HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis.

Background: RNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversity. The automatic detection of RNA-editing from RNA-seq data is computational intensive and limited to small data sets, thus preventing a reliable genome-wide characterisation of such process.

Results: In this work we introduce HPC-REDItools, an upgraded tool for accurate RNA-editing events discovery from large dataset repositories.

Determination of the electronic energy levels of colloidal nanocrystals using field-effect transistors and Ab-initio calculations.

Colloidal nanocrystals electronic energy levels are determined by strong size-dependent quantum confinement. Understanding the configuration of the energy levels of nanocrystal superlattices is vital in order to use them in heterostructures with other materials. A powerful method is reported to determine the energy levels of PbS nanocrystal assemblies by combining the utilization of electric-double-layer-gated transistors and advanced ab-initio theory.

Quantum coherence controls the charge separation in a prototypical artificial light-harvesting system.

The efficient conversion of light into electricity or chemical fuels is a fundamental challenge. In artificial photosynthetic and photovoltaic devices, this conversion is generally thought to happen on ultrafast, femto-to-picosecond timescales and to involve an incoherent electron transfer process. In some biological systems, however, there is growing evidence that the coherent motion of electronic wavepackets is an essential primary step, raising questions about the role of quantum coherence in artificial devices.

Photoexcitation of a light-harvesting supramolecular triad: a time-dependent DFT study.

We present the first time-dependent density functional theory (TDDFT) calculation on a light-harvesting triad carotenoid-diaryl-porphyrin-C(60). Besides the numerical challenge that the ab initio study of the electronic structure of such a large system presents, we show that TDDFT is able to provide an accurate description of the excited-state properties of the system. In particular, we calculate the photoabsorption spectrum of the supramolecular assembly, and we provide an interpretation of the photoexcitation mechanism in terms of the properties of the component moieties.