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A set of oxide and chalcogenide tetrahedral glasses are investigated usingmolecular dynamics simulations. It is shown that unlike stoichiometricselenides such as GeSe$_2$ and SiSe$_2$, germania and silica display largestandard deviations in the associated bond angle distributions. Withinbond-bending constraints theory, this pattern can be interpreted as amanifestation of {\it {broken}} (i.e. ineffective) oxygen bond-bendingconstraints. The same analysis reveals that the changes in the Ge compositionaffects mostly bending around germanium in binary Ge-Se systems, leavingSe-centred bending almost unchanged. In contrast, the corresponding Se twisting(quantified by the dihedral angle) depends on the Ge composition and is reducedwhen the system becomes rigid. Our results establishes the atomic-scalefoundations of the phenomelogical rigidity theory, thereby profoundly extendingits significance and impact on the structural description of network glasses.

Amorphous silicon structures were fabricated using the reverse Monte Carlo technique.

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 [ABSTRACT FROM AUTHOR]

The presence of superclusters based on Cu-centered icosahedra was studied via classical molecular dynamics simulations in Cu64Zr36 metallic glass. Medium-range order was identified by determining the nearest-neighbor histogram and bond-angle distribution of superclusters. A heterogeneous distribution of icosahedra was observed while other common cluster types are distributed homogeneously. The degree of superclustering, as quantified by the number of cap-sharing bonds per icosahedron, was found to depend only on the icosahedron fraction, irrespective of thermal history. This is further supported by a long-time annealing in the supercooled liquid regime, where the number of icosahedra significantly increases and the formation of superclusters is consequently enhanced. While distorted icosahedra are not found in the vicinity of full icosahedra, the Zr-centered (0 0 12 4) clusters show a high spatial correlation to Cu-centered icosahedra. This is indicative of early stages of crystallization into a Cu2Zr Laves phase. [ABSTRACT FROM AUTHOR]

The structure of glassy GeS2 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 GeS2 features a short-range order quite similar to the one found in glassy GeSe2, 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 GeS2 when compared to glassy GeSe2. [ABSTRACT FROM AUTHOR]

In this letter, the strain field below uncapped Ge islands of a different shape on a Si(001) substrate is estimated by molecular dynamics simulations at a realistic scale. Comparison to the Fourier transform maps of transmission electron micrographs, recently reported in literature, shows a very good agreement. We point out that the complex deformation in silicon, just below the edges of the Ge islands, is far from being uniaxial. The stress distribution generated by such a strain determines the range of interdot repulsion. [ABSTRACT FROM AUTHOR]

A set of oxide and chalcogenide tetrahedral glasses is investigated using molecular dynamics simulations. We show that the changes in the Ge composition affect mostly bending around germanium in binary Ge-Se systems, leaving Se-centered bending almost unchanged. In contrast, the corresponding Se twisting (quantified by the dihedral angle) depends on the Ge composition and is reduced when the system becomes rigid. It is also shown that angles involving the fourth neighbor around Ge is found to change when the system enters the stressed rigid phase. The same analysis reveals that unlike stoichiometric selenides such as GeSe2 and SiSe2, germania and silica display large standard deviations in the bond angle distributions. Within bond-bending constraints theory, this pattern can be interpreted as a manifestation of broken (i.e., ineffective) oxygen bond-bending constraints, whereas the silicon and germanium bending in oxides is found to be similar to the one found in flexible and intermediate Ge-Se systems. Our results establish the atomic-scale foundations of the phenomenological rigidity theory, thereby profoundly extending its significance and impact on the structural description of network glasses. [ABSTRACT FROM AUTHOR]

Presence and significance of fivefold configurations in liquid metals are investigated by combining x-ray absorption spectroscopy and computer simulations (molecular dynamics and reverse Monte Carlo) in liquid and undercooled liquid nickel. We show that icosahedral short-range ordering (ISRO), probed by common-neighbor (CNA) and spherical invariant (Ŵ6) analysis, involves a limited fraction (14-18% in undercooled nickel for different structural models) of local atomic configurations. The emerging picture for the liquid structure is that of a mixture of nearly icosahedral structures embedded in a disordered network mainly composed of fragments of highly distorted icosahedra (40-45% of the total), structures reminiscent of the crystalline phase, and other configurations. [ABSTRACT FROM AUTHOR]

We report on DFT-TDDFT studies of the structural, electronic and vibrational properties of B24N24 nanocapsules and the effect of encapsulation of homonuclear diatomic halogens (Cl2, Br2 and I2) and chalcogens (S2 and Se2) on the interaction of the B24N24 nanocapsules with the divalent magnesium cation. In particular, to foretell whether these BN nanostructures could be proper negative electrodes for magnesium-ion batteries, the structural, vibrational and electronic properties, as well as the interaction energy and the cell voltage, which is important for applications, have been computed for each system, highlighting their differences and similarities. The encapsulation of halogen and chalcogen diatomic molecules increases the cell voltage, with an effect enhanced down groups 16 and 17 of the periodic table, leading to better performing anodes and fulfilling a remarkable cell voltage of 3.61 V for the iodine-encapsulated system.

Graphene is an ideal candidate material for spintronics due to its layered structure and peculiar electronic structure. However, in its pristine state, the production of magnetic moments is not trivial. A very appealing approach is the chemical modification of pristine graphene. The main obstacle is the control of the geometrical features and the selectivity of functional groups. The lack of a periodic functionalization pattern of the graphene sheet prevents, therefore, the achievement of long-range magnetic order, thus limiting its use in spintronic devices. In such regards, the stability and the magnitude of the instilled magnetic moment depending on the size and shape of in silico designed graphane islands and ribbons embedded in graphene matrix will be computed and analysed. Our findings thus suggest that a novel and magneto-active graphene derivative nanostructure could become achievable more easily than extended graphone or nanoribbons, with a strong potential for future spintronics applications with a variable spin-current density., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Using first-principles calculations based on density functional theory, we investigated the effects of surface functionalization on the energetic and electronic properties of hydrogenated and chlorinated silicon nanowires oriented along the <112> direction. We show that the band structure is strongly influenced by the diameter of the nanowire, while substantial variations in the formation energy are observed by changing the passivation species. We modeled an octane moiety absorption on the (111) and (110) surface of the silicon nanowire to address the effects on the electronic structure of the chlorinated and hydrogenated systems. We found that the moiety does not substantially affect the electronic properties of the investigated systems. Indeed, the states localized on the molecules are embedded into the valence and conduction bands, with no generation of intragap energy levels and moderated change in the band gap. Therefore, Si-C bonds can enhance protection of the hydrogenated and chlorinated nanowire surfaces against oxidation without substantial modification of the electronic properties. However, we calculated a significant charge transfer from the silicon nanowires to the octane moiety.

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 compounds the problem that the reproduction of knowledge is incomplete, impeding the transparency of science-based targets for the choices made in the energy transition. The FAIR data guiding principles are widely acknowledged as a way forward, but their operationalization is yet to be agreed upon within different research domains. We comprehensively test FAIR data practices in the low carbon energy research domain. 80 databases representative for data needed to support the low carbon energy transition are screened. Automated and manual tests are used to 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 energy data and suggest how to prioritize activities., (© 2022. The Author(s).)

The thermodynamic stability of hydroxylated graphane, that is, fully sp 3 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., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

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.

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.

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.

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.

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(101̅0) 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.

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.

We performed a comparative study of the adsorption of an in vitro selected peptide on two different carbon surfaces: a flat graphene and a curved (0,15) nanotube. The sequence was selected from recent experiments, as the one giving the highest carbon affinity for carbon nanotubes. Rigid docking of the molecule on the two surfaces by a genetic algorithm was followed by molecular dynamics simulations with empirical force fields (OPLS-AA) in water at finite temperature. The total free energies of folding and adhesion and the quality of surface binding were determined, based on a combination of solvation energy, formation of hydrogen bonds, and amount of the apolar (hydrophobic) contact surface between peptide and carbon surface. For both cases, we find a strong adhesion energy and large nonpolar contact surface. Isoleucines and tryptophans are the most strongly bound residues to the two carbon surfaces, the latter one largely dominating. In the case of the carbon nanotube, the peptide shows several competing stable structures, corresponding to different possible molecular foldings, and a propensity to enhance the intramolecular stability by forming new hydrogen bonds. In both systems, different arrangements of the histidine and tryptophan residues enable a better adaptation to the carbon surfaces. These findings suggest that the experimentally observed surface specificity of the peptide on nanotubes may depend on its capability to support multiple strongly bound configurations.

We elucidate the structural properties of amorphous SiSe2 by first-principles molecular dynamics. The calculated structure factor is in very good agreement with experiments, as well as the number of corner- and edge-sharing tetrahedra. By focusing on the sequences of Si atoms linked via intra- and intertetrahedral bonds, we identify the predominant structural motifs. The sequences involving both corner- and edge-sharing connections are significantly more frequent than those formed exclusively by edge-shared Si atoms. Our results clarify a longstanding controversy on the structure of this prototypical disordered network-forming material.