdAl2S4 at near-ambient conditions.Financial support from the Spanish Consolider Ingenio 2010 Program (Project CSD2007-00045) is acknowledged. This work was also supported by Spanish MICCIN under Project MAT2010-21270-C04-03/04 and by Vicerrectorado de Investigacion de la Universitat Politecnica de Valencia under Projects UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11. Supercomputer time was provided by the Red Espanola de Supercomputacion (RES) and the MALTA cluster. J.A.S. acknowledges the Juan de la Cierva fellowship program for financial support. AM. and P.R.-H. acknowledge S. Munoz Rodriguez for providing a data-parsing application.Sans Tresserras, JÁ.; Santamaría Pérez, D.; Popescu, C.; Gomis, O.; Manjón Herrera, FJ.; Vilaplana Cerda, RI.; Muñoz, A.... (2014). Structural and vibrational properties of CdAl2S4 under high pressure: Experimental and theoretical approach. Journal of Physical Chemistry C. 118(28):15363-15374. https://doi.org/10.1021/jp5037926S15363153741182

Phase behaviour of Ag2CrO4 under compression: Structural, vibrational, and optical properties

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp401524sWe have performed an experimental study of the crystal structure, lattice dynamics, and optical properties of silver chromate (Ag2CrO4) at ambient temperature and high pressures. In particular, the crystal structure, Raman-active phonons, and electronic band gap have been accurately determined. When the initial orthorhombic Pnma Ag2CrO4 structure (phase I) is compressed up to 4.5 GPa, a previously undetected phase (phase II) has been observed with a 0.95% volume collapse. The structure of phase II can be indexed to a similar orthorhombic cell as phase I, and the transition can be considered to be an isostructural transition. This collapse is mainly due to the drastic contraction of the a axis (1.3%). A second phase transition to phase III occurs at 13 GPa to a structure not yet determined. First-principles calculations have been unable to reproduce the isostructural phase transition, but they propose the stabilization of a spinel-type structure at 11 GPa. This phase is not detected in experiments probably because of the presence of kinetic barriers. Experiments and calculations therefore seem to indicate that a new structural and electronic description is required to model the properties of silver chromate.This study was supported by the Spanish government MEC under grants MAT2010-21270-C04-01/03/04 and CTQ2009-14596-C02-01, by the Comunidad de Madrid and European Social Fund (S2009/PPQ1551 4161893), by the MALTA Consolider Ingenio 2010 project (CSD2007-00045), and by the Vicerrectorado de Investigacion y Desarrollo of the Universidad Politecnica de Valencia (UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11). A.M. and P.R.-H. acknowledge computing time provided by Red Espanola de Supercomputacion (RES) and MALTA-Cluster. J.A.S. acknowledges Juan de la Cierva Fellowship Program for its financial support. Diamond and ALBA Synchrotron Light Sources are acknowledged for provisions of beam time. We also thank Drs. Peral, Popescu, and Fauth for technical support.Santamaría Pérez, D.; Bandiello, E.; Errandonea, D.; Ruiz-Fuertes, J.; Gomis Hilario, O.; Sans, JÁ.; Manjón Herrera, FJ.... (2013). Phase behaviour of Ag2CrO4 under compression: Structural, vibrational, and optical properties. Journal of Physical Chemistry C. 117(23):12239-12248. https://doi.org/10.1021/jp401524sS12239122481172

Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism

The crystal structure of BT2081 from B. thetaiotaomicron reveals a two-domain protein with a putative carbohydrate-binding site in the C-­terminal domain

Lattice dynamics study of HgGa2Se4 at high pressures

We report on Raman scattering measurements in mercury digallium selenide (HgGa2Se4) up to 25 GPa. We also performed, for the low-pressure defect-chalcopyrite structure, lattice-dynamics ab initio calculations at high pressures which agree with experiments. Measurements evidence that the semiconductor HgGa2Se4 exhibits a pressure-induced phase transition above 19 GPa to a previously undetected structure. This transition is followed by a transformation to a Raman-inactive phase above 23.4 GPa. On downstroke from 25 GPa until 2.5 GPa, a broad Raman spectrum was observed, which has been attributed to a fourth phase, and whose pressure dependence was followed during a second upstroke. Candidate structures for the three phases detected under compression are proposed. Finally, we also report and discuss the decomposition of the sample by laser heating at pressures close to 19 GPa. As possible products of decomposition, we have identified at least the formation of trigonal selenium nanoclusters and cinnabar-type HgSe.This study was supported by the Spanish government MEC under Grant No. MAT2010-21270-004-01/03/04, by MALTA Consolider Ingenio 2010 project (CSD2007-00045), by Generalitat Valenciana through project GVA-ACOMP-2013-012, and by the Vicerrectorado de Investigacion y Desarrollo of the Universidad Politecnica de Valencia (UPV2011-0966 and UPV2011-0914). E.P.-G., J.L.-S., A.M., and P.R.-H. acknowledge computing time provided by Red Espanola de Super-computacion (RES) and MALTA-Cluster.Vilaplana Cerda, RI.; Gomis Hilario, O.; Manjón Herrera, FJ.; Ortiz, HM.; Pérez González, E.; López Solano, J.; Rodríguez Hernández, P.... (2013). Lattice dynamics study of HgGa2Se4 at high pressures. Journal of Physical Chemistry C. 117(30):15773-15781. https://doi.org/10.1021/jp402493rS15773157811173