Tight-binding potentials for transition metals and alloys

Thermodynamic predicting and atomistic modeling the favored compositions for Mg–Ni–Y metallic glasses

For Mg–Ni–Y system, glass formation is jointly studied by thermodynamic calculations and atomistic simulations. The prediction results have extensive implications for the Mg-based family and could be of great help for guiding the composition design.

Mechanical properties and thermal stability of ultrathin molybdenum nanowires

The most stable structures of three ultrathin molybdenum (Mo) nanowires were predicted by the simulated annealing basin-hopping method (SABH) with the penalty algorithm.

Study of structures and thermodynamics of CuNi nanoalloys using a new DFT-fitted atomistic potential

Structure and thermodynamics of CuNi nanoalloys determined by a new DFT-fitted atomistic potential.

Investigation of the mechanical properties and local structural evolution of Ti60Zr10Ta15Si15 bulk metallic glass during tensile deformation: a molecular dynamics study

The investigations on the structural properties and local deformation mechanism of Ti₆₀Zr₁₀Ta₁₅Si₁₅ bulk metallic glass (BMG) have been conducted by using molecular dynamics (MD) simulations for the uniaxial tension process.

Segregation in bimetallic nanoparticles

Theoretical models and experimental results for segregation in bimetallic nanoparticles are discussed and compared in this perspective.

ABCluster: the artificial bee colony algorithm for cluster global optimization

Global optimization of cluster geometries is of fundamental importance in chemistry and an interesting problem in applied mathematics. We apply a swarm-intelligence based heuristic algorithm, i.e. the artificial bee colony algorithm to solve this problem for various kinds of clusters.

Investigation of Zr and Si diffusion behaviors during reactive diffusion – a molecular dynamics study

Molecular dynamics simulation was used to investigate the diffusion behaviors of Zr and Si atoms during a reactive diffusion which produces Zr silicide.

Au13−nAgn clusters: a remarkably simple trend

The planar to three dimensional transition of Au_13−nAg_n clusters is investigated.

Pool-BCGA: a parallelised generation-free genetic algorithm for the ab initio global optimisation of nanoalloy clusters

The Birmingham cluster genetic algorithm is a package that performs global optimisations for homo- and bimetallic clusters based on either first principles methods or empirical potentials. Here, we present a new parallel implementation of the code which employs a pool strategy in order to eliminate sequential steps and significantly improve performance. The new approach meets all requirements of an evolutionary algorithm and contains the main features of the previous implementation. The performance of the pool genetic algorithm is tested using the Gupta potential for the global optimisation of the Au10Pd10 cluster, which demonstrates the high efficiency of the method. The new implementation is also used for the global optimisation of the Au10 and Au20 clusters directly at the density functional theory level.

Temperature-dependent stability of stacking faults in Al, Cu and Ni: first-principles analysis

We present comparative analysis of microscopic mechanisms relevant to plastic deformation of the face-centered cubic (FCC) metals Al, Cu, and Ni, through determination of the temperature-dependent free energies of intrinsic and unstable stacking faults along [1 1̄ 0] and [1 2̄ 1] on the (1 1 1) plane using first-principles density-functional-theory-based calculations. We show that vibrational contribution results in significant decrease in the free energy of barriers and intrinsic stacking faults (ISFs) of Al, Cu, and Ni with temperature, confirming an important role of thermal fluctuations in the stability of stacking faults (SFs) and deformation at elevated temperatures. In contrast to Al and Ni, the vibrational spectrum of the unstable stacking fault (USF[1 2̄ 1]) in Cu reveals structural instabilities, indicating that the energy barrier (γusf) along the (1 1 1)[1 2̄ 1] slip system in Cu, determined by typical first-principles calculations, is an overestimate, and its commonly used interpretation as the energy release rate needed for dislocation nucleation, as proposed by Rice (1992 J. Mech. Phys. Solids 40 239), should be taken with caution.

Validation of classical force fields for the description of thermo-mechanical properties of transition metal materials

It is demonstrated that classical force fields validated through the density functional theory (DFT) calculations of small titanium and nickel clusters can be applied for the description of thermo-mechanical properties of corresponding materials. This has been achieved by means of full-atom molecular dynamics simulations of nanoindentation of amorphous and nanostructured Ti and Ni-Ti materials. The theoretical analysis performed and comparison with experimental data demonstrate that the utilized classical force fields for Ti-Ti, Ni-Ni and Ni-Ti interactions describe reasonably well hardness and the Young's modulus of these materials. This observation is of the general nature and can be utilized for similar numerical exploration of thermo-mechanical properties of a broad range of materials.

Structural order in ultrathin films of the monolayer protected clusters based upon 4 nm gold nanocrystals: an experimental and theoretical study

The structural order in ultrathin films of monolayer protected clusters (MPCs) is important in a number of application areas but can be difficult to demonstrate by conventional methods, particularly when the metallic core dimension, d, is in the intermediate size-range, 1.5 < d < 5.0 nm. Here, improved techniques for the synthesis of monodisperse thiolate-protected gold nanoparticles have made possible the production of dodecane-thiolate saturated ∼4 ± 0.5 nm Au clusters with single-crystal core structure and morphology. An ultrathin ordered film or superlattice of these nanocrystal-core MPCs is prepared and investigated using aberration corrected scanning/transmission electron microscopy (STEM) which allowed imaging of long-range hexagonally ordered superlattices of the nanocrystals, separated by the thiolate groups. The lattice constants determined by direct imaging are in good agreement with those determined by small-angle electron diffraction. The STEM image revealed the characteristic grain boundary (GB) with sigma (Σ) 13 in the interface between two crystals. The formation and structures found are interpreted on the basis of theoretical calculations employing molecular dynamics (MD) simulations and coarse-grained (CG) approach.

Chiral gold nanowires with Boerdijk-Coxeter-Bernal structure

A Boerdijk-Coxeter-Bernal (BCB) helix is made of linearly stacked regular tetrahedra (tetrahelix). As such, it is chiral without nontrivial translational or rotational symmetries. We demonstrate here an example of the chiral BCB structure made of totally symmetrical gold atoms, created in nanowires by direct chemical synthesis. Detailed study by high-resolution electron microscopy illustrates their elegant chiral structure and the unique one-dimensional "pseudo-periodicity". The BCB-type atomic packing mode is proposed to be a result of the competition and compromise between the lattice and surface energy.

Modeling nanoscale inhomogeneities for quantitative HAADF STEM imaging

High-angle annular dark-field scanning transmission electron microscopy in conjunction with image simulation is an important tool to determine the structure of nanomaterials. We show that molecular dynamics calculations can be combined with multislice image simulations to account for the large effects of surface-enhanced thermal vibrations and structural relaxation on image intensities. Application to a catalytically important gold cluster shows that the image intensity is sensitive to these surface dominated effects with important implications for three-dimensional structural characterizations.

Vibrational and electronic excitations in gold nanocrystals

An experimental analysis of all elementary excitations--phonons and electron-holes--in gold nanocrystals has been performed using plasmon resonance Raman scattering. Assemblies of monodisperse, single-crystalline gold nanoparticles, specific substrates and specific experimental configurations have been used. Three types of excitations are successively analyzed: collective quasi-acoustical vibrations of the particles (Lamb's modes), electron-hole excitations (creating the so-called "background" in surface-enhanced Raman scattering) and ensembles of atomic vibrations ("bulk" phonons). The experimental vibrational density of states extracted from the latter contribution is successfully compared with theoretical estimations performed using atomic simulations. The dominant role of surface atoms over the core ones on lattice dynamics is clearly demonstrated. Consequences on the thermodynamic properties of nanocrystals such as the decrease of the characteristic Debye temperature are also considered.

Structure and solid solution properties of Cu-Ag nanoalloys

The nanoparticle phase diagram of an immiscible system is studied at the atomic level. Cu-Ag clusters with sizes 1000 and 2000 atoms, resulting from a global minimum search and belonging to icosahedral and crystalline structural motifs, are considered. We present the statistical analysis of the effect of temperature on the solubility of the two elements based on Metropolis Monte Carlo importance sampling. Our results suggest that the relevance of bulk phase diagrams to nanoparticles is limited to cases where the internal stress distribution does not deviate very much from uniform (e.g. sufficiently large crystalline clusters). In the general case, the principal interdependence between partial phase compositions and the overall cluster composition in nanoparticle phase diagrams need to be taken into account.

Computational design of apolipoprotein E4 inhibitors for Alzheimer's disease therapy from traditional Chinese medicine

Apolipoprotein E4 (Apo E4) is the major genetic risk factor in the causation of Alzheimer's disease (AD). In this study we utilize virtual screening of the world's largest traditional Chinese medicine (TCM) database and investigate potential compounds for the inhibition of ApoE4. We present the top three TCM candidates: Solapalmitine, Isodesacetyluvaricin, and Budmunchiamine L5 for further investigation. Dynamics analysis and molecular dynamics (MD) simulation were used to simulate protein-ligand complexes for observing the interactions and protein variations. Budmunchiamine L5 did not have the highest score from virtual screening; however, the dynamics pose is similar to the initial docking pose after MD simulation. Trajectory analysis reveals that Budmunchiamine L5 was stable over all simulation times. The migration distance of Budmunchiamine L5 illustrates that docked ligands are not variable from the initial docked site. Interestingly, Arg158 was observed to form H-bonds with Budmunchiamine L5 in the docking pose and MD snapshot, which indicates that the TCM compounds could stably bind to ApoE4. Our results show that Budmunchiamine L5 has good absorption, blood brain barrier (BBB) penetration, and less toxicity according to absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction and could, therefore, be safely used for developing novel ApoE4 inhibitors.

Effect of vacancy defects on generalized stacking fault energy of fcc metals

Molecular dynamics (MD) and density functional theory (DFT) studies were performed to investigate the influence of vacancy defects on generalized stacking fault (GSF) energy of fcc metals. MEAM and EAM potentials were used for MD simulations, and DFT calculations were performed to test the accuracy of different common parameter sets for MEAM and EAM potentials in predicting GSF with different fractions of vacancy defects. Vacancy defects were placed at the stacking fault plane or at nearby atomic layers. The effect of vacancy defects at the stacking fault plane and the plane directly underneath of it was dominant compared to the effect of vacancies at other adjacent planes. The effects of vacancy fraction, the distance between vacancies, and lateral relaxation of atoms on the GSF curves with vacancy defects were investigated. A very similar variation of normalized SFEs with respect to vacancy fractions were observed for Ni and Cu. MEAM potentials qualitatively captured the effect of vacancies on GSF.

Microyielding of core-shell crystal dendrites in a bulk-metallic-glass matrix composite

In-situ synchrotron x-ray experiments have been used to follow the evolution of the diffraction peaks for crystalline dendrites embedded in a bulk metallic glass matrix subjected to a compressive loading-unloading cycle. We observe irreversible diffraction-peak splitting even though the load does not go beyond half of the bulk yield strength. The chemical analysis coupled with the transmission electron microscopy mapping suggests that the observed peak splitting originates from the chemical heterogeneity between the core (major peak) and the stiffer shell (minor peak) of the dendrites. A molecular dynamics model has been developed to compare the hkl-dependent microyielding of the bulk metallic-glass matrix composite. The complementary diffraction measurements and the simulation results suggest that the interface, as Maxwell damper, between the amorphous matrix and the (211) crystalline planes relax under prolonged load that causes a delay in the reload curve which ultimately catches up with the original path.

Near-surface strain in icosahedra of binary metallic alloys: segregational versus intrinsic effects

A systematic structural analysis of FePt, CuAu, and Au icosahedral nanoparticles is presented. The uncovered particles are prepared by inert gas condensation and thermally equilibrated through in-flight optical annealing. Aberration-corrected high-resolution transmission electron microscopy reveals that the crystal lattice is significantly expanded near the particle surface. These experimental findings are corroborated by molecular statics simulations that show that this near-surface strain originates from both intrinsic strain due to the icosahedral structure and a partial segregation of the larger of the two alloy constituents to the particle surface.

Anisotropy of electromigration-induced void and island drift

By means of our novel self-learning kinetic Monte Carlo model (Latz et al 2012 J. Phys.: Condens. Matter 24 485005) we study the electromigration-induced drift of monolayer voids and islands on unpassivated surfaces of single crystalline Ag(111) and Ag(001) films at the atomic scale. Regarding the drift velocity, we find a non-monotonic size dependence for small voids. The drift direction is aligned with the electromigration force only along high symmetry directions, while halfway between, the angle enclosed by them is maximal. The magnitude of these directional deviations strongly depends on the system parameter, which are investigated in detail. The simulation results are in accordance with void motion observed in experiments performed on Ag(111).

Atomic scale simulations of pyrochlore oxides with a tight-binding variable-charge model: implications for radiation tolerance

Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd2Ti2O7 and Gd2Zr2O7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd2Ti2O7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd2Zr2O7. Therefore, the defect stability in A2B2O7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd2Ti2O7 amorphization induced by irradiation.

An optimized interatomic potential for Cu-Ni alloys with the embedded-atom method

We have developed a semi-empirical and many-body type model potential using a modified charge density profile for Cu-Ni alloys based on the embedded-atom method (EAM) formalism with an improved optimization technique. The potential is determined by fitting to experimental and first-principles data for Cu, Ni and Cu-Ni binary compounds, such as lattice constants, cohesive energies, bulk modulus, elastic constants, diatomic bond lengths and bond energies. The generated potentials were tested by computing a variety of properties of pure elements and the alloy of Cu, Ni: the melting points, alloy mixing enthalpy, lattice specific heat, equilibrium lattice structures, vacancy formation and interstitial formation energies, and various diffusion barriers on the (100) and (111) surfaces of Cu and Ni.

Structural and electronic properties of tungsten nanoclusters by DFT and basin-hopping calculations

The structural and electronic properties of small tungsten nanoclusters W_n (n = 2–16) were investigated by density functional theory (DFT) calculations.

Theoretical study of small sodium–potassium alloy clusters through genetic algorithm and quantum chemical calculations

Structures regarding the growth of sodium–potassium clusters obtained employing electronic structure methods—from high level coupled cluster calculations to all-electrons correlated MP2 and density functional theory.

Probing the Statistical Validity of the Ductile-to-Brittle Transition in Metallic Nanowires Using GPU Computing

We perform a large-scale statistical analysis (>2000 independent simulations) of the elongation and rupture of gold nanowires, probing the validity and scope of the recently proposed ductile-to-brittle transition that occurs with increasing nanowire length [Wu et al. Nano Lett. 2012, 12, 910-914]. To facilitate a high-throughput simulation approach, we implement the second-moment approximation to the tight-binding (TB-SMA) potential within HOOMD-Blue, a molecular dynamics package which runs on massively parallel graphics processing units (GPUs). In a statistical sense, we find that the nanowires obey the ductile-to-brittle model quite well; however, we observe several unexpected features from the simulations that build on our understanding of the ductile-to-brittle transition. First, occasional failure behavior is observed that qualitatively differs from that predicted by the model prediction; this is attributed to stochastic thermal motion of the Au atoms and occurs at temperatures as low as 10 K. In addition, we also find that the ductile-to-brittle model, which was developed using classical dislocation theory, holds for nanowires as small as 3 nm in diameter. Finally, we demonstrate that the nanowire critical length is higher at 298 K relative to 10 K, a result that is not predicted by the ductile-to-brittle model. These results offer practical design strategies for adjusting nanowire failure and structure and also demonstrate that GPU computing is an excellent tool for studies requiring a large number of independent trajectories in order to fully characterize a system's behavior.

The interpretation of polycrystalline coherent inelastic neutron scattering from aluminium

A new approach to the interpretation and analysis of coherent inelastic neutron scattering from polycrystals (poly-CINS) is presented. This article describes a simulation of the one-phonon coherent inelastic scattering from a lattice model of an arbitrary crystal system. The one-phonon component is characterized by sharp features, determined, for example, by boundaries of the (Q, ω) regions where one-phonon scattering is allowed. These features may be identified with the same features apparent in the measured total coherent inelastic cross section, the other components of which (multiphonon or multiple scattering) show no sharp features. The parameters of the model can then be relaxed to improve the fit between model and experiment. This method is of particular interest where no single crystals are available. To test the approach, the poly-CINS has been measured for polycrystalline aluminium using the MARI spectrometer (ISIS), because both lattice dynamical models and measured dispersion curves are available for this material. The models used include a simple Lennard-Jones model fitted to the elastic constants of this material plus a number of embedded atom method force fields. The agreement obtained suggests that the method demonstrated should be effective in developing models for other materials where single-crystal dispersion curves are not available.

Efficient parallelization of short-range molecular dynamics simulations on many-core systems

This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly inhomogeneous systems like nanodevices or nanostructured materials. In the proposed scheme the calculation of the forces and the generation of neighbor lists are divided into small tasks. The tasks are then executed by a thread pool according to a dependent task schedule. This schedule is constructed in such a way that a particle is never accessed by two threads at the same time. Benchmark simulations on a typical 12-core machine show that the described algorithm achieves excellent parallel efficiencies above 80% for different kinds of systems and all numbers of cores. For inhomogeneous systems the speedups are strongly superior to those obtained with spatial decomposition. Further benchmarks were performed on an Intel Xeon Phi coprocessor. These simulations demonstrate that the algorithm scales well to large numbers of cores.