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A Full Configuration Interaction (Full-CI) algorithm is described. It is an integral-driven approach, with on-the-fly computation of the string-excitation lists that realize the application of the Hamiltonian to the Full-CI vector. The algorithm has been implemented on vector and parallel architectures, both of shared and distributed-memory type. This gave us the possibility of performing large benchmark calculations, with a Full-CI space dimension up to almost ten billion of symmetry-adapted Slater determinants.

A full-configuration interaction (FCI) calculation has been performed for the nitrogen molecule using an ANO [4s3p1d] basis set. The FCI space for such a system contains about 9.68×109 symmetry-adapted Slater determinants. The FCI results are compared with several approximate methods, both of single- and multi-reference type, in order to test their accuracy.

Large-scale full configuration interaction (FCI) calculations are presented on the acetylene molecule using several basis sets. The largest calculation involves more than five billion symmetry-adapted Slater determinants. The FCI results are compared with those obtained using the (SC)2-CI method, that corrects the size-consistency defect of truncated CI schemes. A comparison with other truncated-CI calculations, of both contracted and uncontracted type, is also done.

The implementation of an out-of-core version of a full CI algorithm on the Cray T3D is described. The introduction of heavy I/O activity, necessary to handle larger problems, required particular attention in order to maintain good performance. As an application, the FCI energy of the Be 2 molecule with a [9s2p1d] basis set (all electrons), whose FCI space has a dimension of more than one billion (10 9 ) of symmetry-adapted determinants in D 2h symmetry was computed. A single iteration on the Cray T3D at CINECA (64 processors) required about four hours, 30 minutes of which were spent in I/O operations. 27 iterations were performed and a precision of at least one μhartree in the energy was achieved. Due to the scalability of the code, substantially larger calculations could be performed provided that more processors and a larger amount of disk space were available.

International audience; The fast interconnections of the presently available distributed platforms allow scientists to target highly complex problems by chaining software developed and maintained by experts of the relevant fields. A pillar of such cooperative endeavor in molecular and materials science and technologies is the so-called grid empowered molecular simulator that combines the expertise of molecular science theorists (electronic structure and nuclei dynamics) and experimentalists in order to build and validate ab initio models. This line has prompted an unprecedented level of data format standardization procedures, the bridging of high throughput and high performance platforms, the assemblage of ad hoc designed virtual experiments. In addition this approach has prompted the design and development of tools allowing the evaluation of the quality of the cooperative effort produced by the members of a given research community as well as its rewards to such effort through a credit economy is reported.

A full configuration interaction algorithm on the CRAY T3D massively parallel computer has been implemented. The algorithm shows good scaling behaviour as a function of the number of processors. As an application, we studied a problem that has attracted the attention of several authors in the past, i.e. the determination of the ground state energy of ammonia with a valence double-zeta plus polarization (vdzp) basis set.

GriF is a Workflow Management System designed to support users of the Molecular and Materials Sciences and Technologies COMPCHEM Virtual Organization. In particular, GriF manages the results of the parameter sweeping studies submitted to the Grid. This service has been recently extended to implement seamless access to both High Performance and High Throughput Computing architectures. To this end, the Workflow execution is splitted into single blocks whose execution is most suited to one or the other platform. This has been obtained by implementing a communication channel allowing interoperability between the gLite middleware operating on the Italian Grid Initiative segment accessible to COMPCHEM and the software stack operating on the CINECA machines. As a prototype application a high level ab initio calculation of the potential energy surface of few atom system has been implemented.

An efficient implementation on the CRAY Y-MP of a new full configuration interaction algorithm is illus trated on a model problem. This shows how a careful optimization can lead to huge speedups in CPU times and interesting speedups in the overall elapsed times. The implementation takes full advantage of the algo rithm's characteristics, with a full vectorization of the heaviest innermost loops and parallelization of the im mediately outer loops.

Motivation: Non-coding microRNAs (miRNAs) act as regulators of global protein output. While their major effect is on protein levels of target genes, it has been proven that they also specifically impact on the messenger RNA level of targets. Prominent interest in miRNAs strongly motivates the need for increasing the options available to detect their cellular activity. Results: We used the effect of miRNAs over their targets for the detection of miRNA activity using mRNAs expression profiles. Here we describe the method, called T-REX (from Targets' Reverse EXpression), compare it to other similar applications, show its effectiveness and apply it to build activity maps. We used six different target predictions from each of four algorithms: TargetScan, PicTar, DIANA-microT and DIANA Union. First, we proved the sensitivity and specificity of our technique in miRNA over-expression and knock-out animal models. Then, we used whole transcriptome data from acute myeloid leukemia to show that we could identify critical miRNAs in a real life, complex, clinically relevant dataset. Finally, we studied 66 different cellular conditions to confirm and extend the current knowledge on the role of miRNAs in cellular physiology and in cancer. Availability: Software is available at http://aqua.unife.it and is free for all users with no login requirement. Contact: s.volinia@unife.it Supplementary information: Supplementary data are available at Bioinformatics online.

International audience; IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), is the reference in immunogenetics and immunoinformatics. IMGT standardizes and manages the complex immunogenetic data that include the immunoglobulins (IG) or antibodies, the T cell receptors (TR), the major histocompatibility complex (MHC) and the related proteins of the immune system (RPI), which belong to the immunoglobulin superfamily (IgSF) and the MHC superfamily (MhcSF). The accuracy and consistency of IMGT data and the coherence between the different IMGT components (databases, tools and Web resources) are based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets relying on seven axioms, 'IDENTIFICATION', 'DESCRIPTION', 'CLASSIFICATION', 'NUMEROTATION', 'LOCALIZATION', 'ORIENTATION' and 'OBTENTION', that postulate that objects, processes and relations have to be identified, described, classified, numerotated, localized, orientated, and that the way they are obtained has to be determined. These axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. These axioms have been essential for the conceptualization of the molecular immunogenetics knowledge and for the creation of IMGT. Indeed all the components of the IMGT integrated system have been developed, based on standardized concepts and relations, thus allowing IMGT to bridge biological and computational spheres in bioinformatics. The same axioms can be used to generate concepts for multi-scale level approaches at the molecule, cell, tissue, organ, organism or population level, emphasizing the generalization of the application domain. In that way the Formal IMGT-ONTOLOGY represents a paradigm for the elaboration of ontologies in system biology.

This paper describes the design and implementation of a common data format within abiGrid, a grid-based project that connects different research groups of Quantum Chemists. The research activity of the partners is focused on orbital localization in a Multi-Reference context, since orbital localization is a necessary step towards the development of efficient methods for the treatment of large systems.The goal of abiGrid is to permit the use and interchange of home-made programs, while maintaining the individuality of the different codes that, as research tools, are subject to changes and evolution. Central points of the project are the design of a Common Data format and an extensive use of the Grid technology. In the present contribution the structure of the common data format is described. The format is based on XML, which has already used for chemical applications (CML). The problem of the large amount of data produced by ab-initio calculations is also addressed.

A Full Configuration Interaction algorithm has been optimised for a Cray T3D massively parallel computer. A preliminary version of the code showed good scalability, but also load unbalancing problems and synchronisation overheads. In this paper are described several ways to overcome these problems. A optimal solution has been found to eliminate the need of synchronisation points while load unbalancing appears to depend on the theoretical formulation of the problem. Also in this case some hints are suggested for future works.

The frequency dependence of the dipole electric polarizability and electric shielding tensors of hydrogen and lithium nuclei in the LiH molecule has been studied via some approximations to the polarization propagator method, i.e., STA, TDA, and RPA, allowing for dipole length, velocity, acceleration, and mixed formalisms. The RPA nuclear electric shieldings are in a fairly good agreement with the corresponding experimental data, a discrepancy being observed for the parallel component at the Li nucleus.

By means of symmetry considerations it is shown that aromatic hydrocarbons, perturbed by a magnetic field perpendicular to the molecular plane, are characterized by an interatomic paramagnetic circulation of electrons, flowing around the highest symmetry axis, which is related to the nodal topology of the wave function. An actual calculation confirms that the field of quantum-mechanical current density presents an axial vortex due to σ electrons in benzene, which overcomes the diamagnetic π streamlines. The analysis of the orbital contributions to proton nuclear shielding reveals that σ electrons cause low field shifts, in the NMR spectrum, comparable in magnitude with those arising from π circulation. These results would imply the need for modifying some features of London's ring current model.

The singularities of the quantum-mechanical electron current density induced in a molecule by an external magnetic field are analyzed via the theory of the real autonomous systems of differential equations. Group-theoretical techniques, based on the idea of color symmetry, are developed, which predict the occurrence of singularities about molecular symmetry elements. Plots of induced electron current density have been obtained for the ethylene molecule through accurate coupled SCF calculations. The theoretical magnetic properties of ethylene obtained through this investigation are the most accurate reported so far.

The anisotropy of the nuclear spin–spin coupling tensor, relative to P, H and H, H interacting nuclei, has been investigated by means of extended ab initio calculations in the molecules PH−2, PH3, and PH+4. The coupled Hartree–Fock perturbed scheme has been employed retaining the nonrelativistic Ramsey Hamiltonians. The most important contributions to the anisotropy in the P, H coupling arise from the Fermi contact‐spin‐dipolar cross term, which is partially counterbalanced by the spin‐orbit effect. The discrepancies emerging between computed and experimental J(P,H) in phosphine and phosphonium are interpreted in terms of neglected electron correlation contributions. A dramatic sensitivity of the Fermi contact term of the molecular geometry has been found for PH2−. The calculations show that the P–H coupling is more anisotropic than N–H, which is seemingly due to the enhanced nonsphericity of electron distribution.

Coupled Hartree–Fock perturbation theory has been employed to evaluate the nuclear spin–spin coupling constants between geminal hydrogen and directly bonded X, H atoms. Full tensor matrices have been calculated ab initio, adopting SCF wave functions of near Hartree–Fock quality, determining the average trace and the anisotropy. The results are discussed and compared with those reported for similar systems and with corresponding experimental results.

A first‐order polarization propagator approximation has been adopted to compute the full nuclear spin–spin coupling tensors 1J(X–H) and 2J(H–H) in SiH4 and AlH−4. The higher efficiency of the computational scheme related to the propagator formalism, with respect to the conventional coupled Hartree–Fock method, has been proved. The diamagnetic spin‐dipolar term has been found to provide a larger contribution than the Fermi‐spin‐dipolar cross term to the anisotropy of 1J(X–H). Spin‐dipolar contributions are negligible and the bulk of the average coupling is determined by the Fermi contact term.

Coupled Hartree-Fock perturbation theory is applied in extended ab initio calculations of molecular dipole moments, polarisabilities and first hyperpolarisabilities of first-row hydrides. Their dependence on internuclear separation is also analysed and discussed. Very strong hyperpolarisability gradients and large vibrational corrections are found. The relevance of the present results for interpreting the discrepancies between experimental and theoretical hyperpolarisabilities is pointed out.

Coupled Hartree–Fock perturbation theory, within the framework of an accurate calculation, has been employed to visualize the electronic current density vector field induced by an external uniform magnetic field in the acetylene molecule. The current regime in a plane containing the molecular axis is rather different from those usually accounted for, evidencing the presence of a toroidal vortex in the CH bond. The maps are useful in rationalizing the experimentally observed proton and carbon NMR chemical shifts.

The diamagnetic spin‐orbit contribution to the nuclear spin–spin coupling constants of water has been calculated employing SCF wave functions of increasing accuracy. The results demonstrate that this term is small in the case of direct O–H average coupling constants. On the other hand, a significant contribution (≂−7 Hz) to geminal H–H coupling constant is found. The theoretical results are slightly affected by the characteristics of the basis set employed in the calculations.

The pattern of the electron currents, induced in the benzene molecule by uniform magnetic fields, has been visualized by plotting modulus and direction of the quantum mechanical current density vector evaluated within the coupled Hartree–Fock approximation assuming a basis set of 198 CGTOs. The electron motion is characterized by axial and toroidal vortices and the paramagnetic σ circulation overcomes the diamagnetic π ring current. Intense localized circulations occur about carbon nuclei and carbon–carbon bonds, which give rise to important deshielding effects upon protons. The delocalized currents are most intense in the environment of carbons; delocalized currents are also present, and no actual ’’superconductivity’’ of π electrons can be accounted for. The reported results document that London’s ring current is a rough oversimplification, affected by some unnecessary and unphysical hypotheses.

Code interoperability and the search for domain-specific standard data formats represent critical issues in many areas of computational science. The advent of novel computing infrastructures such as computational grids and clouds make these issues even more urgent. The design and implementation of a common data format for quantum chemistry (QC) and quantum dynamics (QD) computer programs is discussed with reference to the research performed in the course of two Collaboration in Science and Technology Actions. The specific data models adopted, Q5Cost and D5Cost, are shown to work for a number of interoperating codes, regardless of the type and amount of information (small or large datasets) to be exchanged. The codes are either interfaced directly, or transfer data by means of wrappers; both types of data exchange are supported by the Q5/D5Cost library. Further, the exchange of data between QC and QD codes is addressed. As a proof of concept, the H + H2 reaction is discussed. The proposed scheme is shown to provide an excellent basis for cooperative code development, even across domain boundaries. Moreover, the scheme presented is found to be useful also as a production tool in the grid distributed computing environment. © 2013 Wiley Periodicals, Inc.