Local Minimum Energy Configurations Research Articles

Ab initio density-functional studies of 13-atom Cu and Ag clusters

The putative ground-state structures of 13-atom Cu and Ag clusters have been studied using ab initio molecular-dynamics (AIMD) based on density-functional theory (DFT). An ensemble of low-energy configurations, collected along the AIMD trajectory and optimized to nearest local minimum-energy configurations, were studied. An analysis of the results suggests the existence of low-symmetric bilayer structures as strong candidates for the putative ground-state structure of Cu13 and Ag13 clusters. These bilayer structures are markedly different from a buckled bi-planar (BBP) configuration and energetically favorable, by about 0.4–0.5 eV, than the latter proposed earlier by others. Our study reveals that the structure of the resulting putative global-minimum configuration is essentially independent of the nature of basis functions (i.e., plane waves vs. pseudoatomic orbitals) employed in the calculations, for a given exchange-correlation functional. The structural configurations obtained from plane-wave-based DFT calculations show a noticeably tighter or dense first-shell of Cu and Ag atoms. A comparison of our results with recent full-potential DFT simulations is presented.

Generalized stacking fault energies of Cr23C6 carbide: A first-principles study

In many high temperature-resistant Ni-based superalloys, M23C6 carbides form during processing and remain as non-metallic inclusions during the materials use in application. M23C6 type inclusions are principal sites for potential fatigue crack initiation, thus the accurate quantification of their energy barriers for deformation is necessary for in-depth understanding of the overarching mechanical behavior of the material system. In this study, the generalized stacking fault energies (GSFE) are theoretically determined for chromium-rich types of M23C6 carbides (i.e., Cr23C6) in two prominent slip systems: {1 1 1}〈112¯〉 and {1 1 1}〈101¯〉. The results present GSFE curves with double saddle points in both slip systems. The double saddle points of the GSFE curves are explained via the electronic structure of atoms near the slip plane. At deformation quantified by half of a Burgers vector (i.e., 0.5 bp), a pentacyclic charge density distribution appears representing a local minimum energy configuration, which results in a valley of the GSFE curve. Furthermore, the effective coordination number (n) and the distortion index (Δd) of the coordination polyhedrons are employed to characterize the structural change. The analysis reveals that the values of the indexes n and Δd at a displacement value of 0.5 bp are close to the values of a perfect Cr23C6 crystal, while comparatively the distortion index is higher at the saddle points. These results provide new insights into the deformation pathways of M23C6 carbides.

Local structural excitations in model glasses

Structural excitations of model Lennard-Jones glass systems are investigated using the activation-relaxation technique (ART$n$), which explores the potential energy landscape around a local minimum energy configuration by converging to a nearby saddle-point configuration. Performing ART$n$ results in a distribution of barrier energies that is single-peaked for well-relaxed samples. The present work characterizes such atomic-scale excitations in terms of their local structure and environment. It is found that, at zero applied stress, many of the identified events consist of chainlike excitations that can either be extended or ringlike in their geometry. The location and barrier energy of these saddle-point structures are found to correlate with the type of atom involved, and with spatial regions that have low Kelvin eigenshear moduli and are close to the excess free volume within the configuration. Such correlations are, however, weak and more generally the identified local structural excitations are seen to exist throughout the model glass sample. The work concludes with a discussion within the framework of $\ensuremath{\alpha}$ and $\ensuremath{\beta}$ relaxation processes that are known to occur in the undercooled liquid regime.

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

Generation of c-component edge dislocations in α-zirconium during neutron irradiation – An atomistic study

The nucleation and multiplication of c-component edge dislocation segments during neutron irradiation in zirconium and its alloys is known to have important consequences to their in-reactor deformation behavior. Although there are ample experimental observations showing the close correlation between the edge-type and the screw-type of c-dislocations, the relation between them is unclear. In this paper, we performed atomistic study of the interaction between a [0 0 0 1] screw dislocation and a vacancy cluster in the form of a platelet on the basal plane. The local minimum-energy configuration was obtained using the conjugate-gradient method, with boundary relaxation achieved via a modified Green’s function method. Under stress-free conditions, the vacancy clusters maintained their cavity nature. With a [0 0 0 1] screw dislocation in the close neighborhood, vacancy clusters containing more than 23 vacancies collapse into faulted vacancy loops. Interaction at even closer range leads to the disappearance of the vacancy cluster and the development of an edge component on the originally straight screw dislocation in the form of a helical line. The implications of these findings are discussed in relation to the experimentally observed behavior of growth acceleration in zirconium and its alloys.

Pathfinder: A parallel search algorithm for concerted atomistic events

An algorithm has been designed to search for the escape paths with the lowest activation barriers when starting from a local minimum-energy configuration of a many-atom system. The pathfinder algorithm combines: (1) a steered eigenvector-following method that guides a constrained escape from the convex region and subsequently climbs to a transition state tangentially to the eigenvector corresponding to the lowest negative Hessian eigenvalue; (2) discrete abstraction of the atomic configuration to systematically enumerate concerted events as linear combinations of atomistic events; (3) evolutionary control of the population dynamics of low activation-barrier events; and (4) hybrid task + spatial decompositions to implement massive search for complex events on parallel computers. The program exhibits good scalability on parallel computers and has been used to study concerted bond-breaking events in the fracture of alumina.

A molecular interpretation of vitreous boron oxide dynamics

The mobility of vitreous boron oxide is studied by molecular dynamics simulation. A polarization model that incorporates induced dipoles arising both from charges and from other induced dipoles on atoms with nonzero polarizability is used to simulate boron oxide glass at various temperatures above the glass transition temperature. Particle mobility is investigated through the calculation of the self-intermediate scattering function and the mean-squared displacement. The calculations clearly reveal a two-step relaxation with a plateau at intermediate times for all investigated temperatures. With respect to atomic species, boron atoms are less mobile than oxygen atoms at all temperatures within the plateau region. Through analyzing particle trajectories, it is revealed that BO(3) groups move as one unit and follow each other in a stringlike manner. Three connected BO(3) groups comprise a six-membered boroxol ring, which is shown to move in a collective manner, requiring the simultaneous movement of all ring atoms. The boroxol ring is observed to be confined, or caged, during the plateau region, and jumps to a new location at longer times. This observation is linked to the concept of strong versus fragile glass formers and the potential energy landscape. In addition to the caging feature, an overshoot or dip occurs in the plateau regions of the mean-squared displacement and self-intermediate scattering functions respectively. These features are followed by a ringing pattern, previously associated with finite size effects in other strong glass formers, which persist for the duration of the plateau region. Both features are shown to be consistent with the bending of atomic "cages" from the plane of the boroxol ring, and arise due to the displacement of atoms from local minimum energy configurations.

Structural changes at grain boundaries in bcc iron induced by atomic collisions

Symmetrical tilt and twist grain boundary structures have been simulated in bcc iron using a many-body potential of the Finnis–Sinclair form. Initial structures were relaxed to the local minimum energy configuration using molecular dynamics. The width and relative energies of the resulting grain boundaries have been calculated. Collision cascades have been initiated in the structure by imparting initial energy to a single Fe atom and the interaction of the cascade with the grain boundary has been studied again using molecular dynamics simulations. The cascades were chosen where the primary knock-on atom (PKA) had initial energy of 1 keV and the orientation and distance of the PKA were changed in order to generate some statistical information concerning the radiation damage near the interface. The results show an increased radiation damage in the grain boundary region compared to the bulk material. The interstitials that form in the boundary region seem to be stable and do not move away from the boundary during the recrystallisation phase of the collision cascade. Clusters of interstitials are easily produced at the boundary in either structure but the defects induced near the twist boundary are more extensive than those near the tilt boundary.

Modelling radiation effects at grain boundaries in bcc iron

Symmetrical tilt grain boundary structures have been statically simulated in bcc iron using a many body potential of the Finnis–Sinclair form. Different tilt angles were considered and the structures relaxed to the local minimum energy configurations using molecular dynamics. The resulting grain boundaries are classified in terms of their energy and structure. Collision cascades are initiated in the structure by imparting initial energy to a single particle and the interaction of the cascade with the grain boundary has been studied again by using molecular dynamics simulations. The effect of the cascade interaction with one symmetrical tilt grain boundary is reported.

Copper clusters simulated by a many-body tight-binding potential

Abstract We have estimated the classical ground states of copper clusters consisting of 13–1289 atoms using a tight-binding many-body potential. Starting from perfect face-centred-cubic (f.c.c.) and icosahedral structures, each system was allowed to evolve toward its inherent structure (that is the nearest local minimum energy configuration at T = 0K). The (relaxed) icosahedra turned out to be more cohesive for all the directly simulated systems. We have also estimated the critical size at which the f.c.c. structure becomes energetically favourable performing nuclear fits of the ground-state energy for both structures. The icosahedral configuration is more stable for clusters containing less than about 1500 atoms whereas f.c.c. structures are preferred for clusters of larger size. From the simulated phonon spectra, one has that the mean square displacement of an atom depends on the shell it belongs to and that, at least in the pure harmonic approximation, atoms near the centre of the cluster perform small...

The energetics and structure of nickel clusters: Size dependence

The energetics of nickel clusters over a broad size range are explored within the context of the many-body potentials obtained via the embedded atom method. Unconstrained local minimum energy configurations are found for single crystal clusters consisting of various truncations of the cube or octahedron, with and without (110) faces, as well as some monotwinnings of these. We also examine multitwinned structures such as icosahedra and various truncations of the decahedron, such as those of Ino and Marks. These clusters range in size from 142 to over 5000 atoms. As in most such previous studies, such as those on Lennard-Jones systems, we find that icosahedral clusters are favored for the smallest cluster sizes and that Marks’ decahedra are favored for intermediate sizes (all our atomic systems larger than about 2300 atoms). Of course very large clusters will be single crystal face-centered-cubic (fcc) polyhedra: the onset of optimally stable single-crystal nickel clusters is estimated to occur at 17 000 atoms. We find, via comparisons to results obtained via atomistic calculations, that simple macroscopic expressions using accurate surface, strain, and twinning energies can usefully predict energy differences between different structures even for clusters of much smaller size than expected. These expressions can be used to assess the relative energetic merits of various structural motifs and their dependence on cluster size.