119 research outputs found
Direct Observation of Site-specific Valence Electronic Structure at Interface: SiO2/Si Interface
Atom specific valence electronic structures at interface are elucidated
successfully using soft x-ray absorption and emission spectroscopy. In order to
demonstrate the versatility of this method, we investigated SiO2/Si interface
as a prototype and directly observed valence electronic states projected at the
particular atoms of the SiO2/Si interface; local electronic structure strongly
depends on the chemical states of each atom. In addition we compared the
experimental results with first-principle calculations, which quantitatively
revealed the interfacial properties in atomic-scale.Comment: 4 pages, 3 figure
Molecular structural order and anomalies in liquid silica
The present investigation examines the relationship between structural order,
diffusivity anomalies, and density anomalies in liquid silica by means of
molecular dynamics simulations. We use previously defined orientational and
translational order parameters to quantify local structural order in atomic
configurations. Extensive simulations are performed at different state points
to measure structural order, diffusivity, and thermodynamic properties. It is
found that silica shares many trends recently reported for water [J. R.
Errington and P. G. Debenedetti, Nature 409, 318 (2001)]. At intermediate
densities, the distribution of local orientational order is bimodal. At fixed
temperature, order parameter extrema occur upon compression: a maximum in
orientational order followed by a minimum in translational order. Unlike water,
however, silica's translational order parameter minimum is broad, and there is
no range of thermodynamic conditions where both parameters are strictly
coupled. Furthermore, the temperature-density regime where both structural
order parameters decrease upon isothermal compression (the structurally
anomalous regime) does not encompass the region of diffusivity anomalies, as
was the case for water.Comment: 30 pages, 8 figure
Transformation Pathways of Silica under High Pressure
Concurrent molecular dynamics simulations and ab initio calculations show
that densification of silica under pressure follows a ubiquitous two-stage
mechanism. First, anions form a close-packed sub-lattice, governed by the
strong repulsion between them. Next, cations redistribute onto the interstices.
In cristobalite silica, the first stage is manifest by the formation of a
metastable phase, which was observed experimentally a decade ago, but never
indexed due to ambiguous diffraction patterns. Our simulations conclusively
reveal its structure and its role in the densification of silica.Comment: 14 pages, 4 figure
Path integral Monte Carlo simulations of silicates
We investigate the thermal expansion of crystalline SiO in the --
cristobalite and the -quartz structure with path integral Monte Carlo
(PIMC) techniques. This simulation method allows to treat low-temperature
quantum effects properly. At temperatures below the Debye temperature, thermal
properties obtained with PIMC agree better with experimental results than those
obtained with classical Monte Carlo methods.Comment: 27 pages, 10 figures, Phys. Rev. B (in press
Prospects of Transition Interface Sampling simulations for the theoretical study of zeolite synthesis
The transition interface sampling (TIS) technique allows to overcome large
free energy barriers within reasonable simulation time, which is impossible for
straightforward molecular dynamics. Still, the method does not impose an
artificial driving force, but it surmounts the timescale problem by an
importance sampling of true dynamical pathways. Recently, it was shown that the
efficiency of TIS to calculate reaction rates is less sensitive to the choice
of reaction coordinate than those of the standard free energy based techniques.
This could be an important advantage in complex systems for which a good
reaction coordinate is usually very difficult to find. We explain the
principles of this method and discuss some of the promising applications
related to zeolite formation.Comment: 9 pages, accepted for publication in Phys. Chem. Chem. Phys. for the
special issue of the CECAM workshop: Computational aspects of building
blocks, nucleation, and synthesis of porous materials Aug. 29 2006 to Aug. 31
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Genome-Wide Identification of Polycomb Target Genes Reveals a Functional Association of Pho with Scm in Bombyx mori
Polycomb group (PcG) proteins are evolutionarily conserved chromatin modifiers and act together in three multimeric complexes, Polycomb repressive complex 1 (PRC1), Polycomb repressive complex 2 (PRC2), and Pleiohomeotic repressive complex (PhoRC), to repress transcription of the target genes. Here, we identified Polycomb target genes in Bombyx mori with holocentric centromere using genome-wide expression screening based on the knockdown of BmSCE, BmESC, BmPHO, or BmSCM gene, which represent the distinct complexes. As a result, the expressions of 29 genes were up-regulated after knocking down 4 PcG genes. Particularly, there is a significant overlap between targets of BmPho (331 out of 524) and BmScm (331 out of 532), and among these, 190 genes function as regulator factors playing important roles in development. We also found that BmPho, as well as BmScm, can interact with other Polycomb components examined in this study. Further detailed analysis revealed that the C-terminus of BmPho containing zinc finger domain is involved in the interaction between BmPho and BmScm. Moreover, the zinc finger domain in BmPho contributes to its inhibitory function and ectopic overexpression of BmScm is able to promote transcriptional repression by Gal4-Pho fusions including BmScm-interacting domain. Loss of BmPho expression causes relocalization of BmScm into the cytoplasm. Collectively, we provide evidence of a functional link between BmPho and BmScm, and propose two Polycomb-related repression mechanisms requiring only BmPho associated with BmScm or a whole set of PcG complexes
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