Quantum ESPRESSO toward the exascale.

Quantum ESPRESSO is an open-source distribution of computer codes for quantum-mechanical materials modeling, based on density-functional theory, pseudopotentials, and plane waves, and renowned for its performance on a wide range of hardware architectures, from laptops to massively parallel computers, as well as for the breadth of its applications. In this paper, we present a motivation and brief review of the ongoing effort to port Quantum ESPRESSO onto heterogeneous architectures based on hardware accelerators, which will overcome the energy constraints that are currently hindering the way toward exascale computing.

LiGen: a high performance workflow for chemistry driven de novo design.

Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation.

Use of experimental design to optimize docking performance: the case of LiGenDock, the docking module of LiGen, a new de novo design program.

On route toward a novel de novo design program, called LiGen, we developed a docking program, LiGenDock, based on pharmacophore models of binding sites, including a non-enumerative docking algorithm. In this paper, we present the functionalities of LiGenDock and its accompanying module LiGenPocket, aimed at the binding site analysis and structure-based pharmacophore definition. We also report the optimization procedure we have carried out to improve the cognate docking and virtual screening performance of LiGenDock.

Hydroxyl-rich beta-sheet adhesion to the gold surface in water by first-principle simulations.

Proteins able to recognize inorganic surfaces are of paramount importance for living organisms. Mimicking nature, surface-recognizing proteins and peptides have also been man-made by combinatorial biochemistry. However, to date the recognition mechanisms remain elusive, and the underlying physicochemical principles are still unknown.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License.

Acidification of three-dimensional emeraldine polymers: Search for minimum energy paths from base to salt.

We present a numerical simulation of the HCl acidification process of a three-dimensional semiconducting emeraldine base (EB) polymer leading to the corresponding metallic emeraldine salt form. We have searched minimum energy paths connecting the initial configuration, composed of two EB polymer chains per cell each one attached by two HCl molecules, with the Pc2a polaronic configuration which is the final state of the acidification process. For this aim, the variational nudged elastic band method has been adopted.

Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations.

The infrared and Raman spectra of naphthalene crystal with inclusion of anharmonic effects have been calculated by adopting the generalized variational density functional perturbation theory in the framework of Car-Parrinello molecular dynamics simulations. The computational approach has been generalized for cells of arbitrary shape. The intermolecular interactions have been analyzed with and without the van der Waals corrections, showing the importance of such interactions in the naphthalene crystal to reproduce the structural, dynamical, and spectroscopic properties.

Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spectroscopy.

Attempts to resolve the energy-level structure of single DNA molecules by scanning tunnelling spectroscopy span over the past two decades, owing to the unique ability of this technique to probe the local density of states of objects deposited on a surface. Nevertheless, success was hindered by extreme technical difficulties in stable deposition and reproducibility. Here, by using scanning tunnelling spectroscopy at cryogenic temperature, we disclose the energy spectrum of poly(G)-poly(C) DNA molecules deposited on gold.

Optical properties of emeraldine salt polymers from ab initio calculations: comparison with recent experimental data.

We present the absorption coefficient alpha(omega), the transverse dielectric function epsilon(omega), the optical conductivity sigma(omega), and the reflectance R(omega) calculated for an emeraldine salt conducting polymer in its crystalline 3D polaronic structure. We utilize Kohn-Sham density functional theory (DFT) electronic wavefunctions and energies implemented in the expression of the macroscopic transverse dielectric function in the framework of the band theory without the electron-hole interaction. Contributions of intra-band transitions are taken into account by adding a Drude-like term to the dielectric function calculated ab initio.

Full configuration interaction approach to the few-electron problem in artificial atoms.

We present a new high performance configuration interaction code optimally designed for the calculation of the lowest-energy eigenstates of a few electrons in semiconductor quantum dots (also called artificial atoms) in the strong interaction regime. The implementation relies on a single-particle representation, but it is independent of the choice of the single-particle basis and, therefore, of the details of the device and configuration of external fields. Assuming no truncation of the Fock space of Slater determinants generated from the chosen single-particle basis, the code may tackle regimes where Coulomb interaction very effectively mixes many determinants.

Surface trapped excess electrons on ice.

Local trapping of excess electrons at the surface of solid water systems has recently been observed in large water clusters and at the ice/vacuum interface. The existence of stable surface-bound states for the excess electron may have important implications in atmospheric chemistry, electrochemistry, and radiation physics. By means of first-principles molecular dynamics we find that excess electrons induce a structural reconstruction of the ice surface on a time scale of a fraction of a picosecond.

High-pressure dissociation of crystalline para-diiodobenzene: optical experiments and Car-Parrinello calculations.

We have investigated the high-pressure properties of the molecular crystal para-diiodobenzene, by combining optical absorption, reflectance, and Raman experiments with Car-Parrinello simulations. The optical absorption edge exhibits a large red shift from 4 eV at ambient conditions to about 2 eV near 30 GPa. Reflectance measurements up to 80 GPa indicate a redistribution of oscillator strength toward the near-infrared.

Electronic and transport properties of artificial gold chains.

We study the electronic and transport properties of artificial Au atomic chains on a NiAl(110) surface template using state-of-the-art first principles calculations. Au chains display remarkable one-dimensional electronic properties that can be tuned by the selective adsorption of small molecules: a single CO group is shown to modulate the electronic wave functions, acting as a "chemical scissor" along the chain, to strongly modify the coherent transport properties of the system, and to help design one-dimensional nanodevices through artificial profiling of energy barriers.