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The ultimate aim of the EU-funded ImmunoGrid project is to develop a natural-scale model of the human immune system—that is, one that reflects both the diversity and the relative proportions of the molecules and cells that comprise it—together with the grid infrastructure necessary to apply this model to specific applications in the field of immunology. These objectives present the ImmunoGrid Consortium with formidable challenges in terms of complexity of the immune system, our partial understanding about how the immune system works, the lack of reliable data and the scale of computational resources required. In this paper, we explain the key challenges and the approaches adopted to overcome them. We also consider wider implications for the present ambitious plans to develop natural-scale, integrated models of the human body that can make contributions to personalized health care, such as the European Virtual Physiological Human initiative. Finally, we ask a key question: How long will it take us to resolve these challenges and when can we expect to have fully functional models that will deliver health-care benefits in the form of personalized care solutions and improved disease prevention?

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.

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.

The quantum framework of the Grid Empowered Molecular Simulator GEMS has been assembled on the segment of the European Grid devoted to the Computational Chemistry Virtual Organization. The related grid based workflow allows the ab initio evaluation of the dynamics of small systems starting from the calculation of the electronic properties. Interoperability between computational codes across the different stages of the workflow was made possible by the use of the common data formats Q5Cost and D5Cost. Illustrative benchmark runs have been performed on the prototype H + H 2, N + N 2 and O + O 2 gas phase exchange reactions and thermal rate coefficients have been calculated for the last two. Results are discussed in terms of the modeling of the interaction and advantages of using the Grid is highlighted. © 2011 Elsevier B.V. All rights reserved.

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.

A common format for quantum chemistry (QC), enhancing code interoperability and communication between different programs, has been designed and implemented. An XML-based format, QC-ML, is presented for representing quantities such as geometry, basis set, and so on, while an HDF5-based format is presented for the storage of large binary data files. Some preliminary applications that use the format have been implemented and are also described. This activity was carried out within the COST in Chemistry D23 project “MetaChem,” in the Working Group “A meta-laboratory for code integration in ab initio methods.” © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

The dispersion interactions of the Ne2 dimer were studied using both the long-range perturbative and supramolecular approaches: for the long-range approach, full CI or string-truncated CI methods were used, while for the supramolecular treatments, the energy curves were computed by using configuration interaction with single and double excitation (CISD), coupled cluster with single and double excitation, and coupled-cluster with single and double (and perturbative) triple excitations. From the interatomic potential-energy curves obtained by the supramolecular approach, the C6 and C8 dispersion coefficients were computed via an interpolation scheme, and they were compared with the corresponding values obtained within the long-range perturbative treatment. We found that the lack of size consistency of the CISD approach makes this method completely useless to compute dispersion coefficients even when the effect of the basis-set superposition error on the dimer curves is considered. The largest full-CI space we were able to use contains more than 1 billion symmetry-adapted Slater determinants, and it is, to our knowledge, the largest calculation of second-order properties ever done at the full-CI level so far. Finally, a new data format and libraries (Q5Cost) have been used in order to interface different codes used in the present study.

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.

Pitzer's theorem is proved for abelian groups. The expression obtained can be used to perform the two-electron integral transformation taking advantage of molecular symmetry by a single-step procedure.

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.

The frequency dependence of the dipole electric polarizability and electric shielding tensors of hydrogen and fluorine nuclei in the HF molecule has been investigated by means of the lower approximations to the equation-of-motion method---namely, the single-transition approximation (STA), the Tamm-Dancoff approximation (TDA), and the random-phase approximation (RPA)---within the framework of dipole length, velocity, acceleration, and mixed formalisms. Some relations are proved, concerning the relative magnitude of TDA and RPA polarizabilities and Thomas-Reich-Kuhn sum rules in the various formalisms. An interdependence between dynamic polarizabilities and nuclear shielding factors has been found. Good agreement with experimental static shielding factors has been obtained in the RPA calculation.

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.

Coupled Hartree-Fock perturbation theory is applied in accurate ab initio calculations of molecular dipole moment, polarisabilities, first hyperpolarisabilities, electric field gradients and nuclear electric shielding tensors in LiH. Their dependence on internuclear separation is also analysed. According to the theoretical investigations, the molecule is characterised by a very high hyperpolarisability, very strong hyperpolarisability gradients and enhanced electronic shielding about the hydrogen nucleus.

Bond and lone-pair polarizability ellipsoids in water, ammonia and methane have been evaluated within the framework of coupled Hartree–Fock perturbation theory, allowing for high-quality wavefunctions. The results are compared with previous theoretical values and with the earlier semiempirical data reported by Denbigh (Trans. Faraday Soc., 1940, 36, 936). A discussion of nuclear electric shieldings in the same molecules is also presented in order to analyse the role of localized charge distribution.

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.