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. AVAILABILITY: https://github.com/BioinfoUNIBA/REDItools2 . CONCLUSIONS: HPC-REDItools is dramatically faster than the previous version, REDItools, enabling big-data analysis by means of a MPI-based implementation and scaling almost linearly with the number of available cores.

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. Here we investigate the primary charge-transfer process in a supramolecular triad, a prototypical artificial reaction centre. Combining high time-resolution femtosecond spectroscopy and time-dependent density functional theory, we provide compelling evidence that the driving mechanism of the photoinduced current generation cycle is a correlated wavelike motion of electrons and nuclei on a timescale of few tens of femtoseconds. We highlight the fundamental role of the interface between chromophore and charge acceptor in triggering the coherent wavelike electron-hole splitting.