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We present a combined theoretical and computational approach to understanding the shape transition mechanism of Triton X-100 (TX-100) micellar nanoscale aggregates in aqueous solution. The understa...

With the continued digitization of the energy sector, the problem of sunken scholarly data investments and forgone opportunities of harvesting existing data is exacerbating. It adds to the problem that the reproduction of knowledge is incomplete, impeding the transparency of science-based evidence for the choices made in the energy transition. We comprehensively test FAIR data practices in the energy domain with the help of automated and manual tests. We document the state-of-the art and provide insights on bottlenecks from the human and machine perspectives. We propose action items for overcoming the problem with FAIR and open energy data and suggest how to prioritize activities.

To achieve high performance and high energy efficiency on near-future exascale computing systems, three key technology gaps needs to be bridged. These gaps include: energy efficiency and thermal control; extreme computation efficiency via HW acceleration and new arithmetics; methods and tools for seamless integration of reconfigurable accelerators in heterogeneous HPC multi-node platforms. TEXTAROSSA aims at tackling this gap through a co-design approach to heterogeneous HPC solutions, supported by the integration and extension of HW and SW IPs, programming models and tools derived from European research. This work is supported by the TEXTAROSSA project G.A. n.956831, as part of the EuroHPC initiative. Peer Reviewed Article signat per 51 autors/es: Giovanni Agosta, Daniele Cattaneo, William Fornaciari, Andrea Galimberti, Giuseppe Massari, Federico Reghenzani, Federico Terraneo, Davide Zoni, Carlo Brandolese (DEIB – Politecnico di Milano, Italy, name.surname@polimi.it) | Massimo Celino, Francesco Iannone, Paolo Palazzari, Giuseppe Zummo (ENEA, Italy, name.surname@enea.it) | Massimo Bernaschi, Pasqua D’Ambra (Istituto per le Applicazioni del Calcolo (IAC) - CNR, Italy, name.surname@cnr.it) | Sergio Saponara, Marco Danelutto, Massimo Torquati (University of Pisa, Italy, name.surname@unipi.it) | Marco Aldinucci, Yasir Arfat, Barbara Cantalupo, Iacopo Colonnelli, Roberto Esposito, Alberto R. Martinelli, Gianluca Mittone (University of Torino, Italy, name.surname@unito.it) | Olivier Beaumont, Berenger Bramas, Lionel Eyraud-Dubois, Brice Goglin, Abdou Guermouche, Raymond Namyst, Samuel Thibault (Inria - France, name.surname@inria.fr) | Antonio Filgueras, Miquel Vidal, Carlos Alvarez, Xavier Martorell (BSC - Spain, name.surname@bsc.es) | Ariel Oleksiak, Michal Kulczewski (PSNC, Poland, ariel@man.poznan.pl, kulka@man.poznan.pl) | Alessandro Lonardo, Piero Vicini, Francesca Lo Cicero, Francesco Simula, Andrea Biagioni, Paolo Cretaro, Ottorino Frezza, Pier Stanislao Paolucci, Matteo Turisini (INFN Sezione di Roma - Italy, name.surname@roma1.infn.it) | Francesco Giacomini (INFN CNAF - Italy, name.surname@cnaf.infn.it) | Tommaso Boccali (INFN Sezione di Pisa - Italy, name.surname@pi.infn.it) | Simone Montangero (University of Padova and INFN Sezione di Padova - Italy, name.surname@pd.infn.it) | Roberto Ammendola (INFN Sezione di Roma Tor Vergata - Italy, name.surname@roma2.infn.it)

This paper introduces a renewed gateway to ENEAGRID distributed computing resources named Fast Access to Remote Objects 2.0 (FARO 2.0). FARO 2.0 is a tool for application and desktop virtualization with a focus towards user experience (UX), providing trained as well as untrained users with a collection of centralized services that can be seamlessly used on their client through a remote desktop protocol. FARO 2.0 is a JavaFX application whose graphical user interface (GUI) and whose main logics have been implemented through the well-known Web technologies (HTML5, CSS3, Javascript) for easier maintainability and customizability, taking full advantage of the WebView component. The FARO 2.0 framework has been deployed both as a general purpose GUI for remote user access to ENEAGRID resources and as a specialized application or workflow-oriented GUI. They are applied in a set of applicative domains, ranging from materials science to technologies for energy and industry, environmental modeling, and nuclear fusion. Some examples and results are also presented.

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.

International audience; The principles of Findability, Accessibility, Interoperability, and Reusability (FAIR) havebeen put forward to guide optimal sharing of data. The potential for industrial and social innovation is vast. Domain-specific metadata standards are crucial in this context, but are widely missing in the energy sector. This report provides a collaborative response from the low carbon energy research community for addressing the necessity of advancing FAIR metadata standards. We review and test existing metadata practices in the domain based on a series of community workshops. We reflect the perspectives of energy data stakeholders. The outcome is reported in terms of challenges and elicits recommendations for advancing FAIR metadata standards in the energy domain across a broad spectrum of stakeholders.

In the silicon heterojunction solar cells, intrinsic hydrogenated amorphous silicon a-Si:H is used to passivate the crystal silicon c-Si surface to suppress the electrical losses at interfaces and to keep ultralow contact resistivity for the selective transport of one type of carrier only. We use ReaxFF (Reactive Force Field) molecular dynamics to efficiently simulate the thermalisation, quenching, and equilibration processes involving thousands of atoms forming realistic a-Si:H/c-Si interface structures. We generated snapshots of the equilibrated c-Si/a-Si:H interface atom configurations at room temperature. The ab initio characterization has been executed on selected configurations to monitor the electronic properties of the c-Si/a-Si:H interface. The evolution of the intragap states is monitored by analyzing density of states and charge density. This all will allow to design more efficient silicon solar cells belonging to the silicon heterojunction technology.

The surface of nanowires is a source of interest mainly for electrical prospects. Thus, different surface chemical treatments were carried out to develop recipes to control the surface effect. In this work, we succeed in shifting and tuning the semiconductivity of a Si nanowire-based device from n- to p-type. This was accomplished by generating a hole transport layer at the surface by using an electrochemical reaction-based nonequilibrium position to enhance the impact of the surface charge transfer. This was completed by applying different annealing pulses at low temperature (below 400 °C) to reserve the hydrogen bonds at the surface. After each annealing pulse, the surface was characterized by XPS, Kelvin probe measurements, and conductivity measured by FET based on a single Si NW. The mechanism and conclusion were supported experimentally and theoretically. To this end, this strategy has been demonstrated as an essential tool which could pave a new road for regulating semiconductivity and for other low-dimensional nanomaterials., M.B. is thankful for the MAOF Grant from the Council for Higher Education in Israel for new faculty members. A.S. is appreciative of the institutional scholarships for Ph.D. students that they received from Ben-Gurion University of the Negev. W.W. is thankful for the fundamental research funds from the Central Universities (JC2002). L.Z. is thankful for the support of a postdoctoral fellowship from the Jacob Blaustein Center for Scientific Cooperation, the National Natural Science Foundation of China (61904134), and the National Natural Science Foundation of Shaanxi Province (2019JQ-291). The computing resources and the related technical support used for this work have been provided by CRESCO/ENEAGRID High Performance Computing infrastructure and its staff, along with additional support from S. Migliori and S. Giusepponi. E.N.E.A. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 824158 (EoCoE-II). J.A. acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO coordinated project ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya.

We present a first-principles study of the structural, electronic, and optical properties of hydrogenated amorphous silicon (a-Si:H). To this end, atomic configurations of a-Si:H with 72 and 576 atoms respectively are generated using ab initio molecular dynamics, where the larger structures are defect free, closely matching the experimental situation and enabling the comparison of the electronic and optical properties with experimental results. Density functional theory calculations are applied to both configurations in order to obtain the electronic wave functions. These are analyzed and characterized with respect to their localization and their contribution to the density of states, and are used for calculating ab initio absorption spectra of a-Si:H. The results show that both the size and the defect structure of the configurations modify the electronic and optical properties and in particular the value of the band gap. This value could be improved by calculating quasi-particle (QP) corrections to the single-particle spectra using the G0W0 method. We find that the QP corrections can be described by a set of scissors shift parameters, which can also be used in calculations of larger structures. The analysis of individual contributions to the absorption by evaluating the optical matrix elements indicates that strong localization enhances the optical coupling, but has little effect on the average transition probability 〈 | v cv | 2 〉 , for which we find a dependence E 2 + const on the photon energy E, irrespective of the nature of the initial or final state.

We use ab initio molecular dynamics to generate realistic a-Si:H/c-Si interface structures with very low defect-state density by performing a high-temperature annealing. Throughout the annealing, we monitor the evolution of the structural and electronic properties. The analysis of the bonds by means of the electron localization function reveals that dangling bonds move toward the free a-Si:H surface, leaving the interface region itself completely defect free. The hydrogen follows this movement, which indicates that in the case under consideration, hydrogen passivation does not play a significant role at the interface. A configuration with a satisfactory low density of defect states is reached after annealing at 700 K. A detailed characterization of the electronic states in this configuration in terms of their energy, localization, and location reveals that, although no dangling bond states can be found near the interface, localized interface states do exist and are attributed to a potential barrier at the interface. The quantitative description of electronic localization also allows for the determination of the a-Si:H mobility gap, which, together with the c-Si band gap, yields band offsets that are in qualitative agreement with experimental observations.

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

Both mechanical and structural properties of bcc crystal tungsten in presence of mono and divacancy defects has been investigated by using accurate first-principles total energy methods based on density functional theory. A model for tungsten containing a concentration of vacancies of about 2% and 4% has been developed and used to compute the maximum tensile stress required to reach elastic instability under increasing load. Moreover stress effects on the crystalline structure have been characterized in terms of structural displacements.

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.

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.

In order to optimize the optoelectronic properties of novel solar cell architectures, such as the amorphous-crystalline interface in silicon heterojunction devices, we calculate and analyze the local microscopic structure at this interface and in bulk a-Si:H, in particular with respect to the impact of material inhomogeneities. The microscopic information is used to extract macroscopic material properties, and to identify localized defect states, which govern the recombination properties encoded in quantities such as capture cross sections used in the Shockley-Read-Hall theory. To this end, atomic configurations for a-Si:H and a-Si:H/c-Si interfaces are generated using molecular dynamics. Density functional theory calculations are then applied to these configurations in order to obtain the electronic wave functions. These are analyzed and characterized with respect to their localization and their contribution to the (local) density of states. GW calculations are performed for the a-Si:H configuration in order to obtain a quasi-particle corrected absorption spectrum. The results suggest that the quasi-particle corrections can be approximated through a scissors shift of the Kohn-Sham energies., 14 pages, 10 figures, to appear in Springer Lecture Notes in Computer Science, Proceedings of the JHPCS16 conference

A single wurtzite phase of cadmium sulfide cluster is investigated by ab-initio molecular dynamics simulations at different temperatures, ranging from 100 K to 600 K. In this study we propose a possible procedure to characterize the CdS quantum dots system by means of molecular dynamics calculations using a standard Car-Parrinello scheme. In order to ensure the accuracy of the numerical approach, preliminary calculations to test pseudopotentials, cutoff and box size on both single atoms systems and Cd–Cd, S–S, Cd–S dimers have been performed. Calculated binding energies and bond lengths are obtained in good agreement with experimental data. Subsequently, an uncapped CdS cluster with size below 2 nm, 48 atoms of cadmium and 48 atoms of sulfur, in a wurtzite geometry was structurally optimized to minimize internal stresses. The CdS cluster has been carefully characterized structurally at several temperatures up to T = 600 K. At the temperature of 340 K atomic diffusion on the surface allows the onset of a new stable atomic configuration.

Magnesium is one of the most promising materials for hydrogen storage due to its high capacity and low cost. Unfortunately, practical applications are for the moment limited by the slow kinetics and the high operating temperature. Nanostructuring magnesium hydride MgH2, generally by ball milling, introduces plastic deformations and catalysts that highly enhances the H2 absorption and desorption. However a fundamental understanding of the role played by catalysts and interfaces in MgH2 is still lacking. Microscopic characterization of MgH2-Mg system with and without heavy metal catalysts, is achieved by combining accurate SEM observations of samples after partial desorption process and atomic level ab-initio molecular dynamics simulations of MgH2-Mg interfaces. The experimental method is based on low voltage SEM observations of cross sectional powder samples, prepared by a new specific metallographic process. Identification of nucleation sites of the sorption reaction and their correlation with the presence of catalyst particles is achieved by suitable experimental conditions. Moreover ab-initio molecular dynamics clarifies the interplay of interfaces and the deformations induced during desorption by the presence of catalysts that are able to lower binding energies and free hydrogen atoms toward interfaces. Both approaches confirm and characterize the nucleation step in the catalysts driven phase transformation.

A first-principles pseudopotential method is used to investigate the structural and elastic properties of ScAs and ScSb in their ambient B1(NaCl) and in high pressure B2 (CsCl) phases and phonon structures at zero and close to phase transition pressure. The calculated lattice constants, static bulk modulus, first order pressure derivative of the bulk modulus and the elastic constants are reported in B1 and B2 structures and compared with available experimental and other theoretical results. The phonon properties of these two compounds are compared among themselves which reveal that these compounds are predominantly metallic, due to degeneracy of optical frequencies at the zone centre. At high pressure, near the B1 to B2 transition, the LA mode at X-point softens leading to structural instability.

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.

Indications of the Cu2Zr Laves phase are observed in MD simulations of amorphous Cu64Zr36 upon isothermal holding just above the glass transition temperature. The structural evolution towards Cu2Zr is accompanied by an increase in the fraction of Cu-centered icosahedra, which demonstrates that a large icosahedral fraction does not just indicate structural relaxation. The crystal-like regions generate an increase in strength and Young's modulus, and a stronger localized shear band. A universal relation between the fraction of full icosahedra and their interconnectivity is found, and both can be modified simultaneously via changes of temperature or strain.

The structural properties of amorphous SiSe 2 are studied by performing extensive first-principle molecular dynamics simulations. Comparison with experiments in terms of total neutron scattering factor and nuclear magnetic resonance data confirms the reliability of our model. Partial pair correlation functions and ring statistics are used to identify the structural units whose spatial organization gives raise to the intermediate range order. An accurate analysis reveals that amorphous SiSe 2 is largely a chemically ordered system consisting mainly of a network of silicon centered tetrahedra. Different types of connections among the tetrahedra can be identified and classified. In particular edge-sharing connections seem to play a fundamental role in the establishment of the intermediate range order and in the appearance of the first sharp diffraction peak in the total neutron scattering factor.

In a search for the physical origin of the first sharp diffraction peak (FSDP) in the concentration-concentration partial structure factor S-CC (k) of disordered network-forming materials, we perform first-principles molecular dynamics simulations of liquid GeSe4 (l-GeSe4) and liquid SiSe2 (l-SiSe2). These systems are designed to provide clues on the relationship between the appearance of an FSDP in the S-CC(k) structure factor and the degree of chemical order. Short-range chemical order is more pronounced in l-GeSe4 and in l-SiSe2 than in liquid GeSe2. For the latter system, our level of theory does not reproduce the FSDP in the experimentally observed SCC(k) structure factor. We find that a distinct FSDP shows up in the partial structure factor SCC (k) for l-GeSe4. In SCC (k) for l-SiSe2, we also find a feature at the FSDP location, although it is smaller compared to GeSe4. Given the tight correlation existing between chemical order and ionicity, these results suggest that the ionic character of the bonds plays a crucial role in inducing concentration fluctuations at intermediate-range distances.

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.

Arg, Lys and Asp amino acids are known to play a critical role in the adhesion of the RKLPDA engineered peptide on the (101) surface of the titania anatase phase. To understand their contribution to peptide adhesion, we have considered the relevant charge states due to protonation (Arg and Lys) or deprotonation (Asp) occurring in neutral water solution, and studied their adsorption on the (101) anatase TiO2 surface by ab initio total energy calculations based on density functional theory. The adsorption configurations on the hydrated surface are compared to those on the dry surface considering also the presence of the hydration shell around amino acid side-chains. This study explains how water molecules mediate the adsorption of charged amino acids showing that protonated amino acids are chemically adsorbed much more strongly than de-protonated Asp. Moreover it is shown that the polar screening of the hydration shell reduces the adsorption energy of the protonated amino acids to a small extent, thus evidencing that both Arg and Lys strongly adhere on the (101) anatase TiO2 surface in neutral water solution and that they play a major role in the adhesion of the RKLPDA peptide.

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.