Defect calculations in semiconductors through a dielectric-dependent hybrid DFT functional: The case of oxygen vacancies in metal oxides.

We investigate the behavior of oxygen vacancies in three different metal-oxide semiconductors (rutile and anatase TiO2, monoclinic WO3, and tetragonal ZrO2) using a recently proposed hybrid density-functional method in which the fraction of exact exchange is material-dependent but obtained ab initio in a self-consistent scheme. In particular, we calculate charge-transition levels relative to the oxygen-vacancy defect and compare computed optical and thermal excitation/emission energies with the available experimental results, shedding light on the underlying excitation mechanisms and related materials properties. We find that this novel approach is able to reproduce not only ground-state properties and band structures of perfect bulk oxide materials but also provides results consistent with the optical and electrical behavior observed in the corresponding substoichiometric defective systems.

Communication: Hole localization in Al-doped quartz SiO2 within ab initio hybrid-functional DFT.

We investigate the long-standing problem of hole localization at the Al impurity in quartz SiO2, using a relatively recent DFT hybrid-functional method in which the exchange fraction is obtained ab initio, based on an analogy with the static many-body COHSEX approximation to the electron self-energy. As the amount of the admixed exact exchange in hybrid functionals has been shown to be determinant for properly capturing the hole localization, this problem constitutes a prototypical benchmark for the accuracy of the method, allowing one to assess to what extent self-interaction effects are avoided. We obtain good results in terms of description of the charge localization and structural distortion around the Al center, improving with respect to the more popular B3LYP hybrid-functional approach. We also discuss the accuracy of computed hyperfine parameters, by comparison with previous calculations based on other self-interaction-free methods, as well as experimental values. We discuss and rationalize the limitations of our approach in computing defect-related excitation energies in low-dielectric-constant insulators.

Temperature profoundly affects ataxin-3 fibrillogenesis.

Ataxin-3 (AT3) triggers spinocerebellar ataxia type 3 when it carries a polyglutamine stretch expanded beyond a critical threshold. By Fourier transform infrared spectroscopy and atomic force microscopy we previously showed that a normal (AT3Q24) and an expanded (AT3Q55) variant were capable of evolving into oligomers and protofibrils at 37 °C, whereas only the expanded form generated irreversibly aggregated fibrils that also were associated with a network of side-chain glutamine hydrogen bonding [Natalello et al. (2011) PLoS One. 6:e18789]. We report here that AT3Q24, when gradually heated up to 85 °C, undergoes aggregation similar to that observed at 37 °C; in contrast, AT3Q55 only generates large, amorphous aggregates. We propose a possible interpretation of the mechanism by which temperature affects the outcome of fibrillogenesis.

Biosensors and molecular imaging.

The increase in the understanding of the physical and functional properties of the biological material, from the cellular level down to single molecules, owes its success to the development of suitable high-sensitivity platforms to image the biomaterial and analyze its response to specific stimuli. Imaging has indeed reached molecular capabilities, thanks to optical or magnetic markers [1], to the atomic force microscopy (AFM) in surface reconstruction [2], and is nearing success in three-dimensional (3-D) reconstruction thanks to X-ray holography [3].