An isothermal-isobaric Langevin thermostat for simulating nanoparticles under pressure: Application to Au clusters

We present a method for simulating clusters or, molecules subjected to an external pressure, which is exerted by a pressure-transmitting medium. It is based on the canoninical Langevin thermostat, but extended in such a way that the Brownian forces are allowed to operate only from the region exterior to the cluster. We show that the frictional force of the Langevin thermostat is linked to the pressure of the reservoir in a unique way, and that this property manifests itself when the particle it acts upon is not pointlike but has finite dimensions. By choosing appropriately the strength of the random forces and the friction coefficient, both temperature and pressure can be controlled independently. We illustrate the capabilities of this new method by calculating the compressibility of small gold clusters under pressure.

Neutral and Charged 1-Butyl-3-methylimidazolium Triflate Clusters: Equilibrium Concentration in the Vapor Phase and Thermal Properties of Nanometric Droplets

Ground state energy, structure, and harmonic vibrational modes of 1-butyl-3-methylimidazolium triflate ([bmim][Tf]) clusters have been computed using an all-atom empirical potential model. Neutral and charged species have been considered up to a size (30 [bmim][Tf] pairs) well into the nanometric range. Free energy computations and thermodynamic modeling have been used to predict the equilibrium composition of the vapor phase as a function of temperature and density. The results point to a nonnegligible concentration of very small charged species at pressures (P ~ 0.01 Pa) and temperatures (T 600 K) at the boundary of the stability range of [bmim][Tf]. Thermal properties of nanometric neutral droplets have been investigated in the 0 T 700 K range. A near-continuous transition between a liquidlike phase at high T and a solidlike phase at low T takes place at T ~ 190 K in close correspondence with the bulk glass point Tg ~ 200 K. Solidification is accompanied by a transition in the dielectric properties of the droplet, giving rise to a small permanent dipole embedded into the solid cluster. The simulation results highlight the molecular precursors of several macroscopic properties and phenomena and point to the close competition of Coulomb and dispersion forces as their common origin.

Model calculations for copper clusters on Au(111) surfaces

Using the semi-empirical embedded-atom method, the structure of small copper clusters on Au(111) surfaces has been investigated both by static and dynamic calculations. By varying the size of roughly circular clusters, the edge energy per atom is obtained; it agrees quite well with estimates based on experimental results. Small three-dimensional clusters tend to have the shape of a pyramid, whose sides are oriented in the directions of small surface energy. The presence of a cluster is found to distort the underlying lattice of adsorbed copper atoms. (C) 2002 Published by Elsevier Science B.V.

Desmoplastic Small Round Cell Tumor of Major Salivary Glands: Report of 1 Case and a Review of the Literature

Desmoplastic small round cell tumor is a rare malignant neoplasm mostly occurring in the vicinity of or within the peritoneal cavity, and is uncommon in the head and neck region. Tumor location within a major salivary gland is exceptional. We report a case of a 41-year-old Chinese man with a history of diabetes mellitus and end-stage renal failure on peritoneal dialysis with a desmoplastic small round cell tumor occurring in the left submandibular gland. Fine-needle aspiration cytology showed variably cohesive clusters of small cells with hyperchromatic nuclei and fine granular chromatin. On histology the neoplasm displayed classic features of a desmoplastic small round cell tumor with angulated nests of small round blue cells in a fibromyxoid/desmoplastic stroma. Neoplastic cells were immunoreactive for cytokeratins (AE1/3), desmin (paranuclear dot-like), WT-1 (nuclear), epithelial membrane antigen, and CD56. EWS gene translocation and EWS-WT1 gene fusion were detected by fluorescence in situ hybridization and reverse transcriptase polymerase chain reaction, respectively. The case presented is the sixth case of and the oldest reported patient with a desmoplastic small round cell tumor occurring in a major salivary gland to date. Desmoplastic small round cell tumor should be considered in the differential diagnosis of a salivary gland neoplasm with a basaloid or small cell pattern on fine-needle aspiration cytology.

The VLT-FLAMES survey of massive stars: observations centered on the Magellanic Cloud clusters NGC 330, NGC 346, NGC 2004, and the N11 region

We present new observations of 470 stars using the Fibre Large Array Multi-Element Spectrograph ( FLAMES) instrument in fields centered on the clusters NGC330 and NGC346 in the Small Magellanic Cloud (SMC), and NGC2004 and the N11 region in the Large Magellanic Cloud (LMC). A further 14 stars were observed in the N11 and NGC330 fields using the Ultraviolet and Visual Echelle Spectrograph (UVES) for a separate programme. Spectral classifications and stellar radial velocities are given for each target, with careful attention to checks for binarity. In particular, we have investigated previously unexplored regions around the central LH9/LH10 complex of N11, finding similar to 25 new O-type stars from our spectroscopy. We have observed a relatively large number of Be-type stars that display permitted Fe II emission lines. These are primarily not in the cluster cores and appear to be associated with classical Be-type stars, rather than pre main-sequence objects. The presence of the Fe II emission, as compared to the equivalent width of Ha, is not obviously dependent on metallicity. We have also explored the relative fraction of Be- to normal B-type stars in the field-regions near to NGC330 and NGC2004, finding no strong evidence of a trend with metallicity when compared to Galactic results. A consequence of service observations is that we have reasonable time-sampling in three of our FLAMES fields. We find lower limits to the binary fraction of O- and early B-type stars of 23 to 36%. One of our targets (NGC346-013) is especially interesting with a massive, apparently hotter, less luminous secondary component.

Exploring the free energy surfaces of clusters using reconnaissance metadynamics

A new approach is proposed for exploring the low-energy structures of small to medium-sized aggregates of atoms and molecules. This approach uses the recently proposed reconnaissance metadynamics method [G. A. Tribello, M. Ceriotti, and M. Parrinello. Proc. Natl. Acad. Sci. U.S.A. 107(41), 17509 (2010)] in tandem with collective variables that describe the average structure of the coordination sphere around the atoms/molecules. We demonstrate this method on both Lennard-Jones and water clusters and show how it is able to quickly find the global minimum in the potential energy surface, while exploring the finite temperature free energy surface. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3628676]

Large- and small-scale structure of the intermediate- and high-velocity clouds towards the LMC and SMC.

We employ Ca II K and Na I D interstellar absorption-line spectroscopy of early-type stars in the Large and Small Magellanic Clouds (LMC, SMC) to investigate the large- and small-scale structure in foreground intermediate- and high-velocity clouds (I/HVCs). Data include FLAMES-GIRAFFE Ca II K observations of 403 stars in four open clusters, plus FEROS or UVES spectra of 156 stars in the LMC and SMC. The FLAMES observations are amongst the most extensive probes to date of Ca II structures on ∼20 arcsec scales in Magellanic I/HVCs. From the FLAMES data within a 0 ∘.∘.∘.5 field of view, the Ca II K equivalent width in the I/HVC components towards three clusters varies by factors of ≥10. There are no detections of molecular gas in absorption at intermediate or high velocities, although molecular absorption is present at LMC and Galactic velocities towards some sightlines. The FEROS/UVES data show Ca II K I/HVC absorption in ∼60 per cent of sightlines. The range in the Ca II/Na I ratio in I/HVCs is from –0.45 to +1.5 dex, similar to previous measurements for I/HVCs. In 10 sightlines we find Ca II/O I ratios in I/HVC gas ranging from 0.2 to 1.5 dex below the solar value, indicating either dust or ionization effects. In nine sightlines I/HVC gas is detected in both H I and Ca II at similar velocities, implying that the two elements form part of the same structure.

Immunogold Detection of L-glutamate and D-serine in Small Synaptic-Like Microvesicles in Adult Hippocampal Astrocytes.

Glutamate and the N-methyl-D-aspartate receptor ligand D-serine are putative gliotransmitters. Here, we show by immunogold cytochemistry of the adult hippocampus that glutamate and D-serine accumulate in synaptic-like microvesicles (SLMVs) in the perisynaptic processes of astrocytes. The estimated concentration of fixed glutamate in the astrocytic SLMVs is comparable to that in synaptic vesicles of excitatory nerve terminals (∼45 and ∼55 mM, respectively), whereas the D-serine level is about 6 mM. The vesicles are organized in small spaced clusters located near the astrocytic plasma membrane. Endoplasmic reticulum is regularly found in close vicinity to SLMVs, suggesting that astrocytes contain functional nanodomains, where a local Ca(2+) increase can trigger release of glutamate and/or D-serine.

Calculation of the electronic properties of neutral and ionized divalent-metal clusters

The electronic properties of neutral and ionized divalent-metal clusters have been studied using a microscopic theory, which takes into account the interplay between van der Waals (vdW) and covalent bonding in the neutral clusters, and the competition between hole delocalization and polarization energy in the ionized clusters. By calculating the ground-state energies of neutral and ionized. Hg_n clusters, we determine the size dependence of the bond character and the ionization potential I_p(n). For neutral Hg_n clusters we obtain a transition from van del Waals to covalent behaviour at the critical size n_c ~ 10-20 atoms. Results for I_p(Hg_n) with n \le 20 are in good agreement with experiments, and suggest that small Hg_n^+ clusters can be viewed as consisting of a positive trimer core Hg_3^+ surrounded by n - 3 polarized neutral atoms.

On the localization of electrons and holes in Hg_n and rare-gas clusters

We have used a microscopic theory to study the size dependence of the degree of localization of the valence electrons and holes in neutral an ionized rare-gas and Hg_n clusters. We discuss under which circumstances localization of the electrons and holes is favoured. We have calculated the ionization potential of Xe_n, Kr_n and small Hg_n clusters. Good agreement with experiments is obtained. We have also determined the dependence of the ionization potential on cluster structure.

Theoretical study of magnetism, structure and chemical order in transition-metal alloy clusters

Research on transition-metal nanoalloy clusters composed of a few atoms is fascinating by their unusual properties due to the interplay among the structure, chemical order and magnetism. Such nanoalloy clusters, can be used to construct nanometer devices for technological applications by manipulating their remarkable magnetic, chemical and optical properties. Determining the nanoscopic features exhibited by the magnetic alloy clusters signifies the need for a systematic global and local exploration of their potential-energy surface in order to identify all the relevant energetically low-lying magnetic isomers. In this thesis the sampling of the potential-energy surface has been performed by employing the state-of-the-art spin-polarized density-functional theory in combination with graph theory and the basin-hopping global optimization techniques. This combination is vital for a quantitative analysis of the quantum mechanical energetics. The first approach, i.e., spin-polarized density-functional theory together with the graph theory method, is applied to study the Fe$_m$Rh$_n$ and Co$_m$Pd$_n$ clusters having $N = m+n \leq 8$ atoms. We carried out a thorough and systematic sampling of the potential-energy surface by taking into account all possible initial cluster topologies, all different distributions of the two kinds of atoms within the cluster, the entire concentration range between the pure limits, and different initial magnetic configurations such as ferro- and anti-ferromagnetic coupling. The remarkable magnetic properties shown by FeRh and CoPd nanoclusters are attributed to the extremely reduced coordination number together with the charge transfer from 3$d$ to 4$d$ elements. The second approach, i.e., spin-polarized density-functional theory together with the basin-hopping method is applied to study the small Fe$_6$, Fe$_3$Rh$_3$ and Rh$_6$ and the larger Fe$_{13}$, Fe$_6$Rh$_7$ and Rh$_{13}$ clusters as illustrative benchmark systems. This method is able to identify the true ground-state structures of Fe$_6$ and Fe$_3$Rh$_3$ which were not obtained by using the first approach. However, both approaches predict a similar cluster for the ground-state of Rh$_6$. Moreover, the computational time taken by this approach is found to be significantly lower than the first approach. The ground-state structure of Fe$_{13}$ cluster is found to be an icosahedral structure, whereas Rh$_{13}$ and Fe$_6$Rh$_7$ isomers relax into cage-like and layered-like structures, respectively. All the clusters display a remarkable variety of structural and magnetic behaviors. It is observed that the isomers having similar shape with small distortion with respect to each other can exhibit quite different magnetic moments. This has been interpreted as a probable artifact of spin-rotational symmetry breaking introduced by the spin-polarized GGA. The possibility of combining the spin-polarized density-functional theory with some other global optimization techniques such as minima-hopping method could be the next step in this direction. This combination is expected to be an ideal sampling approach having the advantage of avoiding efficiently the search over irrelevant regions of the potential energy surface.

Lethal Closeness: The Evolution of a Small-World Drug Trafficking Network

The evolution of the drug trafficking network –so-called– ‘Cartel del Norte del Valle’, is studied using network analysis methods. We found that the average length between any pair of its members was bounded by 4 –an attribute of smallworld networks. In this tightly connected network, informational shocks induce fear and the unleashing of searches of threatening nodes, using available paths. Lethal violence ensues in clusters of increasing sizes that fragment the network, without compromising, however, the survival of the largest component, which proved to be resilient to massive violence. In spite of a success from the point of view of head counting, the US’ socialization program for drug traffickers did not effectively change the cyclical dynamics of the drug dealing business: war survivors took over what was left from the old network initiating a new cycle of business and violence.

A new interpretation of the bonding properties and UV–vis spectra of [M3(CO)12] clusters (M = Ru, Os): a TD-DFT study

DFT and TD-DFT calculations (ADF program) were performed in order to analyze the electronic structure of the [M-3(CO)(12)] clusters (M = Ru, Os) and interpret their electronic spectra. The highest occupied molecular orbitals are M-M bonding (sigma) involving different M-M bonds, both for Ru and Os. They participate in low-energy excitation processes and their depopulation should weaken M-M bonds in general. While the LUMO is M-NI and M-CO anti-bonding (sigma*), the next, higher-lying empty orbitals have a main contribution from CO (pi*) and either a small (Ru) or an almost negligible one (Os) from the metal atoms. The main difference between the two clusters comes from the different nature of these low-energy unoccupied orbitals that have a larger metal contribution in the case of ruthenium. The photochemical reactivity of the two clusters is reexamined and compared to earlier interpretations.

Supramolecular structures of enzyme clusters

The structural characterization of subtilisin mesoscale clusters, which were previously shown to induce supramolecular order in biocatalytic self-assembly of Fmocdipeptides, was carried out by synchrotron small-angle X-ray, dynamic, and static light scattering measurements. Subtilisin molecules self-assemble to form supramolecular structures in phosphate buffer solutions. Structural arrangement of subtilisin clusters at 55 degrees Centigrade was found to vary systematically with increasing enzyme concentration. Static light scattering measurements showed the cluster structure to be consistent with a fractal-like arrangement, with fractal dimension varying from 1.8 to 2.6 with increasing concentration for low to moderate enzyme concentrations. This was followed by a structural transition around the enzyme concentration of 0.5 mg mL-1 to more compact structures with significantly slower relaxation dynamics, as evidenced by dynamic light scattering measurements. These concentration-dependent supramolecular enzyme clusters provide tunable templates for biocatalytic self-assembly.

Measurement of the epicycle frequency in the Galactic disc and initial velocities of open clusters

A new method to measure the epicycle frequency kappa in the Galactic disc is presented. We make use of the large data base on open clusters completed by our group to derive the observed velocity vector (amplitude and direction) of the clusters in the Galactic plane. In the epicycle approximation, this velocity is equal to the circular velocity given by the rotation curve, plus a residual or perturbation velocity, of which the direction rotates as a function of time with the frequency kappa. Due to the non-random direction of the perturbation velocity at the birth time of the clusters, a plot of the present-day direction angle of this velocity as a function of the age of the clusters reveals systematic trends from which the epicycle frequency can be obtained. Our analysis considers that the Galactic potential is mainly axis-symmetric, or in other words, that the effect of the spiral arms on the Galactic orbits is small; in this sense, our results do not depend on any specific model of the spiral structure. The values of kappa that we obtain provide constraints on the rotation velocity of the in particular, V(0) is found to be 230 +/- 15 km s(-1) even if the scale (R(0) = 7.5 kpc) of the Galaxy is adopted. The measured kappa at the solar radius is 43 +/- 5 km s(-1) kpc(-1). The distribution of initial velocities of open clusters is discussed.