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Electronic structure, elasticity, Debye temperature and anisotropy of cubic WO3 from first-principles calculation.

ABSTRACT: The electron structure, elastic constant, Debye temperature and anisotropy of elastic wave velocity for cubic WO3 are studied using CASTEP based on density functional theory. The optimized structure is consistent with previous work and the band gap is obtained by computing the electronic structure; the top of the valence band is not at the same point as the bottom of the conduction band, which is an indirect band-gap oxide. Electronic properties are studied from the calculation of band structure, densities of states and charge densities. The bulk and shear moduli, Young's modulus, hardness and Poisson's ratio for WO3 are studied by the elastic constants. We calculated acoustic wave velocities in different directions and estimated the Debye temperature from the acoustic velocity. The anisotropy of WO3 was analysed from the point of view of a pure wave and quasi wave.

SUBMITTER: Liu X

PROVIDER: S-EPMC6030277 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Electronic structure, elasticity, Debye temperature and anisotropy of cubic WO<sub>3</sub> from first-principles calculation.

Liu Xing X Fan Hui-Qing HQ

Royal Society open science 20180620 6

The electron structure, elastic constant, Debye temperature and anisotropy of elastic wave velocity for cubic WO<sub>3</sub> are studied using CASTEP based on density functional theory. The optimized structure is consistent with previous work and the band gap is obtained by computing the electronic structure; the top of the valence band is not at the same point as the bottom of the conduction band, which is an indirect band-gap oxide. Electronic properties are studied from the calculation of ban ...[more]

PMID: 30110454

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Project description:We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in tethered particle motion (TPM) experiments, and it accounts for all the entropic forces present in such experiments. Our model has no free parameters; it characterizes DNA elasticity using information obtained in other kinds of experiments. It assumes a harmonic elastic energy function (or wormlike chain type elasticity), but our Monte Carlo calculation scheme is flexible enough to accommodate arbitrary elastic energy functions. We show how to compute both the 'looping J factor' (or equivalently, the looping free energy) for various DNA construct geometries and LacI concentrations, as well as the detailed probability density function of bead excursions. We also show how to extract the same quantities from recent experimental data on TPM, and then compare to our model's predictions. In particular, we present a new method to correct observed data for finite camera shutter time and other experimental effects. Although the currently available experimental data give large uncertainties, our first-principles predictions for the looping free energy change are confirmed to within about 1 k(B)T, for loops of length around 300 basepairs. More significantly, our model successfully reproduces the detailed distributions of bead excursion, including their surprising three-peak structure, without any fit parameters and without invoking any alternative conformation of the LacI tetramer. Indeed, the model qualitatively reproduces the observed dependence of these distributions on tether length (e.g., phasing) and on LacI concentration (titration). However, for short DNA loops (around 95 basepairs) the experiments show more looping than is predicted by the harmonic-elasticity model, echoing other recent experimental results. Because the experiments we study are done in vitro, this anomalously high looping cannot be rationalized as resulting from the presence of DNA-bending proteins or other cellular machinery. We also show that it is unlikely to be the result of a hypothetical 'open' conformation of the LacI tetramer.

Dataset Information

Electronic structure, elasticity, Debye temperature and anisotropy of cubic WO3 from first-principles calculation.

Publications

Electronic structure, elasticity, Debye temperature and anisotropy of cubic WO<sub>3</sub> from first-principles calculation.

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