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. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented.

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. In particular, we applied the design of experiments (DoE) methodology to screen the set of user-adjustable parameters to identify those having the largest influence on the accuracy of the results (which ensure the best performance in pose prediction and in virtual screening approaches) and then to choose their optimal values. The results are also compared with those obtained by two popular docking programs, namely, Glide and AutoDock for pose prediction, and Glide and DOCK6 for Virtual Screening.

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. Selectivity of gold-binding peptides (cysteine-free and rich in hydroxyl amino acids) is particularly puzzling, since the most relevant gold surface, Au(111), is known to be chemically inert and atomically flat. Using atomistic first-principle simulations we show that weak chemical interactions of dative-bond character confer to a prototype secondary structure (an antiparallel beta-sheet made of hydroxyl amino acids) and its hydration layer the capability of discriminating among gold surface sites. Our results highlight the unexpected role of hydration water in this process, suggesting that hydrophilic amino acids and their hydration shell cooperate to contribute to protein-gold surface recognition.

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. We provide a pictorial representation of the acidification process at T=0 K, monitoring the EB protonation and the evolution of the polymeric chains and of the positions of the Cl(-) counterions on the lowest potential energy surface. To include also temperature effects, we have explored the potential energy surface around the final equilibrium configuration, heating the system and following its dynamics by the Car-Parrinello procedure.

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.

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. Comparison with optical properties, recently measured on high-quality emeraldine salts (Lee, K.; Cho, S.; Park, S. H.; Heeger, A. J.; Lee, C.-W.; Lee, S. H. Nature 2006, 441, 65), and with optical absorption spectra, recorded on other emeraldine salts, is very satisfactory. The calculated spectra are discussed in terms of energy-band structure, density of states, inter- and intra-band transitions, and transverse dielectric function.

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. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

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. The tunnelling current-voltage (I-V) characteristics and their derivative (dI/dV-V) curves at 78 K exhibit a clear gap and a peak structure around the gap. Limited fluctuations in the I-V curves are observed and statistically characterized. By means of ab initio density functional theory calculations, the character of the observed peaks is generally assigned to groups of orbitals originating from the different molecular components, namely the nucleobases, the backbone and the counterions.

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. Typical strongly correlated systems lead to very large diagonalization problems; in our implementation, the secular equation is reduced to its minimal rank by exploiting the symmetry of the effective-mass interacting Hamiltonian, including square total spin. The resulting Hamiltonian is diagonalized via parallel implementation of the Lanczos algorithm. The code gives access to both wave functions and energies of first excited states. Excellent code scalability in a parallel environment is demonstrated; accuracy is tested for the case of up to eight electrons confined in a two-dimensional harmonic trap as the density is progressively diluted up to the Wigner regime, where correlations become dominant. Comparison with previous quantum Monte Carlo simulations in the Wigner regime demonstrates power and flexibility of the method.

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. The surface molecular rearrangement leads to an increase of the number of dangling OH bonds pointing towards the vacuum and to the appearance of an electrostatic barrier preventing the penetration of the electron in the bulk. Both factors imply a remarkable stability for the surface-bound excess electron, with respect to its decay into the bulk solvated state.

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. The calculations, which describe correctly the two known molecular crystal phases at ambient pressure, predict a nonmolecular metallic phase, stable at high pressure. This high-density phase is characterized by an extended three-dimensional network, in which chemically bound iodine atoms form layers connected by hydrocarbon bridges. Experimentally, Raman spectra of samples recovered after compression show vibrational modes of elemental solid iodine. This result points to a pressure-induced molecular dissociation process which leads to the formation of domains of iodine and disordered carbon.

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.