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This document summarises the views expressed by the Italian Computing and Data Initiative (ICDI) in response to the open consultation for the EOSC Strategic Research and Innovation Agenda (SRIA), closed on the 31st of August. It provides insightful input and suggestions about the current draft of the SRIA document shared with the wider EOSC community, with the aim of helping to shape the future vision of the European Open Science Cloud.

In this work molecular simulations are used to probe the gas adsorption properties of amorphous chalcogenide nanopores. A realistic atom-scale model, derived by first-principles calculations, of glassy chalcogenide surface is considered for the present study. Nitrogen adsorption and condensation at 77 K in pores of different widths are simulated for characterization purposes. The adsorption of carbon dioxide, methane, hydrogen, and their mixtures is investigated at 298 K. Analysis of the adsorption data shows nice agreement with the prediction of obtained using the Ideal Adsorbed Solution Theory. A detailed comparison with experimental literature data is also proposed and discussed. We also address the effect of the surface chemistry on the gas adsorption by studying both bare and hydrogenated chalcogenide surfaces. We show here that porous glassy chalcogenide exhibits highly selective gas adsorption properties and can strongly discriminate among gases on the basis of their interaction with the chalcogenide surface.

In this paper we describe the parallelization of a molecu­lar dynamics code, based on a Tight-Binding Hamiltonian, on a DMMP parallel platform. The data-parallel implementation has been carried out within the HPF framework, and tested on IBM SP2 architectures. The integration of an optimized parallel library routine (PESSL) for the full diagonalization of large symmetric matrices is also described. The scalability of this approach, the performance of the parallel code and that of the PESSL routine are shown. © Springer-Verlag Berlin Heidelberg 1998.

A genetic algorithm for ground-state structure optimization of a Palladium atomic cluster has been developed and ported on a SIMDMIMD parallel platform. The SIMD part of the parallel platform is represented by a Quadrics/APE100 consisting of 512 floating point units while the MIMD part is formed by a cluster of workstations. The proposed algorithm contains a part where the genetic operators are applied to the elements of the population and a part which performs a further local relaxation and the fitness calculation via Molecular Dynamics. These parts have been implemented on the MIMD part and on the SIMD one, respectively. Results have been compared to those generated by using a Simulated Annealing technique. © Springer-Verlag Berlin Heidelberg 1996.

A Molecular Dynamics code, utilized for the study of atomistic models of metallic nanostructured materials, has been ported on MIMD platforms by means of the PVM message passing libraries. The nanostructured materials represent a challenging problem for the parallelization strategies due to their intrinsic dishomogeneity and to the slow relaxation toward the equilibrium configuration. The interaction potential, derived from the second moment approximation of a tight-binding Hamiltonian, the Parrinello-Rahman-Nosé and the VI order predictor-corrector Gear algorithms are implemented efficiently in the parallel code. The parallelization strategies utilized and the molecular dynamics code are described in detail. Benchmarks on several MIMD platforms allow performances evaluation and future improvements. © Springer-Verlag Berlin Heidelberg 1996.

The thermodynamic stability of hydroxylated graphane, that is, fully sp3 graphene derivatives coordinated with -H and -OH groups, has been recently demonstrated by ab initio calculations. Within the density functional theory approach, we investigate the electronic property modifications of graphane by progressive hydroxylation, that is, by progressively substituting -H with -OH groups. When 50% of graphane is hydroxylated, the energy bandgap reaches its largest value of 6.68 eV. The electronic affinity of 0.8 eV for graphane can widely change in the 0.28-1.60 eV range depending on the geometric configuration. Hydroxylated graphane has two interfaces with vacuum, hence its electron affinity can be different on each interface with the formation of an intrinsic dipole perpendicular to the monolayer. We envisage the possibility of using hydroxylated graphane allotropes with tunable electronic affinity to serve as interfacial layers in 2D material-based heterojunctions.

Laser-driven proton acceleration, as produced during the interaction of a high-intensity (I > 1 × 1018 W/cm2), short pulse (

Development of characterization methods and tools to address structural, electronic and optical properties of materials from the atomic-scale models. Characterization procedures to assess the reliability of the numerical models. Application of MDFT code to supercapacitor materials screening. Coupling of codes to increase accurateness of the computed properties. Modeling of materials at different lenght scales. Description of applications via continuous models. Model settings to design large scale simulations to address accurately macroscopic properties., H2020

The solubilization mechanism of lipid membranes in the presence of Triton X-100 (TX-100) is investigated at molecular resolution using molecular dynamics (MD) simulations. Thanks to the large time and length scales accessible by the hybrid particle-field formulation of the models employed here, the complex process of membrane solubilization has been studied, with the goal of verifying the three stage model reported in the literature. DPPC lipid bilayers and vesicles have been studied at different concentrations of the TX-100 detergent employing coarse grained (CG) models. Systems up to ∼600.000 beads, corresponding to more than 2 millions heavy atoms, have been simulated. Moreover, in order to clarify several experimental pieces of evidence, both slow and fast detergent partition scenarios have been investigated. Flat and curved (vesicles) lipid bilayer surfaces, interacting with TX-100, have been considered to study the curvature effects on the detergent partition rate in the membrane. Shape and conformational changes of mixed DPPC/TX-100 vesicles, as a function of TX-100 content, have also been studied. In particular, high curvature surfaces, corresponding to a higher local TX-100 content, promote a membrane rupture. In flat lipid surfaces, on the time scale simulated the detergent partition is almost absent, following a different pathway of the solubilization membrane mechanism. © 2017 the Owner Societies.

Optimization of all numerical codes ported in the infrastructure and used for supercapacitors, PV and batteries. The scope of deliverable D3.2 is to report the new advances in the field of materials for energy that comes from the search of new methodologies and models that could be more efficient on the new generation of computer hardware for exascale. In this respect, deliverable D3.2 is a transversal deliverable that report the new advances related to activities described in task T3.2, T3.3 and T3.4., H2020

Corrosion property of iron in high temperature stagnant liquid lead has been studied using molecular dynamics method. The method was used to predict the limit values of the injected oxygen into the liquid lead for maximum corrosion inhibition of iron. It is from experimental results, in order to inhibit the corrosion at possible lowest rate then a stable self-healing protective iron oxide layer should be developed at the surface of steel continuously. In this research we investigated the iron corrosion and it can be predicted that the protective oxide layer may be formed by injecting oxygen within the range of 5.35 × 10-2 wt% to 8.95 × 10-2 wt% (for observed temperature 750 C). The oxygen 5.35 × 10-2 wt% is the lower limit to prevent high dissolution of iron while the oxygen content of 8.95 × 10-2 wt% is the upper limit to avoid high precipitation of lead oxide. We also guess that effect of oxygen injection into liquid lead creates a thin oxygen barrier that separating the liquid lead and iron oxides from direct interaction. The iron oxides layer and oxygen barrier then may be regarded as double corrosion inhibition. © 2013 Elsevier Ltd. All rights reserved.

Doping of MgH2 with transition metals and their oxides is well-known procedure to improve its hydrogen (de) sorption properties, namely to lower the temperature of desorption and to achieve the kinetics speedup. In order to assess the influence Ti and TiO2 doping has on H mobility and to characterize structurally and electronically observed differences, MgH2-Mg interface doped with both Ti and TiO2 have been studied using ab-initio interface molecular dynamics and bulk calculations. Results suggest different mechanisms of MgH2 structure destabilization. The presence of dopants significantly stabilize MgH2-Mg interface, which is confirmed by work of adhesion computation. Calculated formation energies show that interface system with doped TiO2 is more stable. In terms of H mobility, molecular dynamics simulations confirm that Ti doping is more effective than TiO2 in lowering the desorption temperature. The mobility of hydrogen atoms close to dopant is much higher in the case of Ti than in the case of TiO2. Electronic structure characterization reveals that oxygen atoms with high electron affinity forms more pronounced ionic bonding with Ti and the other neighbor Mg atoms. This in turn cause a shorter Ti-H bonds in first coordination than in the case of Ti doping and further reduction of H atoms mobility. This is in accordance with molecular dynamics predictions. (C) 2016 Elsevier B.V. All rights reserved.

The interface of biological molecules with inorganic surfaces has been the subject of several recent studies. Experimentally some amino acids are evidenced to play a critical role in the adhesion and selectivity on oxide surfaces; however, detailed information on how the water molecules on the hydrated surface are able to mediate the adsorption is still missing. Accurate total energy ab initio calculations based on dispersion-corrected density functional theory have been performed to investigate the adsorption of selected amino acids on the hydrated ZnO(101¯0) surface, and the results are presented and discussed in this paper. We have also investigated the role played by water in the determination of the most energetically favorable adsorption configurations of the selected amino acids. We have found that for some amino acids the most energetically favorable configurations involve the deprotonation of the molecule if the water screening is not effective. © 2015 American Chemical Society.

The corrosion of structural materials used in fast nuclear reactor design is a current major problem. It is due to the use of liquid metal as a coolant candidate in the heat transfer system. The liquid metal as lead-bismuth eutectic was found to make high corrosion to structural material as steel. One of the solutions of this problem is to inject some inhibitor into liquid metal. In this current work we simulate the effect of nitrogen injection as inhibitor candidate. The simulation will predict the proper concentration of injected nitrogen and also observe the microscopic structure of the material before and after injection to know the ability of nitrogen as an inhibitor. The simulation follows the molecular dynamics method and for preliminary study we use iron material rather than steel. We also use lennard-jones potential for simplification of the study. It is from our simulation we see nitrogen shows better corrosion mitigation compare with oxygen as in our previous study. The effective inhibition can be achieved by injecting at least 0.056wt.% nitrogen. This amount seems to be able to reduce the corrosion level of iron till about 99.5% for high corrosion at temperature 750 °C. © Published under licence by IOP Publishing Ltd.

A multiscale scheme is proposed and validated for Triton X-100 (TX-100), which is a detergent widely employed in biology. The hybrid particle field formulation of the model allows simulations of large-scale systems. The coarse-grained (CG) model, accurately validated in a wide range of concentrations, shows a critical micelle concentration, shape transition in isotropic micellar phase, and appearance of hexagonal ordered phase in the experimental ranges reported in the literature. The fine resolution of the proposed CG model allows one to obtain, by a suitable reverse mapping procedure, atomistic models of micellar assemblies and of the hexagonal phase. In particular, atomistic models of the micelles give structures in good agreement with experimental pair distance distribution functions and hydrodynamic measurements. The picture emerging by detailed analysis of simulated systems is quite complex. Polydisperse mixtures of spherical-, oblate-, and prolate-shaped aggregates have been found. The shape and the micelle behavior are mainly dictated by the aggregation number (Nagg). Micelles with low Nagg values (∼40) are spherical, while those with high Nagg values (∼140 or larger) are characterized by prolate ellipsoidal shapes. For intermediate Nagg values (∼70), fluxional micelles alternating between oblate and prolate shapes are found. The proposed model opens the way to investigations of several mechanisms involving TX-100 assembly in protein and membrane biophysics. © 2015 American Chemical Society.

The low-density (LDA) to high-density (HDA) transformation in amorphous Ge at high pressure is studied by first-principles molecular dynamics simulations in the framework of density functional theory. Previous experiments are accurately reproduced, including the presence of a well-defined LDA-HDA transition above 8 GPa. The LDA-HDA density increase is found to be about 14%. Pair and bond-angle distributions are obtained in the 0-16 GPa pressure range and allowed us a detailed analysis of the transition. The local fourfold coordination is transformed in an average HDA sixfold coordination associated with different local geometries as confirmed by coordination number analysis and shape of the bond-angle distributions. © 2016 IOP Publishing Ltd.

The characterization of self-diffusion in MgO grain boundaries is a materials science problem of general interest, being relevant to the stability and reactivity of MgO layers in artificial nanostructures as well as to the understanding of mass transport and morphological evolution in polycrystalline metal oxides which are employed in many technological applications. In addition, atomic transport in MgO is a key factor to describe the rheology of the Earth’s lower mantle. In this work, we tackle the problem using a classical molecular dynamics model and finite-temperature simulations. To this purpose, we first design a stable grain boundary structure, which is meant to be representative of general internal interfaces in nanocrystalline MgO. The Mg and O self-diffusion coefficients along this grain boundary are then determined as a function of temperature by calculating the mean-square ionic displacement in the boundary region. Two different diffusion regimes at low and high temperature are identified, allowing to obtain the relevant activation enthalpies for migration from the temperature dependance of the diffusion coefficients. Our results prove that Mg diffusion along MgO grain boundaries is sufficiently fast to explain the recently reported development of MgO hollow structures during repeated hydrogen sorption cycles in Mg/MgO nanoparticles.

Magnesium hydride is a very promising material for solid-state hydrogen storage. However, some drawbacks have to be overcome to use it in real applications. The use of catalysts is a viable solution to lower the desorption temperature and increase the overall kinetics. An accurate model has been developed to study the mechanism of action of the catalyst and how it interacts with the interface MgH2-Mg, through which H atoms diffuse. The accurate evaluation of the work of adhesion and defect energy formation, versus the distance from the interface are linked to the atomic-scale structural distortion induced by the catalyst. Moreover, molecular dynamics simulations at several temperature provide a clear description of the desorption mechanism and an estimate of the desorption temperature. © 2015 Hydrogen Energy Publications, LLC.

Corrosion of structural materials in high temperature molten lead-bismuth eutectic is a major problem for design of PbBi cooled reactor. One technique to inhibit corrosion process is to inject oxygen into coolant. In this paper we study and focus on a way of inhibiting the corrosion of iron using molecular dynamics method. For the simulation results we concluded that effective corrosion inhibition of iron may be achieved by injection 0.0532 wt% to 0.1156 wt% oxygen into liquid lead-bismuth. At this oxygen concentration the structure of iron material will be maintained at about 70% in bcc crystal structure during interaction with liquid metal. © 2014 AIP Publishing LLC.

The structure of glassy GeS${}_{2}$ is studied in the framework of density functional theory, by using a fully self-consistent first-principles molecular dynamics (FPMD) scheme. A comparative analysis is performed with previous molecular dynamics data obtained within the Harris functional (HFMD) total energy approach. The calculated total neutron structure factor exhibits an unprecedented agreement with the experimental counterpart. In particular, the height of the first sharp diffraction peak (FSDP) improves considerably upon the HFMD results. Both the Ge and the S subnetworks are affected by a consistent number of miscoordinations, coexisting with the main tetrahedral structural motif. Glassy GeS${}_{2}$ features a short-range order quite similar to the one found in glassy GeSe${}_{2}$, a notable exception being the larger number of edge-sharing connections. An electronic structure localization analysis, based on the Wannier functions formalism, provides evidence of a more enhanced ionic character in glassy GeS${}_{2}$ when compared to glassy GeSe${}_{2}$.

Hydrogen desorption from hydride matrix is still an open field of research. Extensive, density functional theory based, ab-initio molecular dynamics simulations of MgH2-Mg interface catches the atomic level structural mechanism leading to hydrogen desorption. The numerical model estimates the desorption temperature for an interface with Fe catalyst in excellent agreement with experimental results. Formation energies and the analysis of the structural data reveal the role played by the catalysts to lower the desorption temperature. © 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

In this work total and partial density of states were calculated for small single wurtzite CdS nanoparticle, quantum dots, with diameter below 2 nm, performing DFT pseudopotentials calculations with generalized gradient approximation. The cluster was previously heated at different temperatures ranging from 100 to 600 K-, by means of Car-Parrinello ab-initio molecular dynamics, finding a stable phase after 340 K. Another stable phase is reached at higher temperature, more than 480 K, where surface migrations play an important role in the determination of final atomic configuration. Density of states was obtained for the structures heated at 100 K, 280 K 330 K, 340 K, 480 K and 570 K and substantial modifications were found after 340 K where the superficial effects cause some alterations of the intermediate electronic states around the band gap. From the partial density of states it has been clearly showed that the atoms on the surface have a main role on the formation of the intermediate states on the band gap. This effect is meaningful for small particles where the fraction of the surface atoms is greater than the fraction of the core atoms.Copyright © 2013 American Scientific Publishers.

The upper threshold of hydrogen adsorption in Li-doped and hydrogenated carbon nanotube densely packed arrays is calculated to check the ability of such systems to fulfill the target indicated by the United States Department of Energy (DOE). To this aim, model potential parameters have been obtained by Density Functional Theory and have been used to calculate the adsorption isotherms in honeycomb arrays containing up to seven tubes by means of Grand-Canonical Monte Carlo simulations. A hybrid model has been developed involving both atomistic potentials for short-range interactions and integrated potentials for hydrogen interacting with distant tubes. In the pressure range explored, it is shown that the hydrogen adsorption performances of Li-doped carbon nanotubes arranged in close packed honeycomb arrays, while being enhanced with respect to pristine carbon nanotubes, are still well below the DOE targets. © Springer Science+Business Media 2013.

We analyze from a computational viewpoint the conformational and dynamical properties of the interesting oligopeptide that is reported to bind specifically to titania surfaces. First-principles simulations based on Density Functional Theory (DFT) and classical Molecular Dynamics (MD) are carried out to investigate both the structure and the stability of single amino acids and of the full peptide on the (101) surface of TiO2 in the anatase crystalline structure. Moreover the strength of the adhesion is estimated by pulling the peptide away from the surface. Our results shed light on the role played by some amino acids that are known to be essential in selective adsorption on TiO2, as well as on the peptide structural conformation upon the surface.Copyright © 2013 American Scientific Publishers.