Medium-sized Clusters Research Articles

Simple maintenance of Beowulf clusters in an academic environment

We present our experiences with an evolving installation system for small- to medium-sized clusters which are typically used in academic settings to support a combination of teaching and research. ...

Theoretical exploration of pump and probe in medium-sized Na clusters

We investigate pump and probe dynamics in simple metal clusters of medium size. Test cases areNa9+ andNa41+.The initial pulse ionizes the cluster and excites ionic motion by a sudden increaseof Coulomb pressure. The subsequent ionic breathing motion can be directlymapped by the probe pulses if the analysing frequency stays sufficiently below theplasmon resonance peak at all times. Pump and probe experiments could thusprovide direct access to ionic dynamics in electronically excited metalclusters, in the spirit of pump and probe experiments on small molecules.

Nonorthogonal tight-binding model for germanium

We present a pair of nonorthogonal tight-binding (TB) models for germanium within the NRL-TB approach. One uses an ${\mathrm{sp}}^{3}$ basis, and is optimized for total-energy calculations by fitting to the total energy and band structures of several high-symmetry lattice structures. The other uses an ${\mathrm{sp}}^{3}{d}^{5}$ basis to accurately reproduce the diamond lattice band structure, including three conduction bands. We present tests of the ${\mathrm{sp}}^{3}$ TB model on bulk properties, including high-symmetry lattice structure energies and volumes and the diamond lattice elastic constants, phonons, and band structure. We also present results for point defect formation and relaxation energies and low index surface energies and stresses, many of which have not been calculated using the density-functional theory (DFT), as well as some medium size clusters. Taking advantage of the computational efficiency of the TB approach, we go beyond the capabilities of standard density-functional theory, combining it with molecular dynamics to simulate finite temperature properties of Ge. We get good agreement with experiment for the atomic mean-squared displacement and the melting point approximated using the Lindemann criterion, as well as the linear thermal-expansion coefficient. In another demonstration of the efficiency of the TB approach, we present results for the structure and electronic properties of a high angle twist grain boundary (GB). In agreement with DFT simulation we see a range of structures with comparable energies, all with electronic states deep in the band gap. In contrast to previous work we find some different geometries with perfect fourfold coordination of all atoms in the GB. Despite the perfect coordination, these structures also have deep electronic states in the gap, indicating that the GB will be electrically active.

Properties of small- to medium-sized mercury clusters from a combined ab initio, density-functional, and simulated-annealing study.

Relativistic coupled-cluster and second-order many-body perturbation theories were used to construct two- and three-body potentials for the interaction between mercury atoms. A subsequent combined simulated-annealing downhill simplex and conjugate gradient-optimization procedure gave global minima for mercury clusters with up to 30 atoms. The calculations reveal magic cluster numbers of 6, 13, 19, 23, 26, and 29 atoms. At these cluster sizes, the static dipole polarizability obtained from density-functional theory has a minimum. The calculations also reveal a fast convergence of the polarizability towards the bulk limit in contrast to the singlet-triplet gap or the ionization potential.

Stability and reactivity patterns of medium-sized vanadium oxide cluster cations VxOy+ (4  x  14)

Gas-phase vanadium oxide clusters VxOy+ in the size range 4 ⩽ x ⩽ 14 have been produced via laser vaporisation in a continuous flow of He/O2 carrier gas. The cluster distributions were subsequently characterised by their scattering behaviour at low-density gas targets (10−4 − 2 × 10−3 mbar). The experimental scattering cross sections were used to study differences in the interactions with rare gases, hydrocarbons (alkanes: methane, propane, n-butane and alkenes: ethene, propene, but-1-ene) and also small inorganic molecules (N2, O2, CO, NO, SO2). The compositions of the dominant oxide clusters reveal the predominance of vanadium atoms in the formal oxidation states +4 and +5. The interaction patterns of these oxide clusters with rare gases show no indications for fragmentation at collision energies corresponding to a cluster beam velocity of 900 ms−1. Clusters with a composition of (V2O5)n+ have increased cross sections for the interaction with alkanes and alkenes. Indeed, for the alkenes stable adducts have been detected under the applied scattering conditions. The increased cross sections have been interpreted in terms of a strong reactivity towards hydrocarbons, which is in agreement with previous results on smaller vanadium oxide clusters (R. C. Bell, K. A. Zemski, K. P. Kerns, H. T. Deng and A. W. Castleman, Jr., J. Phys. Chem. A, 1998, 102, 1733).

Electric field induced transitions in water clusters

The influence of an external uniform electrostatic field on the internal energy and polarization of a medium-sized water cluster, consisting of 40 molecules is studied at four temperatures: 150, 170, 200, and 240 K, by means of the Monte Carlo method. The external field is slowly varied in the 0.5×10 7–7×10 7 V/cm range. The system shows an abrupt change of its properties at some critical value of the field, E tr, where a transition from a normal (solid-like or liquid-like) to a superpolarized cluster state is observed. This process has the character of a first-order phase transition and is accompanied by the absorption of heat. For intermediate field strengths, polarization has been found to increase with increasing temperature, an effect, which through a simple analytical model has been shown to be the result of the interplay between the strength of the attractive water–water interactions and the strength of the external field. Also E tr has been found to decrease with increasing temperature, in contrast to the behavior dictated by the Clausius–Clayperon equation for field-induced transitions between equilibrium states.

Phyllodes Tumor of the Breast

To develop more useful criteria for differentiating benign phyllodes tumor (BPT) from fibroadenoma (FA) of the breast on fine needle aspiration cytology (FNAC), with a focus on architectural features of epithelial clusters. The smears of 18 cases obtained by preoperative FNAC, each with tissue-proven BPT, were compared to those of 25 cases of FA. Several features of epithelial clusters in both groups were studied, with histologic correlation. BPT exhibited large epithelial clusters longer than 1 mm, with a wavy or folded shape, that could be distinguished from the small or medium-sized clusters with tubular, blunt-branching or monolayered contours in FA. This appearance of BPT was equivalent to the characteristic phyllodes pattern of its histology. The size and shape of epithelial clusters are important diagnostic clues in addition to several findings that have been described as differentiating BPT from FA on FNAC.

Pinning and implantation of size-selected metal clusters: a topical review

This paper presents a topical review of the deposition of size-selected metal clusters, specifically Ag N +, on graphite, which has been explored via a combination of molecular dynamics (MD) simulations and scanning tunnelling microscopy (STM) experiments. The size-selected metal clusters were fabricated by a magnetron sputtering, gas aggregation cluster beam source. It has been shown that the clusters are pinned to the surface when the impact energy exceeds a critical value, which is proportional to the cluster size. At very high cluster impact energies, the clusters penetrate the graphite surface and become implanted. For medium size clusters ( N=20–200 atoms), it was found via the MD simulations that the implantation depth varies linearly with the impact energy and cluster size as D∼ E/ N 2/3. For small clusters, e.g. Ag 7 +, both MD simulations and experiment revealed a linear dependence of the implantation depth on cluster velocity rather than cluster impact energy.

Partitioning Method Applied to X-Ray Absorption Near Edge Structure Calculations

So far we have developed an efficient technique to calculate the X-ray absorption near edge structure (XANES) spectra based on partitioning method to include important full multiple scatterings but exclude unimportant scatterings. In this paper we discuss some techniques to obtain rapid convergence of partial summation and give some illustrative examples applied to medium size (about 50) and large clusters (>100 atoms). The best approach to obtain good convergence to full MS calculation and high efficiency depends on cluster size. Though full MS calculations need much time , that is drastically shortened to less than 10–30% for the large clusters by use of the present methods.

Computation of Large Systems with Economic Basis Set: Simulation of Diamond Metallization Using Titanium

Economic basis sets for ab initio calculations of systems involving titanium (Ti) atom have been studied. The basis set in which the polarization and diffuse functions are applied only to Ti and its nearest neighboring atoms is shown to give reliable binding energies and geometries for various carbon-based compounds. Such a basis set is used as the economic basis set for calculations of medium-sized clusters simulating Ti and diamond interactions. For large clusters composed of Ti and C atoms, the more economic basis set 6-31G is considered for obtaining reliable energetics with the correction using high-level single-point energy calculations with 6-31+G*. The approach to determine the economic basis set is expected to be useful for a general system containing transition metal element. With the economic basis sets, simulations of diamond metallization have revealed reasonable behavior of the Ti atomic interaction with diamond film. On the basis of the determined energetics of Ti deposition, the high Ti concentration in CVD diamond after metallization is conjectured to occupy the grain boundaries rather than the bulk of diamond grain. For a Ti atom with high kinetic energy, the Ti atom may penetrate through a diamond (001) surface more easily than through a diamond (111) surface. In the diamond bulk, the Ti atom may energetically favor to substitute a C site more than diffusion.

Structure and electronic properties ofGen(n=2–25)clusters from density-functional theory

The geometrical and electronic structures of the germanium clusters with up to 25 atoms are studied by using density-functional theory with the generalized gradient approximation. The ${\mathrm{Ge}}_{n}$ clusters follow a prolate growth pattern with $n>~13.$ For medium-sized clusters, we find two kinds of competing structures, stacked layered structures and compact structures. The stacked layered structures with capped tetrahedron ${\mathrm{Ge}}_{9}$ cluster are more stable than compact structures and other stacked structures. The size dependence of cluster binding energies, highest-occupied and lowest-unoccupied molecular orbital gap, and ionization potentials are discussed and compared with experiments.

Magic number behavior for heat capacities of medium-sized classical Lennard-Jones clusters

Monte Carlo methods were used to calculate heat capacities as functions of temperature for classical atomic clusters of aggregate sizes 25⩽N⩽60 that were bound by pairwise Lennard-Jones potentials. The parallel tempering method was used to overcome convergence difficulties due to quasiergodicity in the solid-liquid phase-change regions. All of the clusters studied had pronounced peaks in their heat capacity curves, most of which corresponded to their solid-liquid phase-change regions. The heat capacity peak height and location exhibited two general trends as functions of cluster size: for N=25 to 36, the peak temperature slowly increased, while the peak height slowly decreased, disappearing by N=37; for N=30, a very small secondary peak at very low temperature emerged and quickly increased in size and temperature as N increased, becoming the dominant peak by N=36. Superimposed on these general trends were smaller fluctuations in the peak heights that corresponded to “magic number” behavior, with local maxima found at N=36, 39, 43, 46, and 49, and the largest peak found at N=55. These magic numbers were a subset of the magic numbers found for other cluster properties, and can be largely understood in terms of the clusters’ underlying geometries. Further insights into the melting behavior of these clusters were obtained from quench studies and by examining rms bond length fluctuations.

Targeting of liver tumour in rats by selective delivery of holmium-166 loaded microspheres: a biodistribution study

Intra-arterial administration of beta-emitting particles that become trapped in the vascular bed of a tumour and remain there while delivering high doses, represents a unique approach in the treatment of both primary and metastatic liver tumours. Studies on selective internal radiation therapy of colorectal liver metastases using yttrium-90 glass microspheres have shown encouraging results. This study describes the biodistribution of 40-microm poly lactic acid microspheres loaded with radioactive holmium-166, after intra-arterial administration into the hepatic artery of rats with implanted liver tumours. Radioactivity measurements showed >95% retention of injected activity in the liver and its resident tumour. The average activity detected in other tissues was < or =0.1%ID/g, with incidental exceptions in the lungs and stomach. Very little 166Ho activity was detected in kidneys (<0.1%ID/g), thereby indicating the stability of the microspheres in vivo. Tumour targeting was very effective, with a mean tumour to liver ratio of 6. 1+/-2.9 for rats with tumour (n=15) versus 0.7+/-0.5 for control rats (n=6; P<0.001). These ratios were not significantly affected by the use of adrenaline. Histological analysis showed that five times as many large (>10) and medium-sized (4-9) clusters of microspheres were present within tumour and peritumoural tissue, compared with normal liver. Single microspheres were equally dispersed throughout the tumour, as well as normal liver parenchyma.

Thermal properties of medium-sized Ge clusters

The thermal behavior of germanium clusters is studied by using tight-binding molecular dynamics. The lowest energy structures of Ge n clusters up to 21 atoms are optimized with a genetic algorithm. Some high symmetric layered structures are found in medium-sized clusters and large clusters can be constructed from small cluster subunits. We discuss the melting temperature as a function of the cluster size. Even-odd alternation is found in the size range n=11–17. The Ge n clusters with n=7, 12 and 19 have particularly high melting points, which correspond to the relatively high stabilities of their ground state structures. We find that the large clusters can be dissociated into small clusters upon heating and an interesting two-stage melting behavior is revealed in the case of Ge 21.

Spectroscopic evidence for the tricapped trigonal prism structure of semiconductor clusters

We have obtained photoelectron spectra (PES) for silicon cluster anions with up to 20 atoms. Efficient cooling of species in the source has allowed us to resolve multiple features in the PES for all sizes studied. Spectra for an extensive set of low-energy Si(-)(n) isomers found by a global search have been simulated using density functional theory and pseudopotentials. Except for n = 12, calculations for Si(-)(n) ground states agree with the measurements. This does not hold for other plausible geometries. Hence PES data validate the tricapped trigonal prism morphologies for medium-sized Si clusters.

Observing FcepsilonRI signaling from the inside of the mast cell membrane.

We have determined the membrane topography of the high-affinity IgE receptor, FcstraightepsilonRI, and its associated tyrosine kinases, Lyn and Syk, by immunogold labeling and transmission electron microscopic (TEM) analysis of membrane sheets prepared from RBL-2H3 mast cells. The method of Sanan and Anderson (Sanan, D.A., and R.G.W. Anderson. 1991. J. Histochem. Cytochem. 39:1017-1024) was modified to generate membrane sheets from the dorsal surface of RBL-2H3 cells. Signaling molecules were localized on the cytoplasmic face of these native membranes by immunogold labeling and high-resolution TEM analysis. In unstimulated cells, the majority of gold particles marking both FcepsilonRI and Lyn are distributed as small clusters (2-9 gold particles) that do not associate with clathrin-coated membrane. Approximately 25% of FcepsilonRI clusters contain Lyn. In contrast, there is essentially no FcepsilonRI-Syk colocalization in resting cells. 2 min after FcepsilonRI cross-linking, approximately 10% of Lyn colocalizes with small and medium-sized FcepsilonRI clusters (up to 20 gold particles), whereas approximately 16% of Lyn is found in distinctive strings and clusters at the periphery of large receptor clusters (20-100 gold particles) that form on characteristically osmiophilic membrane patches. While Lyn is excluded, Syk is dramatically recruited into these larger aggregates. The clathrin-coated pits that internalize cross-linked receptors bud from membrane adjacent to the Syk-containing receptor complexes. The sequential association of FcstraightepsilonRI with Lyn, Syk, and coated pits in topographically distinct membrane domains implicates membrane segregation in the regulation of FcstraightepsilonRI signaling.

Ionization Bands and Electron Affinities of Mixed Boron−Nitrogen BnNnClusters (n= 3,4,5)

The ionization bands and electron affinities of medium-size BnNn clusters (n = 3, 4, 5) have been investigated by means of one-particle Green's function calculations using the outer-valence Green's function (OVGF) approximation or the third-order algebraic diagrammatic construction [ADC(3)] scheme. Despite their structural similarity with isoelectronic cumulenic carbon chains and rings, these clusters do not exhibit a significant breakdown of the orbital picture of ionization, with the exception of the N2s bands (eb > 25 eV), which relate exclusively to complex sets of shake-up lines. The main (one-hole) ionization bands provide specific signatures for ring topologies based on n equivalent vertices, whereas a reduction of the curvature of N−B−N bridges with increasing system size can be followed from the N2s bands. The B3N3- anion is slightly stable against electron loss, whereas negative vertical electron affinities are obtained for B4N4 and B5N5.

Structures of Germanium Clusters: Where the Growth Patterns of Silicon and Germanium Clusters Diverge

We have performed a systematic ground state geometry search for ${\mathrm{Ge}}_{n}$ neutrals and cations in the $n\ensuremath{\le}16$ size range using density functional theory--local density approximation and gradient-corrected methods. Like their silicon analogs, medium-sized Ge clusters are stacks of tricapped trigonal prism subunits. However, the structures of ${\mathrm{Ge}}_{n}$ and ${\mathrm{Si}}_{n}$ for $n\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}13$ and $n\ensuremath{\ge}15$ differ in details. The onset of the structural divergence between the growth patterns of Si and Ge clusters is confirmed by the measurements of gas phase ion mobilities, fragmentation pathways, and dissociation energies.

Structure of hydrogenated silicon clusters. Medium-sized clusters

The structures of the SinHm clusters containing 10 to 70 silicon atoms and different numbers of hydrogen atoms are calculated in the MINDO/3 approximation using the Monte Carlo technique. The geometry optimization of the clusters showed the existence of several structural varieties that determine the optimal geometry of the clusters differing in size and hydrogen content. Small clusters (n < 20) with various geometrical configurations often have a hollow structure if the number of silicon atoms in the cluster is more than 12. For 20 ≤ n < 60 and the hydrogen content m ≤ n, hollow spheroidal geometry is most favorable. Staring from n ≈ 56−60, diamond structures are more favorable. The ratio c = m/n < 1, at which the spheroidal structure remains optimal, decreases with further increase in n.

Effect of embedding and cluster size on the ab initio study of potassium adsorption at rutile(110)

The results of Hartree–Fock ab initio model calculations for the adsorption of a single potassium atom on a bridging oxygen site of the rutile(110) surface are presented. The surface is simulated with small clusters Ti2O4 and Ti4O8, either embedded in a finite array of total ion potentials and point charges or saturated with H, OH, and H2O. The effect of the different embedding techniques on physical aspects of the adsorption process is discussed in terms of electronic structure and energetics. Comparison of available experimental data and previous theoretical studies with the present results show that medium-sized model clusters give a reasonable description of the adsorption process, independent of the embedding method. For very small models, even the qualitative picture of the K—TiO2 interaction changes when different embedding techniques are used. These results can be generalized to develop rules for designing cluster models for metal adsorption on rutile surfaces. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 127–132, 1999