Total energy calculation of high pressure selenium: The origin of incommensurate modulations in Se-IV and the instability of proposed Se-II

We present calculation of the high pressure crystal structures in selenium, including rational approximants to the recently reported incommensurate phases. We show how the incommensurate phases can be intuitively explained in terms of imaginary phonon frequencies arising from Kohn anomalies in the putative undistorted phase. We also find inconsistencies between the calculated and experimental Se-II phase - the calculations show it to be a metastable metal while the experiment finds a stable semiconductor. We propose that the experimentally reported structure is probably in error.Comment: 4 pages 4 figure

Magmatic overpressures, volatile exsolution and potential explosivity of fissure eruptions inferred via dike aspect ratios

Buoyant magmas abundant in exsolved volatiles (bubbles) drive the rapid upward-propagation of feeder dikes from magma chambers. The consequence of a feeder dike reaching the surface can result in an explosive volcanic eruption depending, partly, on the retention of volatiles. Therefore, timely detection of the vesicularity and overpressure of the magma during feeder dike ascent is critical for the prediction of the explosivity of any future eruption. In this study, we evaluated the explosivity of eruptions based on field investigations of the erupted products and the overpressure of magma in the conduit based on the dimensions of exposed feeder dikes. We found a positive correlation between the explosivity of eruptions and the magma overpressure generated in the conduit during recent fissure eruptions of Miyakejima volcano. Because the buoyancy of low-density magma produces positive overpressure at the dike’s top, feeder dikes with highly-vesiculated magmas possess high amounts of overpressure. An enlargement of the opening width of a feeder dike by magmatic overpressure results in a higher flux of vesiculated magma, which causes vigorous explosive activity. Our results suggest the possibility of forecasting the explosivity of an impending eruption if the width (or opening) of an ascending feeder dike is monitored in real-time through measurements of ground deformation and seismicity induced by the dike

Krylov Subspace Method for Molecular Dynamics Simulation based on Large-Scale Electronic Structure Theory

For large scale electronic structure calculation, the Krylov subspace method is introduced to calculate the one-body density matrix instead of the eigenstates of given Hamiltonian. This method provides an efficient way to extract the essential character of the Hamiltonian within a limited number of basis set. Its validation is confirmed by the convergence property of the density matrix within the subspace. The following quantities are calculated; energy, force, density of states, and energy spectrum. Molecular dynamics simulation of Si(001) surface reconstruction is examined as an example, and the results reproduce the mechanism of asymmetric surface dimer.Comment: 7 pages, 3 figures; corrected typos; to be published in Journal of the Phys. Soc. of Japa

Ferromagnetism in semiconductors and oxides: prospects from a ten years' perspective

Over the last decade the search for compounds combining the resources of semiconductors and ferromagnets has evolved into an important field of materials science. This endeavour has been fuelled by continual demonstrations of remarkable low-temperature functionalities found for ferromagnetic structures of (Ga,Mn)As, p-(Cd,Mn)Te, and related compounds as well as by ample observations of ferromagnetic signatures at high temperatures in a number of non-metallic systems. In this paper, recent experimental and theoretical developments are reviewed emphasising that, from the one hand, they disentangle many controversies and puzzles accumulated over the last decade and, on the other, offer new research prospects.Comment: review, 13 pages, 8 figures, 109 reference

Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins

<p>Abstract</p> <p>Background</p> <p><it>Bupleurum chinense </it>DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of <it>B. chinense</it>, but relatively little is known about saikosaponin biosynthesis. The 454 pyrosequencing technology provides a promising opportunity for finding novel genes that participate in plant metabolism. Consequently, this technology may help to identify the candidate genes involved in the saikosaponin biosynthetic pathway.</p> <p>Results</p> <p>One-quarter of the 454 pyrosequencing runs produced a total of 195, 088 high-quality reads, with an average read length of 356 bases (NCBI SRA accession SRA039388). A <it>de novo </it>assembly generated 24, 037 unique sequences (22, 748 contigs and 1, 289 singletons), 12, 649 (52.6%) of which were annotated against three public protein databases using a basic local alignment search tool (E-value ≤1e-10). All unique sequences were compared with NCBI expressed sequence tags (ESTs) (237) and encoding sequences (44) from the <it>Bupleurum </it>genus, and with a Sanger-sequenced EST dataset (3, 111). The 23, 173 (96.4%) unique sequences obtained in the present study represent novel <it>Bupleurum </it>genes. The ESTs of genes related to saikosaponin biosynthesis were found to encode known enzymes that catalyze the formation of the saikosaponin backbone; 246 cytochrome P450 (<it>P450</it>s) and 102 glycosyltransferases (<it>GT</it>s) unique sequences were also found in the 454 dataset. Full length cDNAs of 7 <it>P450</it>s and 7 uridine diphosphate <it>GT</it>s (<it>UGT</it>s) were verified by reverse transcriptase polymerase chain reaction or by cloning using 5' and/or 3' rapid amplification of cDNA ends. Two <it>P450</it>s and three <it>UGT</it>s were identified as the most likely candidates involved in saikosaponin biosynthesis. This finding was based on the coordinate up-regulation of their expression with <it>β-AS </it>in methyl jasmonate-treated adventitious roots and on their similar expression patterns with <it>β-AS </it>in various <it>B. chinense </it>tissues.</p> <p>Conclusions</p> <p>A collection of high-quality ESTs for <it>B. chinense </it>obtained by 454 pyrosequencing is provided here for the first time. These data should aid further research on the functional genomics of <it>B. chinense </it>and other <it>Bupleurum </it>species. The candidate genes for enzymes involved in saikosaponin biosynthesis, especially the <it>P450</it>s and <it>UGT</it>s, that were revealed provide a substantial foundation for follow-up research on the metabolism and regulation of the saikosaponins.</p

Geochemistry of lavas from the 2005–2006 eruption at the East Pacific Rise, 9°46′N–9°56′N : implications for ridge crest plumbing and decadal changes in magma chamber compositions

Author Posting. © American Geophysical Union, 2010. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 11 (2010): Q05T09, doi:10.1029/2009GC002977.Detailed mapping, sampling, and geochemical analyses of lava flows erupted from an ∼18 km long section of the northern East Pacific Rise (EPR) from 9°46′N to 9°56′N during 2005–2006 provide unique data pertaining to the short-term thermochemical changes in a mid-ocean ridge magmatic system. The 2005–2006 lavas are typical normal mid-oceanic ridge basalt with strongly depleted incompatible trace element patterns with marked negative Sr and Eu/Eu* anomalies and are slightly more evolved than lavas erupted in 1991–1992 at the same location on the EPR. Spatial geochemical differences show that lavas from the northern and southern limits of the 2005–2006 eruption are more evolved than those erupted in the central portion of the fissure system. Similar spatial patterns observed in 1991–1992 lavas suggest geochemical gradients are preserved over decadal time scales. Products of northern axial and off-axis fissure eruptions are consistent with the eruption of cooler, more fractionated lavas that also record a parental melt component not observed in the main suite of 2005–2006 lavas. Radiogenic isotopic ratios for 2005–2006 lavas fall within larger isotopic fields defined for young axial lavas from 9°N to 10°N EPR, including those from the 1991–1992 eruption. Geochemical data from the 2005–2006 eruption are consistent with an invariable mantle source over the spatial extent of the eruption and petrogenetic processes (e.g., fractional crystallization and magma mixing) operating within the crystal mush zone and axial magma chamber (AMC) before and during the 13 year repose period. Geochemical modeling suggests that the 2005–2006 lavas represent differentiated residual liquids from the 1991–1992 eruption that were modified by melts added from deeper within the crust and that the eruption was not initiated by the injection of hotter, more primitive basalt directly into the AMC. Rather, the eruption was driven by AMC pressurization from persistent or episodic addition of more evolved magma from the crystal mush zone into the overlying subridge AMC during the period between the two eruptions. Heat balance calculations of a hydrothermally cooled AMC support this model and show that continual addition of melt from the mush zone was required to maintain a sizable AMC over this time interval.This work has been supported by NSF grants OCE‐0525863 and OCE‐0732366 (D. J. Fornari and S. A. Soule), OCE‐0636469 (K. H. Rubin), and OCE‐ 0138088 (M. R. Perfit), as well as postdoctoral fellowship funds from the University of Florida