The behavior of small helium clusters near free surfaces in tungsten

NASA Astrophysics Data System (ADS)

Barashev, A. V.; Xu, H.; Stoller, R. E.

2014-11-01

The results of a computational study of helium-vacancy clusters in tungsten are reported. A recently developed atomistic kinetic Monte Carlo method employing empirical interatomic potentials was used to investigate the behavior of clusters composed of three interstitial-helium atoms near {1 1 1}, {1 1 0} and {1 0 0} free surfaces. Multiple configurations were examined and the local energy landscape was characterized to determine cluster mobility and the potential for interactions with the surface. The clusters were found to be highly mobile if far from the surface, but were attracted and bound to the surface when within a distance of a few lattice parameters. When near the surface, the clusters were transformed into an immobile configuration due to the creation of a Frenkel pair; the vacancy was incorporated into what became a He3-vacancy complex. The corresponding interstitial migrated to and became an adatom on the free surface. This process can contribute to He retention, and may be responsible for the observed deterioration of the plasma-exposed tungsten surfaces.

System and method for merging clusters of wireless nodes in a wireless network

DOEpatents

Budampati, Ramakrishna S [Maple Grove, MN; Gonia, Patrick S [Maplewood, MN; Kolavennu, Soumitri N [Blaine, MN; Mahasenan, Arun V [Kerala, IN

2012-05-29

A system includes a first cluster having multiple first wireless nodes. One first node is configured to act as a first cluster master, and other first nodes are configured to receive time synchronization information provided by the first cluster master. The system also includes a second cluster having one or more second wireless nodes. One second node is configured to act as a second cluster master, and any other second nodes configured to receive time synchronization information provided by the second cluster master. The system further includes a manager configured to merge the clusters into a combined cluster. One of the nodes is configured to act as a single cluster master for the combined cluster, and the other nodes are configured to receive time synchronization information provided by the single cluster master.

Neck formation and deformation effects in a preformed cluster model of exotic cluster decays

NASA Astrophysics Data System (ADS)

Kumar, Satish; Gupta, Raj K.

1997-01-01

Using the nuclear proximity approach and the two center nuclear shape parametrization, the interaction potential between two deformed and pole-to-pole oriented nuclei forming a necked configuration in the overlap region is calculated and its role is studied for the cluster decay half-lives. The barrier is found to move to a larger relative separation, with its proximity minimum lying in the neighborhood of the Q value of decay and its height and width reduced considerably. For cluster decay calculations in the preformed cluster model of Malik and Gupta, due to deformations and orientations of nuclei, the (empirical) preformation factor is found to get reduced considerably and agrees nicely with other model calculations known to be successful for their predictions of cluster decay half-lives. Comparison with the earlier case of nuclei treated as spheres suggests that the effects of both deformations and neck formation get compensated by choosing the position of cluster preformation and the inner classical turning point for penetrability calculations at the touching configuration of spherical nuclei.

Structures and energetics of hydrated deprotonated cis-pinonic acid anion clusters and their atmospheric relevance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Gao-Lei; Zhang, Jun; Valiev, Marat

2017-01-01

Pinonic acid, a C10-monocarboxylic acid with a hydrophilic –CO 2H group and a hydrophobic hydrocarbon backbone, is a key intermediate oxidation product of α-pinene – an important monoterpene compound in biogenic emission processes that influences the atmosphere. Molecular interaction between cis-pinonic acid and water is essential for understanding its role in the formation and growth of pinene-derived secondary organic aerosols. In this work, we studied the structures, energetics, and optical properties of hydrated clusters of cis-pinonate anion (cPA–), the deprotonated form of cis-pinonic acid, by negative ion photoelectron spectroscopy and ab initio theoretical calculations. Our results show that cPA– canmore » adopt two different structural configurations – open and folded. In the absence of waters, the open configuration has the lowest energy and provides the best agreement with the experiment. The addition waters, which mainly interact with the negatively charged -CO 2– group, gradually stabilize the folded configuration and lower its energy difference relative to the most stable open-configured structure. Thermochemical and equilibrium hydrate distribution analysis suggests that the mono- and di- hydrates are likely to exist in humid atmospheric environment with high populations. The detailed molecular description of cPA– hydrated clusters unraveled in this study provides a valuable reference for understanding the initial nucleation process and aerosol formation involving organics containing both hydrophilic and hydrophobic groups, as well as for analyzing the optical properties of those organic aerosols.« less

Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation.

PubMed

Blanco, Marco A; Sahin, Erinc; Robinson, Anne S; Roberts, Christopher J

2013-12-19

Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semiquantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work (Grüenberger et al., J. Phys. Chem. B 2013, 117, 763), this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental value of B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-Crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependence on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino-acids/surface patches that form interprotein contacts at conditions that favor dimerization of gD-Crys. The resulting regions agree with previously found aggregation-prone sites, as well as suggesting new ones that may be important.

Coarse-Grained Model for Colloidal Protein Interactions, B22, and Protein Cluster Formation

PubMed Central

Blanco, Marco A.; Sahin, Eric; Robinson, Anne S.; Roberts, Christopher J.

2014-01-01

Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semi-quantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work, this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental values of the B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependance on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino-acids / surface patches that form inter-protein contacts at conditions that favor dimerization of gD-Crys. The resulting regions agree with previously found aggregation-prone sites, as well as suggesting new ones that may be important. PMID:24289039

Structural features of small benzene clusters (C6H6)n (n ≤ 30) as investigated with the all-atom OPLS potential.

PubMed

Takeuchi, Hiroshi

2012-10-18

The structures of the simplest aromatic clusters, benzene clusters (C(6)H(6))(n), are not well elucidated. In the present study, benzene clusters (C(6)H(6))(n) (n ≤ 30) were investigated with the all-atom optimized parameters for liquid simulation (OPLS) potential. The global minima and low-lying minima of the benzene clusters were searched with the heuristic method combined with geometrical perturbations. The structural features and growth sequence of the clusters were examined by carrying out local structure analyses and structural similarity evaluation with rotational constants. Because of the anisotropic interaction between the benzene molecules, the local structures consisting of 13 molecules are considerably deviated from regular icosahedron, and the geometries of some of the clusters are inconsistent with the shapes constructed by the interior molecules. The distribution of the angle between the lines normal to two neighboring benzene rings is anisotropic in the clusters, whereas that in the liquid benzene is nearly isotropic. The geometries and energies of the low-lying configurations and the saddle points between them suggest that most of the configurations previously detected in supersonic expansions take different orientations for one to four neighboring molecules.

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations.

PubMed

Alexandrova, Anastassia N; Boldyrev, Alexander I; Li, Xiang; Sarkas, Harry W; Hendricks, Jay H; Arnold, Susan T; Bowen, Kit H

2011-01-28

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.

Cluster-collision frequency. I. The long-range intercluster potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amadon, A.S.; Marlow, W.H.

1991-05-15

In recent years, gas-borne atomic and molecular clusters have emerged as subjects of basic physical and chemical interest and are gaining recognition for their importance in numerous applications. To calculate the evolution of the mass distribution of these clusters, their thermal collision rates are required. For computing these collision rates, the long-range interaction energy between clusters is required and is the subject of this paper. Utilizing a formulation of the iterated van der Waals interaction over discrete molecules that can be shown to converge with increasing numbers of atoms to the Lifshitz--van der Waals interaction for condensed matter, we calculatemore » the interaction energy as a function of center-of-mass separation for identical pairs of clusters of 13, 33, and 55 molecules of carbon tetrachloride in icosahedral and dodecahedral configurations. Two different relative orientations are chosen for each pair of clusters, and the energies are compared with energies calculated from the standard formula for continuum matter derived by summing over pair interactions with the Hamaker constant calculated according to Lifshitz theory. The results of these calculations give long-range interaction energies that assume typical adhesion-type values at cluster contact, unlike the unbounded results for the Lifshitz-Hamaker model. The relative difference between the discrete molecular energies and the continuum energies vanishes for {ital r}{sup *}{approx}2, where {ital r}{sup *} is the center-of-mass separation distance in units of cluster diameter. For larger separations, the relative difference changes sign, showing a value of approximately 15%, with the difference diminishing for increasing-sized clusters.« less

Diffusion reordering kinetics in lattice-gas systems: Time evolution of configurational entropy and internal energy

NASA Astrophysics Data System (ADS)

Weinketz, Sieghard

1998-07-01

The reordering kinetics of a diffusion lattice-gas system of adsorbates with nearest- and next-nearest-neighbor interactions on a square lattice is studied within a dynamic Monte Carlo simulation, as it evolves towards the equilibrium from a given initial configuration, at a constant temperature. The diffusion kinetics proceeds through adsorbate hoppings to empty nearest-neighboring sites (Kawasaki dynamics). The Monte Carlo procedure allows a ``real'' time definition from the local transition rates, and the configurational entropy and internal energy can be obtained from the lattice configuration at any instant t by counting the local clusters and using the C2 approximation of the cluster variation method. These state functions are then used in their nonequilibrium form as a direct measure of reordering along the time. Different reordering processes are analyzed within this approach, presenting a rich variety of behaviors. It can also be shown that the time derivative of entropy (times temperature) is always equal to or lower than the time derivative of energy, and that the reordering path is always strongly dependent on the initial order, presenting in some cases an ``invariance'' of the entropy function to the magnitude of the interactions as far as the final order is unaltered.

Photoabsorption in sodium clusters: first principles configuration interaction calculations

NASA Astrophysics Data System (ADS)

Priya, Pradip Kumar; Rai, Deepak Kumar; Shukla, Alok

2017-05-01

We present systematic and comprehensive correlated-electron calculations of the linear photoabsorption spectra of small neutral closed- and open-shell sodium clusters (Nan, n = 2 - 6), as well as closed-shell cation clusters (Nan+, n = 3, 5). We have employed the configuration interaction (CI) methodology at the full CI (FCI) and quadruple CI (QCI) levels to compute the ground, and the low-lying excited states of the clusters. For most clusters, besides the minimum energy structures, we also consider their energetically close isomers. The photoabsorption spectra were computed under the electric-dipole approximation, employing the dipole-matrix elements connecting the ground state with the excited states of each isomer. Our calculations were tested rigorously for convergence with respect to the basis set, as well as with respect to the size of the active orbital space employed in the CI calculations. These calculations reveal that as far as electron-correlation effects are concerned, core excitations play an important role in determining the optimized ground state geometries of various clusters, thereby requiring all-electron correlated calculations. But, when it comes to low-lying optical excitations, only valence electron correlation effects play an important role, and excellent agreement with the experimental results is obtained within the frozen-core approximation. For the case of Na6, the largest cluster studied in this work, we also discuss the possibility of occurrence of plasmonic resonance in the optical absorption spectrum. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-70728-3

Self-Organization of Metal Nanoparticles in Light: Electrodynamics-Molecular Dynamics Simulations and Optical Binding Experiments.

PubMed

McCormack, Patrick; Han, Fei; Yan, Zijie

2018-02-01

Light-driven self-organization of metal nanoparticles (NPs) can lead to unique optical matter systems, yet simulation of such self-organization (i.e., optical binding) is a complex computational problem that increases nonlinearly with system size. Here we show that a combined electrodynamics-molecular dynamics simulation technique can simulate the trajectories and predict stable configurations of silver NPs in optical fields. The simulated dynamic equilibrium of a two-NP system matches the probability density of oscillations for two optically bound NPs obtained experimentally. The predicted stable configurations for up to eight NPs are further compared to experimental observations of silver NP clusters formed by optical binding in a Bessel beam. All configurations are confirmed to form in real systems, including pentagonal clusters with five-fold symmetry. Our combined simulations and experiments have revealed a diverse optical matter system formed by anisotropic optical binding interactions, providing a new strategy to discover artificial materials.

INTERACTION OF INTERSTITIAL CLUSTERS WITH RHENIUM, OSMIUM, AND TANTALUM IN TUNGSTEN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Nandipati, Giridhar; Kurtz, Richard J.

2016-09-01

In the previous semi annual report, we explored the stability of interstitial clusters in W up to size seven. In this report, we study the binding of those clusters to Re, Os, and Ta atoms. For each cluster size, the three most stable configurations are considered to average the binding property. The average binding energy to a Re decreases from 0.79 eV for a size-1 cluster (a [111] dumbbell) to 0.65 eV for a size-7 cluster. For Os, the binding decreases from 1.61 eV for a [111] dumbbell to 1.34 eV for a size-7 cluster. Tantalum is repulsive to interstitialmore » clusters with binding energy ranges from -0.61 eV for a [111] dumbbell to -0.5 eV for a size-7 cluster.« less

Valence ionized states of iron pentacarbonyl and eta5-cyclopentadienyl cobalt dicarbonyl studied by symmetry-adapted cluster-configuration interaction calculation and collision-energy resolved Penning ionization electron spectroscopy.

PubMed

Fukuda, Ryoichi; Ehara, Masahiro; Nakatsuji, Hiroshi; Kishimoto, Naoki; Ohno, Koichi

2010-02-28

Valence ionized states of iron pentacarbonyl Fe(CO)(5) and eta(5)-cyclopentadienyl cobalt dicarbonyl Co(eta(5)-C(5)H(5))(CO)(2) have been studied by ultraviolet photoelectron spectroscopy, two-dimensional Penning ionization electron spectroscopy (2D-PIES), and symmetry-adapted cluster-configuration interaction calculations. Theory provided reliable assignments for the complex ionization spectra of these molecules, which have metal-carbonyl bonds. Theoretical ionization energies agreed well with experimental observations and the calculated wave functions could explain the relative intensities of PIES spectra. The collision-energy dependence of partial ionization cross sections (CEDPICS) was obtained by 2D-PIES. To interpret these CEDPICS, the interaction potentials between the molecules and a Li atom were examined in several coordinates by calculations. The relation between the slope of the CEDPICS and the electronic structure of the ionized states, such as molecular symmetry and the spatial distribution of ionizing orbitals, was analyzed. In Fe(CO)(5), an attractive interaction was obtained for the equatorial CO, while the interaction for the axial CO direction was repulsive. For Co(eta(5)-C(5)H(5))(CO)(2), the interaction potential in the direction of both Co-C-O and Co-Cp ring was attractive. These anisotropic interactions and ionizing orbital distributions consistently explain the relative slopes of the CEDPICS.

An optimized full-configuration-interaction nuclear orbital approach to a ``hard-core'' interaction problem: Application to (3He)N-Cl2(B) clusters (N<=4)

NASA Astrophysics Data System (ADS)

de Lara-Castells, M. P.; Villarreal, P.; Delgado-Barrio, G.; Mitrushchenkov, A. O.

2009-11-01

An efficient full-configuration-interaction nuclear orbital treatment has been recently developed as a benchmark quantum-chemistry-like method to calculate ground and excited "solvent" energies and wave functions in small doped ΔEest clusters (N ≤4) [M. P. de Lara-Castells, G. Delgado-Barrio, P. Villarreal, and A. O. Mitrushchenkov, J. Chem. Phys. 125, 221101 (2006)]. Additional methodological and computational details of the implementation, which uses an iterative Jacobi-Davidson diagonalization algorithm to properly address the inherent "hard-core" He-He interaction problem, are described here. The convergence of total energies, average pair He-He interaction energies, and relevant one- and two-body properties upon increasing the angular part of the one-particle basis set (expanded in spherical harmonics) has been analyzed, considering Cl2 as the dopant and a semiempirical model (T-shaped) He-Cl2(B) potential. Converged results are used to analyze global energetic and structural aspects as well as the configuration makeup of the wave functions, associated with the ground and low-lying "solvent" excited states. Our study reveals that besides the fermionic nature of H3e atoms, key roles in determining total binding energies and wave-function structures are played by the strong repulsive core of the He-He potential as well as its very weak attractive region, the most stable arrangement somehow departing from the one of N He atoms equally spaced on equatorial "ring" around the dopant. The present results for N =4 fermions indicates the structural "pairing" of two H3e atoms at opposite sides on a broad "belt" around the dopant, executing a sort of asymmetric umbrella motion. This pairing is a compromise between maximizing the H3e-H3e and the He-dopant attractions, and suppressing at the same time the "hard-core" repulsion. Although the He-He attractive interaction is rather weak, its contribution to the total energy is found to scale as a power of three and it thus increasingly affects the pair density distributions as the cluster grows in size.

Collective Flows of 16O+16O Collisions with α-Clustering Configurations

NASA Astrophysics Data System (ADS)

Guo, Chen-Chen; He, Wan-Bing; Ma, Yu-Gang

2017-08-01

The main purpose of the present paper is to discuss whether or not the collective flows in heavy-ion collision at Fermi energy can be taken as a tool to investigate the cluster configuration in light nuclei. In practice, within an Extended Quantum Molecular Dynamics model, four $\\alpha$-clustering (linear chain, kite, square, and tetrahedron) configurations of $^{16}$O are employed in the initialization, $^{16}$O+$^{16}$O around Fermi energy (40 - 60 MeV$/$nucleon) with impact parameter 1 - 3 fm are simulated, the directed and elliptic flows are analyzed. It is found that collective flows are influenced by the different $\\alpha$-clustering configurations, and the directed flow of free protons is more sensitive to the initial cluster configuration than the elliptic flow. Nuclear reaction at Fermi energy can be taken a useful way to study cluster configuration in light nuclei.

A DIM model for sodium cluster-ions interacting with a charged conducting sphere

NASA Astrophysics Data System (ADS)

Kuntz, P. J.

A diatomics-in-molecules (DIM) model for the energy, shape and charge distribution of metal cluster ions in the presence of a charged insulated conducting sphere is presented. The electrostatic interaction between the sphere and the cluster-ion is introduced in a self-consistent manner which allows the sphere to be polarized by the ion and the ion by the sphere. This interaction appears in the diagonal elements of the model Hamiltonian matrix in such a way that the lowest eigenvalue includes the correct electrostatic energy for the charge distribution in the ground state. The model is applied to the calculation of fusion barriers for Na+2 and Na+3 ions. When both the charge distribution and the geometric configuration of the cluster-ion are allowed to relax freely, the energy as a function of distance from the sphere is nearly the same as that calculated from the electrostatic energy alone, which implies that details of the molecular structure of the cluster-ion can be neglected in calculating fusion barriers from charge polarization alone. That the fusion barriers lie sufficiently far away from the sphere so that the molecule does not dissociate under the influence of the Coulomb interaction confirms that it is meaningful to speak of two separate entities at the barrier position.

A machine learning approach to graph-theoretical cluster expansions of the energy of adsorbate layers

NASA Astrophysics Data System (ADS)

Vignola, Emanuele; Steinmann, Stephan N.; Vandegehuchte, Bart D.; Curulla, Daniel; Stamatakis, Michail; Sautet, Philippe

2017-08-01

The accurate description of the energy of adsorbate layers is crucial for the understanding of chemistry at interfaces. For heterogeneous catalysis, not only the interaction of the adsorbate with the surface but also the adsorbate-adsorbate lateral interactions significantly affect the activation energies of reactions. Modeling the interactions of the adsorbates with the catalyst surface and with each other can be efficiently achieved in the cluster expansion Hamiltonian formalism, which has recently been implemented in a graph-theoretical kinetic Monte Carlo (kMC) scheme to describe multi-dentate species. Automating the development of the cluster expansion Hamiltonians for catalytic systems is challenging and requires the mapping of adsorbate configurations for extended adsorbates onto a graphical lattice. The current work adopts machine learning methods to reach this goal. Clusters are automatically detected based on formalized, but intuitive chemical concepts. The corresponding energy coefficients for the cluster expansion are calculated by an inversion scheme. The potential of this method is demonstrated for the example of ethylene adsorption on Pd(111), for which we propose several expansions, depending on the graphical lattice. It turns out that for this system, the best description is obtained as a combination of single molecule patterns and a few coupling terms accounting for lateral interactions.

One-electron pseudo-potential investigation of NO(X2Π)-Arn clusters (n = 1,2,3,4)

NASA Astrophysics Data System (ADS)

Hammami, H.; Ben Mohamed, F. E.; Mohamed, D.; Ben El Hadj Rhouma, M.; Al Mogren, M. M.; Hochlaf, M.

2017-10-01

In this work, we investigate the minimal energy and low-lying isomers of the ground state of NOArn clusters using a hybrid pseudo-potential model, where a single electron quantum description is combined with the classical argon-argon pair potential and an expansion in terms of the Legendre polynomials. In such model, we use two centres of polarisation for NO+, where we considered for each nuclear configuration an analytic dipole polarisation for N+ and O+. The reliability of our model is checked by comparison of the NO(X2Π)-Ar potential energy surface with that deduced using the multireference configuration interaction (MRCI+Q) approach. The results of this formalism agree quite well with the MRCI ones over a wide range of nuclear arrangements.

Anisotropy of the Coulomb Interaction between Folded Proteins: Consequences for Mesoscopic Aggregation of Lysozyme

PubMed Central

Chan, Ho Yin; Lankevich, Vladimir; Vekilov, Peter G.; Lubchenko, Vassiliy

2012-01-01

Toward quantitative description of protein aggregation, we develop a computationally efficient method to evaluate the potential of mean force between two folded protein molecules that allows for complete sampling of their mutual orientation. Our model is valid at moderate ionic strengths and accounts for the actual charge distribution on the surface of the molecules, the dielectric discontinuity at the protein-solvent interface, and the possibility of protonation or deprotonation of surface residues induced by the electric field due to the other protein molecule. We apply the model to the protein lysozyme, whose solutions exhibit both mesoscopic clusters of protein-rich liquid and liquid-liquid separation; the former requires that protein form complexes with typical lifetimes of approximately milliseconds. We find the electrostatic repulsion is typically lower than the prediction of the Derjaguin-Landau-Verwey-Overbeek theory. The Coulomb interaction in the lowest-energy docking configuration is nonrepulsive, despite the high positive charge on the molecules. Typical docking configurations barely involve protonation or deprotonation of surface residues. The obtained potential of mean force between folded lysozyme molecules is consistent with the location of the liquid-liquid coexistence, but produces dimers that are too short-lived for clusters to exist, suggesting lysozyme undergoes conformational changes during cluster formation. PMID:22768950

Theoretical study of the H2 reaction with a Pt4 (111) cluster

NASA Astrophysics Data System (ADS)

Cruz, A.; Bertin, V.; Poulain, E.; Benitez, J. I.; Castillo, S.

2004-04-01

The Cs symmetry reaction of the H2 molecule on a Pt4 (111) clusters, has been studied using ab initio multiconfiguration self-consistent field plus extensive multireference configuration interaction variational and perturbative calculations. The H2 interaction by the vertex and by the base of a tetrahedral Pt4 cluster were studied in ground and excited triplet and singlet states (closed and open shells), where the reaction curves are obtained through many avoided crossings. The Pt4 cluster captures and activates the hydrogen molecule; it shows a similar behavior compared with other Ptn (n=1,2,3) systems. The Pt4 cluster in their lowest five open and closed shell electronic states: 3B2, 1B2, 1A1 3A1, 1A1, respectively, may capture and dissociate the H2 molecule without activation barriers for the hydrogen molecule vertex approach. For the threefolded site reaction, i.e., by the base, the situation is different, the hydrogen adsorption presents some barriers. The potential energy minima occur outside and inside the cluster, with strong activation of the H-H bond. In all cases studied, the Pt4 cluster does not absorb the hydrogen molecule.

Spin-orbit coupling effect on structural and magnetic properties of ConRh13-n (n = 0-13) clusters

NASA Astrophysics Data System (ADS)

Bai, Xi; Lv, Jin; Zhang, Fu-Qiang; Jia, Jian-Feng; Wu, Hai-Shun

2018-04-01

The effect of spin-orbit interaction on the structures and magnetism of ConRh13-n (n = 0-13) clusters have been systematically investigated by using the spin-orbit coupling (SOC) implementation of the density functional theory (DFT). The results calculated without SOC (NSOC) show that Rh13 prefers the double simple-cubic configuration, and icosahedron is the favorable structure for n = 1-9, while n ≥ 10, clusters favor the hexagonal bilayer structure. The inclusion of SOC in calculation does not change the geometries of clusters. Compared with that in NSOC calculation, although the binding energy per atom in clusters with same composition decreases in SOC calculation, the relative stability of clusters with different compositions does not change. An interesting result is that the spin moments of clusters for n = 1-9 are almost constant (21 μB). Spin-orbit interaction recovers orbital moment and its anisotropy by removing crystal-field effect in calculation. The destruction of bonding symmetry and relaxation of bonding account for high anisotropies of orbital moments in Co11Rh2 and CoRh12 clusters. With atomic composition (Co/Rh) around 4/9-5/8 and 9/4, the Co-Rh clusters exhibit high magnetic anisotropy energies.

Impurity-doped Si10 cluster: Understanding the structural and electronic properties from first-principles calculations

NASA Astrophysics Data System (ADS)

Majumder, Chiranjib; Kulshreshtha, S. K.

2004-12-01

Structural and electronic properties of metal-doped silicon clusters ( MSi10 , M=Li , Be, B, C, Na, Mg, Al, and Si) have been investigated via ab initio molecular dynamics simulation under the formalism of the density functional theory. The exchange-correlation energy has been calculated using the generalized gradient approximation method. Several stable isomers of MSi10 clusters have been identified based on different initial configurations and their relative stabilities have been analyzed. From the results it is revealed that the location of the impurity atom depends on the nature of interaction between the impurity atom and the host cluster and the size of the impurty atom. Whereas Be and B atoms form stable isomers, the impurity atom being placed at the center of the bicapped tetragonal antiprism structure of the Si10 cluster, all other elements diffuse outside the cage of Si10 cluster. Further, to understand the stability and the chemical bonding, the LCAO-MO based all electron calculations have been carried out for the lowest energy isomers using the hybrid B3LYP energy functional. Based on the interaction energy of the M atoms with Si10 clusters it is found that p-p interaction dominates over the s-p interaction and smaller size atoms interact more strongly. Based on the binding energy, the relative stability of MSi10 clusters is found to follow the order of CSi10>BSi10>BeSi10>Si11>AlSi10>LiSi10>NaSi10>MgSi10 , leading one to infer that while the substitution of C, B and Be enhances the stability of the Si11 cluster, others have an opposite effect. The extra stability of the BeSi10 clusters is due to its encapsulated close packed structure and large energy gap between the HOMO and LUMO energy levels.

Transonic Navier-Stokes computations of strake-generated vortex interactions for a fighter-like configuration

NASA Technical Reports Server (NTRS)

Reznick, Steve

1988-01-01

Transonic Euler/Navier-Stokes computations are accomplished for wing-body flow fields using a computer program called Transonic Navier-Stokes (TNS). The wing-body grids are generated using a program called ZONER, which subdivides a coarse grid about a fighter-like aircraft configuration into smaller zones, which are tailored to local grid requirements. These zones can be either finely clustered for capture of viscous effects, or coarsely clustered for inviscid portions of the flow field. Different equation sets may be solved in the different zone types. This modular approach also affords the opportunity to modify a local region of the grid without recomputing the global grid. This capability speeds up the design optimization process when quick modifications to the geometry definition are desired. The solution algorithm embodied in TNS is implicit, and is capable of capturing pressure gradients associated with shocks. The algebraic turbulence model employed has proven adequate for viscous interactions with moderate separation. Results confirm that the TNS program can successfully be used to simulate transonic viscous flows about complicated 3-D geometries.

Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions.

PubMed

Tauer, Tony P; Sherrill, C David

2005-11-24

The benzene dimer is the simplest prototype of pi-pi interactions and has been used to understand the fundamental physics of these interactions as they are observed in more complex systems. In biological systems, however, aromatic rings are rarely found in isolated pairs; thus, it is important to understand whether aromatic pairs remain a good model of pi-pi interactions in clusters. In this study, ab initio methods are used to compute the binding energies of several benzene trimers and tetramers, most of them in 1D stacked configurations. The two-body terms change only slightly relative to the dimer, and except for the cyclic trimer, the three- and four-body terms are negligible. This indicates that aromatic clusters do not feature any large nonadditive effects in their binding energies, and polarization effects in benzene clusters do not greatly change the binding that would be anticipated from unperturbed benzene-benzene interactions, at least for the 1D stacked systems considered. Three-body effects are larger for the cyclic trimer, but for all systems considered, the computed binding energies are within 10% of what would be estimated from benzene dimer energies at the same geometries.

Interfacial energetics of two-dimensional colloidal clusters generated with a tunable anharmonic interaction potential

NASA Astrophysics Data System (ADS)

Hilou, Elaa; Du, Di; Kuei, Steve; Biswal, Sibani Lisa

2018-02-01

Interfacial characteristics are critical to various properties of two-dimensional (2D) materials such as band alignment at a heterojunction and nucleation kinetics in a 2D crystal. Despite the desire to harness these enhanced interfacial properties for engineering new materials, unexpected phase transitions and defects, unique to the 2D morphology, have left a number of open questions. In particular, the effects of configurational anisotropy, which are difficult to isolate experimentally, and their influence on interfacial properties are not well understood. In this work, we begin to probe this structure-thermodynamic relationship, using a rotating magnetic field to generate an anharmonic interaction potential in a 2D system of paramagnetic particles. At low magnetic field strengths, weakly interacting colloidal particles form non-close-packed, fluidlike droplets, whereas, at higher field strengths, crystallites with hexagonal ordering are observed. We examine spatial and interfacial properties of these 2D colloidal clusters by measuring the local bond orientation order parameter and interfacial stiffness as a function of the interaction strength. To our knowledge, this is the first study to measure the tunable interfacial stiffness of a 2D colloidal cluster by controlling particle interactions using external fields.

Improving the distinguishable cluster results: spin-component scaling

NASA Astrophysics Data System (ADS)

Kats, Daniel

2018-06-01

The spin-component scaling is employed in the energy evaluation to improve the distinguishable cluster approach. SCS-DCSD reaction energies reproduce reference values with a root-mean-squared deviation well below 1 kcal/mol, the interaction energies are three to five times more accurate than DCSD, and molecular systems with a large amount of static electron correlation are still described reasonably well. SCS-DCSD represents a pragmatic approach to achieve chemical accuracy with a simple method without triples, which can also be applied to multi-configurational molecular systems.

Formation of prismatic loops from C15 Laves phase interstitial clusters in body-centered cubic iron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yongfeng; Bai, Xian-Ming; Tonks, Michael R.

2015-03-01

This Letter reports the transition of C15 phase self-interstitial clusters to loops in body-centered-cubic Iron. Molecular dynamics simulations are performed to evaluate the relative stabilities of difference interstitial cluster configurations including C15 phase structure and <100> and <111>/2 loops. Within a certain size range, C15 cluster are found more stable than loops, and the relative stabilities are reversed beyond that range. In accordance to the crossover in relative stabilities, C15 clusters may grow by absorbing individual interstitials at small sizes and transitions into loops eventually. The transition takes place by nucleation and reaction of <111>/2 loop segments. These observations explainmore » the absence of C15 phase interstitial clusters predicted by density-functional-theory calculations in previous experimental observations. More importantly, the current results provide a new formation mechanism of <100> loops which requires no interaction of loops.« less

InCHlib - interactive cluster heatmap for web applications.

PubMed

Skuta, Ctibor; Bartůněk, Petr; Svozil, Daniel

2014-12-01

Hierarchical clustering is an exploratory data analysis method that reveals the groups (clusters) of similar objects. The result of the hierarchical clustering is a tree structure called dendrogram that shows the arrangement of individual clusters. To investigate the row/column hierarchical cluster structure of a data matrix, a visualization tool called 'cluster heatmap' is commonly employed. In the cluster heatmap, the data matrix is displayed as a heatmap, a 2-dimensional array in which the colour of each element corresponds to its value. The rows/columns of the matrix are ordered such that similar rows/columns are near each other. The ordering is given by the dendrogram which is displayed on the side of the heatmap. We developed InCHlib (Interactive Cluster Heatmap Library), a highly interactive and lightweight JavaScript library for cluster heatmap visualization and exploration. InCHlib enables the user to select individual or clustered heatmap rows, to zoom in and out of clusters or to flexibly modify heatmap appearance. The cluster heatmap can be augmented with additional metadata displayed in a different colour scale. In addition, to further enhance the visualization, the cluster heatmap can be interconnected with external data sources or analysis tools. Data clustering and the preparation of the input file for InCHlib is facilitated by the Python utility script inchlib_clust . The cluster heatmap is one of the most popular visualizations of large chemical and biomedical data sets originating, e.g., in high-throughput screening, genomics or transcriptomics experiments. The presented JavaScript library InCHlib is a client-side solution for cluster heatmap exploration. InCHlib can be easily deployed into any modern web application and configured to cooperate with external tools and data sources. Though InCHlib is primarily intended for the analysis of chemical or biological data, it is a versatile tool which application domain is not limited to the life sciences only.

Mapping the phase inhomogeneity across first order spin flop transition

NASA Astrophysics Data System (ADS)

Tripathi, Malvika; Majumder, Supriyo; Choudhary, R. J.; Phase, D. M.

2018-04-01

As a consequence of spin reorientation phase transition (SRPT, TSRPT = 34K) in SmCrO3, the two phases, high temperature uncompensated anti-ferromagnetic Γ4 configuration and low temperature collinear anti-ferromagnetic phase Γ1 coexist in the vicinity of transition. The observed unexpectedly huge coercivity (Hc ˜2T) below SRPT at 25K questions on the behavior of two co-existing phases. In the present study, we have used the FORC diagrams to monitor the distribution of clusters related to different phases and to understand the nature of interaction among the clusters of distinct phases. We observed that the nature of interaction has indeed magnetic effect and the pining across phase boundaries may cause the enhancement of coercivity at 25K.

High Level ab initio Predictions of the Energetics of mCO2•(H2O)n (n = 1-3, m = 1-12) Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thanthiriwatte, Sahan; Duke, Jessica R.; Jackson, Virgil E.

Electronic structure calculations at the correlated molecular orbital theory and density functional theory levels have been used to generate a reliable set of clustering energies for up to three water molecules in carbon dioxide clusters up to n = 12. The structures and energetics are dominated by Lewis acid-base interactions with hydrogen bonding interactions playing a lesser energetic role. The actual binding energies are somewhat larger than might be expected. The correlated molecular orbital MP2 method and density functional theory with the ωB97X exchange-correlation functional provide good results for the energetics of the clusters but the B3LYP and ωB97X-D functionalsmore » do not. Seven CO2 molecules form the first solvent shell about a single H2O with four CO2 molecules interacting with the H2O via Lewis acid-base interactions, two CO2 interacting with the H2O by hydrogen bonds, and the seventh CO2 completing the shell. The Lewis acid-base and weak hydrogen bond interactions between the water molecules and the CO2 molecules are strong enough to disrupt the trimer ring configuration for as few as seven CO2 molecules. Calculated 13C NMR chemical shifts for mCO2•(H2O)n show little change with respect to the number of H2O or CO2 molecules in the cluster. The O-H stretching frequencies do exhibit shifts that can provide information about the interactions between water and CO2 molecules.« less

A first principles investigation of the oxygen adsorption on Zr(0001) surface using cluster expansions

NASA Astrophysics Data System (ADS)

Samin, Adib J.; Taylor, Christopher D.

2017-11-01

The design of corrosion resistant zircalloys is important for a variety of technological applications ranging from medicine to the nuclear industry. Since corrosion resistance is mainly attributed to the formation of a surface oxide layer, developing a detailed understanding of this process may assist in future corrosion resistance design. In this work, we conduct a systematic multi-scale investigation of the early stages of oxide formation. This was accomplished by first using a database of fully relaxed DFT calculations to build a cluster-expansion description of the potential function. The developed potential was reasonably good at predicting DFT energies as evidenced by the cross-validation score of 4.4 meV/site. The effective cluster expansion parameters were indicative of repulsive adsorbate interactions in the adlayer in agreement with the literature. The potential then allowed for a systematic investigation of the oxygen configurations on the Zr(0001) surface via Monte Carlo simulations. The adsorption energy was recorded as a function of coverage and an increasing trend was observed in agreement with DFT predictions and the repulsive nature of interactions in the adlayer. The convex hull diagram was recorded indicating the most stable configuration to occur around a coverage of 0.6 ML. The adsorption isotherm was also recorded and contrasted for two temperatures relevant for different applications.

Clustering and propulsion of isotropic catalytic swimmers

NASA Astrophysics Data System (ADS)

Varma, Akhil; Montenegro-Johnson, Thomas D.; Michelin, Sebastien

2017-11-01

Catalytic micro-swimmers such as phoretic particles use local gradients in solute concentration for propulsion. An isolated isotropic phoretic particle generates a uniform concentration field on its surface and hence cannot propel on its own. Symmetry of this field is broken by the presence of at least another similar particle in the system, which leads to phoretic attraction or repulsion. Phoretic attraction drives the clustering of identical homogeneous particles into stable clusters of various configurations which may self-propel or rotate due to their geometric asymmetry. Using full numerical simulations and analytic approximations based on pairwise interactions of the particles, we study the cluster formation and its impact on the statistics of the propulsion properties. We finally analyze the effect of background noise on the results. European Research Council (Grant Agreement 714027).

Frustration and thermalization in an artificial magnetic quasicrystal

NASA Astrophysics Data System (ADS)

Shi, Dong; Budrikis, Zoe; Stein, Aaron; Morley, Sophie A.; Olmsted, Peter D.; Burnell, Gavin; Marrows, Christopher H.

2018-03-01

Artificial frustrated systems offer a playground to study the emergent properties of interacting systems. Most work to date has been on spatially periodic systems, known as artificial spin ices when the interacting elements are magnetic. Here we have studied artificial magnetic quasicrystals based on quasiperiodic Penrose tiling patterns of interacting nanomagnets. We construct a low-energy configuration from a step-by-step approach that we propose as a ground state. Topologically induced emergent frustration means that this configuration cannot be constructed from vertices in their ground states. It has two parts, a quasi-one-dimensional `skeleton' that spans the entire pattern and is capable of long-range order, surrounding `flippable' clusters of macrospins that lead to macroscopic degeneracy. Magnetic force microscopy imaging of Penrose tiling arrays revealed superdomains that are larger for more strongly coupled arrays, especially after annealing the array above its blocking temperature.

Frustration and thermalization in an artificial magnetic quasicrystal

DOE PAGES

Shi, Dong; Budrikis, Zoe; Stein, Aaron; ...

2017-12-11

Here, artificial frustrated systems offer a playground to study the emergent properties of interacting systems. Most work to date has been on spatially periodic systems, known as artificial spin ices when the interacting elements are magnetic. Here we have studied artificial magnetic quasicrystals based on quasiperiodic Penrose tiling patterns of interacting nanomagnets. We construct a low-energy configuration from a step-by-step approach that we propose as a ground state. Topologically induced emergent frustration means that this configuration cannot be constructed from vertices in their ground states. It has two parts, a quasi-one-dimensional ‘skeleton’ that spans the entire pattern and is capablemore » of long-range order, surrounding ‘flippable’ clusters of macrospins that lead to macroscopic degeneracy. Magnetic force microscopy imaging of Penrose tiling arrays revealed superdomains that are larger for more strongly coupled arrays, especially after annealing the array above its blocking temperature.« less

Frustration and thermalization in an artificial magnetic quasicrystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Dong; Budrikis, Zoe; Stein, Aaron

Here, artificial frustrated systems offer a playground to study the emergent properties of interacting systems. Most work to date has been on spatially periodic systems, known as artificial spin ices when the interacting elements are magnetic. Here we have studied artificial magnetic quasicrystals based on quasiperiodic Penrose tiling patterns of interacting nanomagnets. We construct a low-energy configuration from a step-by-step approach that we propose as a ground state. Topologically induced emergent frustration means that this configuration cannot be constructed from vertices in their ground states. It has two parts, a quasi-one-dimensional ‘skeleton’ that spans the entire pattern and is capablemore » of long-range order, surrounding ‘flippable’ clusters of macrospins that lead to macroscopic degeneracy. Magnetic force microscopy imaging of Penrose tiling arrays revealed superdomains that are larger for more strongly coupled arrays, especially after annealing the array above its blocking temperature.« less

Cluster approach to the prediction of thermodynamic and transport properties of ionic liquids

NASA Astrophysics Data System (ADS)

Seeger, Zoe L.; Kobayashi, Rika; Izgorodina, Ekaterina I.

2018-05-01

The prediction of physicochemical properties of ionic liquids such as conductivity and melting point would substantially aid the targeted design of ionic liquids for specific applications ranging from solvents for extraction of valuable chemicals to biowaste to electrolytes in alternative energy devices. The previously published study connecting the interaction energies of single ion pairs (1 IP) of ionic liquids to their thermodynamic and transport properties has been extended to larger systems consisting of two ion pairs (2 IPs), in which many-body and same-ion interactions are included. Routinely used cations, of the imidazolium and pyrrolidinium families, were selected in the study coupled with chloride, tetrafluoroborate, and dicyanamide. Their two ion pair clusters were subjected to extensive configuration screening to establish most stable structures. Interaction energies of these clusters were calculated at the spin-ratio scaled MP2 (SRS-MP2) level for the correlation interaction energy, and a newly developed scaled Hartree-Fock method for the rest of energetic contributions to interaction energy. A full geometry screening for each cation-anion combination resulted in 192 unique structures, whose stability was assessed using two criteria—widely used interaction energy and total electronic energy. Furthermore, the ratio of interaction energy to its dispersion component was correlated with experimentally observed melting points in 64 energetically favourable structures. These systems were also used to test the correlation of the dispersion contribution to interaction energy with measured conductivity.

Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers.

PubMed

Galeano, B K; Ranatunga, W; Gakh, O; Smith, D Y; Thompson, J R; Isaya, G

2017-06-21

Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.

Meiotic events in Oenothera - a non-standard pattern of chromosome behaviour.

PubMed

Golczyk, Hieronim; Musiał, Krystyna; Rauwolf, Uwe; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

2008-11-01

The genus Oenothera shows an intriguing extent of permanent translocation heterozygosity. Reciprocal translocations of chromosome arms in species or populations result in various kinds of chromosome multivalents in diakinesis. Early meiotic events conditioning such chromosome behaviour are poorly understood. We found a surprising uniformity of the leptotene-diplotene period, regardless of the chromosome configuration at diakinesis (ring of 14, 7 bivalents, mixture of bivalents and multivalents). It appears that the earliest chromosome interactions at Oenothera meiosis are untypical, since they involve pericentromeric regions. During early leptotene, proximal chromosome parts cluster and form a highly polarized Rabl configuration. Telomeres associated in pairs were seen at zygotene. The high degree of polarization of meiotic nuclei continues for an exceptionally long period, i.e., during zygotene-pachytene into the diplotene contraction stage. The Rabl-polarized meiotic architecture and clustering of pericentromeres suggest a high complexity of karyotypes, not only in structural heterozygotes but also in bivalent-forming homozygous species.

Burnout and demographic characteristics of workers experiencing different types of work-home interaction.

PubMed

Merecz, Dorota; Andysz, Aleksandra

2014-12-01

The purpose of this study was to explore configurations of positive versus negative interactions between work and home (WHI) and their relation to burnout and demographic characteristics. Sample of 533 Polish workers were interviewed by means of self-administered questionnaires (SWING and MBI-GS). Demographic and work characteristics were also controlled. Cluster analysis distinguished 5 types of WHIs: positive WHI (18%), negative WHI (15.9%), no interaction (29.3%), mutual positive interactions (15.4%) and positive HWI (21.4%). The quality of WHI was associated with number of work hours and tenure at main place of employment. The effect of gender on the quality of work-home interaction was not significant. Configuration of WHIs affected the level of burnout. Again, there was no significant difference between men and women in terms of burnout and its sub-dimensions. The least burned-out were people from positive WHI, positive HWI and mutual positive interaction groups. The most burned-out were people who experienced negative WHI the most often. In this group, predominance of men working more than 10 h per day was observed. The majority of study group (71%) experienced rather integration than segmentation of both spheres. Our results suggest that segmentation is not an universal and effective strategy of coping with work and home demands - it may prevent the positive home-work spillover, which can be buffer or remedy against stress or burnout. We consider cluster analysis the appropriate method in research on relation to work-family balance issue, which may be useful in unraveling relationships between this phenomenon and attitudes and behaviors.

Relativistic all-order many-body calculation of energies, wavelengths, and M 1 and E 2 transition rates for the 3 dn configurations in tungsten ions

NASA Astrophysics Data System (ADS)

Safronova, M. S.; Safronova, U. I.; Porsev, S. G.; Kozlov, M. G.; Ralchenko, Yu.

2018-01-01

Energy levels, wavelengths, magnetic-dipole and electric-quadrupole transition rates between the low-lying states are evaluated for W51 + to W54 + ions with 3 dn (n =2 to 5) electronic configurations by using an approach combining configuration interaction with the linearized coupled-cluster single-double method. The QED corrections are directly incorporated into the calculations and their effect is studied in detail. Uncertainties of the calculations are discussed. This study of such highly charged ions with the present method opens the way for future applications allowing an accurate prediction of properties for a very wide range of highly charged ions aimed at providing precision benchmarks for various applications.

α clustering with a hollow structure: Geometrical structure of α clusters from platonic solids to fullerene shape

NASA Astrophysics Data System (ADS)

Tohsaki, Akihiro; Itagaki, Naoyuki

2018-01-01

We study α -cluster structure based on the geometric configurations with a microscopic framework, which takes full account of the Pauli principle, and which also employs an effective internucleon force including finite-range three-body terms suitable for microscopic α -cluster models. Here, special attention is focused upon the α clustering with a hollow structure; all the α clusters are put on the surface of a sphere. All the platonic solids (five regular polyhedra) and the fullerene-shaped polyhedron coming from icosahedral structure are considered. Furthermore, two configurations with dual polyhedra, hexahedron-octahedron and dodecahedron-icosahedron, are also scrutinized. When approaching each other from large distances with these symmetries, α clusters create certain local energy pockets. As a consequence, we insist on the possible existence of α clustering with a geometric shape and hollow structure, which is favored from Coulomb energy point of view. Especially, two configurations, that is, dual polyhedra of dodecahedron-icosahedron and fullerene, have a prominent hollow structure compared with the other six configurations.

The Cluster Variation Method: A Primer for Neuroscientists.

PubMed

Maren, Alianna J

2016-09-30

Effective Brain-Computer Interfaces (BCIs) require that the time-varying activation patterns of 2-D neural ensembles be modelled. The cluster variation method (CVM) offers a means for the characterization of 2-D local pattern distributions. This paper provides neuroscientists and BCI researchers with a CVM tutorial that will help them to understand how the CVM statistical thermodynamics formulation can model 2-D pattern distributions expressing structural and functional dynamics in the brain. The premise is that local-in-time free energy minimization works alongside neural connectivity adaptation, supporting the development and stabilization of consistent stimulus-specific responsive activation patterns. The equilibrium distribution of local patterns, or configuration variables , is defined in terms of a single interaction enthalpy parameter ( h ) for the case of an equiprobable distribution of bistate (neural/neural ensemble) units. Thus, either one enthalpy parameter (or two, for the case of non-equiprobable distribution) yields equilibrium configuration variable values. Modeling 2-D neural activation distribution patterns with the representational layer of a computational engine, we can thus correlate variational free energy minimization with specific configuration variable distributions. The CVM triplet configuration variables also map well to the notion of a M = 3 functional motif. This paper addresses the special case of an equiprobable unit distribution, for which an analytic solution can be found.

The Cluster Variation Method: A Primer for Neuroscientists

PubMed Central

Maren, Alianna J.

2016-01-01

Effective Brain–Computer Interfaces (BCIs) require that the time-varying activation patterns of 2-D neural ensembles be modelled. The cluster variation method (CVM) offers a means for the characterization of 2-D local pattern distributions. This paper provides neuroscientists and BCI researchers with a CVM tutorial that will help them to understand how the CVM statistical thermodynamics formulation can model 2-D pattern distributions expressing structural and functional dynamics in the brain. The premise is that local-in-time free energy minimization works alongside neural connectivity adaptation, supporting the development and stabilization of consistent stimulus-specific responsive activation patterns. The equilibrium distribution of local patterns, or configuration variables, is defined in terms of a single interaction enthalpy parameter (h) for the case of an equiprobable distribution of bistate (neural/neural ensemble) units. Thus, either one enthalpy parameter (or two, for the case of non-equiprobable distribution) yields equilibrium configuration variable values. Modeling 2-D neural activation distribution patterns with the representational layer of a computational engine, we can thus correlate variational free energy minimization with specific configuration variable distributions. The CVM triplet configuration variables also map well to the notion of a M = 3 functional motif. This paper addresses the special case of an equiprobable unit distribution, for which an analytic solution can be found. PMID:27706022

Circular single domains in hemispherical Permalloy nanoclusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Araujo, Clodoaldo I. L de, E-mail: dearaujo@ufv.br; Fonseca, Jakson M.; Sinnecker, João P.

2014-11-14

We have studied ferromagnetic Permalloy clusters obtained by electrodeposition on n-type silicon. Magnetization measurements reveal hysteresis loops almost independent on temperature and very similar in shape to those obtained in nanodisks with diameter bigger than 150 nm. The spin configuration for the ground state, obtained by micromagnetic simulation, shows topological vortices with random chirality and polarization. This behavior in the small diameter clusters (∼80 nm) is attributed to the Dzyaloshinskii-Moriya interaction that arises in its hemispherical geometries. This magnetization behavior can be utilized to explain the magnetoresistance measured with magnetic field in plane and out of sample plane.

Tile-based Level of Detail for the Parallel Age

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niski, K; Cohen, J D

Today's PCs incorporate multiple CPUs and GPUs and are easily arranged in clusters for high-performance, interactive graphics. We present an approach based on hierarchical, screen-space tiles to parallelizing rendering with level of detail. Adapt tiles, render tiles, and machine tiles are associated with CPUs, GPUs, and PCs, respectively, to efficiently parallelize the workload with good resource utilization. Adaptive tile sizes provide load balancing while our level of detail system allows total and independent management of the load on CPUs and GPUs. We demonstrate our approach on parallel configurations consisting of both single PCs and a cluster of PCs.

Dynamics of fragment formation in neutron-rich matter

NASA Astrophysics Data System (ADS)

Alcain, P. N.; Dorso, C. O.

2018-01-01

Background: Neutron stars are astronomical systems with nucleons subjected to extreme conditions. Due to the longer range Coulomb repulsion between protons, the system has structural inhomogeneities. Several interactions tailored to reproduce nuclear matter plus a screened Coulomb term reproduce these inhomogeneities known as nuclear pasta. These structural inhomogeneities, located in the crusts of neutron stars, can also arise in expanding systems depending on the thermodynamic conditions (temperature, proton fraction, etc.) and the expansion velocity. Purpose: We aim to find the dynamics of the fragment formation for expanding systems simulated according to the little big bang model. This expansion resembles the evolution of merging neutron stars. Method: We study the dynamics of the nucleons with semiclassical molecular dynamics models. Starting with an equilibrium configuration, we expand the system homogeneously until we arrive at an asymptotic configuration (i.e., very low final densities). We study, with four different cluster recognition algorithms, the fragment distribution throughout this expansion and the dynamics of the cluster formation. Results: Studying the topology of the equilibrium states, before the expansion, we reproduced the known pasta phases plus a novel phase we called pregnocchi, consisting of proton aggregates embedded in a neutron sea. We have identified different fragmentation regimes, depending on the initial temperature and fragment velocity. In particular, for the already mentioned pregnocchi, a neutron cloud surrounds the clusters during the early stages of the expansion, resulting in systems that give rise to configurations compatible with the emergence of the r process. Conclusions: We showed that a proper identification of the cluster distribution is highly dependent on the cluster recognition algorithm chosen, and found that the early cluster recognition algorithm (ECRA) was the most stable one. This approach allowed us to identify the dynamics of the fragment formation. These calculations pave the way to a comparison between Earth experiments and neutron star studies.

Geometric structure of percolation clusters.

PubMed

Xu, Xiao; Wang, Junfeng; Zhou, Zongzheng; Garoni, Timothy M; Deng, Youjin

2014-01-01

We investigate the geometric properties of percolation clusters by studying square-lattice bond percolation on the torus. We show that the density of bridges and nonbridges both tend to 1/4 for large system sizes. Using Monte Carlo simulations, we study the probability that a given edge is not a bridge but has both its loop arcs in the same loop and find that it is governed by the two-arm exponent. We then classify bridges into two types: branches and junctions. A bridge is a branch iff at least one of the two clusters produced by its deletion is a tree. Starting from a percolation configuration and deleting the branches results in a leaf-free configuration, whereas, deleting all bridges produces a bridge-free configuration. Although branches account for ≈43% of all occupied bonds, we find that the fractal dimensions of the cluster size and hull length of leaf-free configurations are consistent with those for standard percolation configurations. By contrast, we find that the fractal dimensions of the cluster size and hull length of bridge-free configurations are given by the backbone and external perimeter dimensions, respectively. We estimate the backbone fractal dimension to be 1.643 36(10).

Formation and decay of resonance states in 9Be and 9B nuclei: Microscopic three-cluster model investigations

NASA Astrophysics Data System (ADS)

Vasilevsky, V. S.; Katō, K.; Takibayev, N. Zh.

2017-09-01

We study the nature of the low-lying resonance states in mirror nuclei 9Be and 9B. Investigations are performed within a three-cluster model. The model makes use of the hyperspherical harmonics, which provides a convenient description of the three-cluster continuum. The dominant three-cluster configurations α +α +n and α +α +p in 9Be and 9B, respectively, are taken into account. Dominant decay channels for all resonance states in 9Be and 9B are explored. Much attention is paid to the controversial 1 /2+ resonance states in both nuclei. We study effects of the Coulomb interaction on the energy and width of three-cluster resonances in the mirror nuclei 9Be and 9B. We also search for the Hoyle-analog state, which is a key step for alternative ways to synthesize 9Be and 9B in triple collisions of clusters in a stellar environment.

Nuclear Potential Clustering As a New Tool to Detect Patterns in High Dimensional Datasets

NASA Astrophysics Data System (ADS)

Tonkova, V.; Paulus, D.; Neeb, H.

2013-02-01

We present a new approach for the clustering of high dimensional data without prior assumptions about the structure of the underlying distribution. The proposed algorithm is based on a concept adapted from nuclear physics. To partition the data, we model the dynamic behaviour of nucleons interacting in an N-dimensional space. An adaptive nuclear potential, comprised of a short-range attractive (strong interaction) and a long-range repulsive term (Coulomb force) is assigned to each data point. By modelling the dynamics, nucleons that are densely distributed in space fuse to build nuclei (clusters) whereas single point clusters repel each other. The formation of clusters is completed when the system reaches the state of minimal potential energy. The data are then grouped according to the particles' final effective potential energy level. The performance of the algorithm is tested with several synthetic datasets showing that the proposed method can robustly identify clusters even when complex configurations are present. Furthermore, quantitative MRI data from 43 multiple sclerosis patients were analyzed, showing a reasonable splitting into subgroups according to the individual patients' disease grade. The good performance of the algorithm on such highly correlated non-spherical datasets, which are typical for MRI derived image features, shows that Nuclear Potential Clustering is a valuable tool for automated data analysis, not only in the MRI domain.

A Chandra X-ray census of the interacting binaries in old open clusters - NGC 188

NASA Astrophysics Data System (ADS)

Vats, Smriti; Van Den Berg, Maureen

2017-01-01

We present a new X-ray study of NGC 188, one of the oldest open clusters known in the Milky Way (7 Gyr). Our X-ray observation using the Chandra X-ray Observatory is aimed at uncovering the population of close interacting binaries in the cluster. We detect 84 X-ray sources with a limiting X-ray luminosity, LX ~ 4×1029 erg s-1 (0.3-7 keV), of which 28 are within the half-mass radius. Of these, 13 are proper-motion or radial-velocity cluster members, wherein we identify a mix of active binaries (ABs) and blue straggler stars (BSSs). We also identify one tentative cataclysmic variable (CV) candidate which is a known short-period photometric variable, but whose membership to NGC 188 is unknown. We have compared the X-ray luminosity per unit of cluster mass (i.e. the X-ray emissivity) of NGC 188 with those of other old Galactic open clusters and dense globular clusters (47 Tuc, NGC 6397). Our findings confirm the earlier result that old open clusters have higher X-ray emissivities than the globular clusters (LX ≥1×1030 erg s-1). This may be explained by dynamical encounters in globulars, which could have a net effect of destroying binaries, or the typically higher metallicities of open clusters. We find one intriguing X-ray source in NGC 188 that is a BSS and cluster member, whose X-ray luminosity cannot be explained by its currently understood binary configuration. Its X-ray detection invokes the need for a third companion in the system.

Two-dimensional and three-dimensional Coulomb clusters in parabolic traps

DOE Office of Scientific and Technical Information (OSTI.GOV)

D'yachkov, L. G., E-mail: dyachk@mail.ru; Myasnikov, M. I., E-mail: miasnikovmi@mail.ru; Petrov, O. F.

2014-09-15

We consider the shell structure of Coulomb clusters in an axially symmetric parabolic trap exhibiting a confining potential U{sub c}(ρ,z)=(mω{sup 2}/2)(ρ{sup 2}+αz{sup 2}). Assuming an anisotropic parameter α = 4 (corresponding to experiments employing a cusp magnetic trap under microgravity conditions), we have calculated cluster configurations for particle numbers N = 3 to 30. We have shown that clusters with N ≤ 12 initially remain flat, transitioning to three-dimensional configurations as N increases. For N = 8, we have calculated the configurations of minimal potential energy for all values of α and found the points of configuration transitions. For N = 13 and 23, we discuss the influence of bothmore » the shielding and anisotropic parameter on potential energy, cluster size, and shell structure.« less

Performance monitoring for new phase dynamic optimization of instruction dispatch cluster configuration

DOEpatents

Balasubramonian, Rajeev [Sandy, UT; Dwarkadas, Sandhya [Rochester, NY; Albonesi, David [Ithaca, NY

2012-01-24

In a processor having multiple clusters which operate in parallel, the number of clusters in use can be varied dynamically. At the start of each program phase, the configuration option for an interval is run to determine the optimal configuration, which is used until the next phase change is detected. The optimum instruction interval is determined by starting with a minimum interval and doubling it until a low stability factor is reached.

Bootstrap Percolation on Homogeneous Trees Has 2 Phase Transitions

NASA Astrophysics Data System (ADS)

Fontes, L. R. G.; Schonmann, R. H.

2008-09-01

We study the threshold θ bootstrap percolation model on the homogeneous tree with degree b+1, 2≤ θ≤ b, and initial density p. It is known that there exists a nontrivial critical value for p, which we call p f , such that a) for p> p f , the final bootstrapped configuration is fully occupied for almost every initial configuration, and b) if p< p f , then for almost every initial configuration, the final bootstrapped configuration has density of occupied vertices less than 1. In this paper, we establish the existence of a distinct critical value for p, p c , such that 0< p c < p f , with the following properties: 1) if p≤ p c , then for almost every initial configuration there is no infinite cluster of occupied vertices in the final bootstrapped configuration; 2) if p> p c , then for almost every initial configuration there are infinite clusters of occupied vertices in the final bootstrapped configuration. Moreover, we show that 3) for p< p c , the distribution of the occupied cluster size in the final bootstrapped configuration has an exponential tail; 4) at p= p c , the expected occupied cluster size in the final bootstrapped configuration is infinite; 5) the probability of percolation of occupied vertices in the final bootstrapped configuration is continuous on [0, p f ] and analytic on ( p c , p f ), admitting an analytic continuation from the right at p c and, only in the case θ= b, also from the left at p f .

Identifying Few-Molecule Water Clusters with High Precision on Au(111) Surface.

PubMed

Dong, Anning; Yan, Lei; Sun, Lihuan; Yan, Shichao; Shan, Xinyan; Guo, Yang; Meng, Sheng; Lu, Xinghua

2018-06-01

Revealing the nature of a hydrogen-bond network in water structures is one of the imperative objectives of science. With the use of a low-temperature scanning tunneling microscope, water clusters on a Au(111) surface were directly imaged with molecular resolution by a functionalized tip. The internal structures of the water clusters as well as the geometry variations with the increase of size were identified. In contrast to a buckled water hexamer predicted by previous theoretical calculations, our results present deterministic evidence for a flat configuration of water hexamers on Au(111), corroborated by density functional theory calculations with properly implemented van der Waals corrections. The consistency between the experimental observations and improved theoretical calculations not only renders the internal structures of absorbed water clusters unambiguously, but also directly manifests the crucial role of van der Waals interactions in constructing water-solid interfaces.

B =5 Skyrmion as a two-cluster system

NASA Astrophysics Data System (ADS)

Gudnason, Sven Bjarke; Halcrow, Chris

2018-06-01

The classical B =5 Skyrmion can be approximated by a two-cluster system in which a B =1 Skyrmion is attached to a core B =4 Skyrmion. We quantize this system, allowing the B =1 to freely orbit the core. The configuration space is 11 dimensional but simplifies significantly after factoring out the overall spin and isospin degrees of freedom. We exactly solve the free quantum problem and then include an interaction potential between the Skyrmions numerically. The resulting energy spectrum is compared to the corresponding nuclei—the helium-5/lithium-5 isodoublet. We find approximate parity doubling not seen in the experimental data. In addition, we fail to obtain the correct ground-state spin. The framework laid out for this two-cluster system can readily be modified for other clusters and in particular for other B =4 n +1 nuclei, of which B =5 is the simplest example.

A multi purpose source chamber at the PLEIADES beamline at SOLEIL for spectroscopic studies of isolated species: cold molecules, clusters, and nanoparticles.

PubMed

Lindblad, Andreas; Söderström, Johan; Nicolas, Christophe; Robert, Emmanuel; Miron, Catalin

2013-11-01

This paper describes the philosophy and design goals regarding the construction of a versatile sample environment: a source capable of producing beams of atoms, molecules, clusters, and nanoparticles in view of studying their interaction with short wavelength (vacuum ultraviolet and x-ray) synchrotron radiation. In the design, specific care has been taken of (a) the use standard components, (b) ensuring modularity, i.e., that swiftly switching between different experimental configurations was possible. To demonstrate the efficiency of the design, proof-of-principle experiments have been conducted by recording x-ray absorption and photoelectron spectra from isolated nanoparticles (SiO2) and free mixed clusters (Ar/Xe). The results from those experiments are showcased and briefly discussed.

Activity of a social dynamics model

NASA Astrophysics Data System (ADS)

Reia, Sandro M.; Neves, Ubiraci P. C.

2015-10-01

Axelrod's model was proposed to study interactions between agents and the formation of cultural domains. It presents a transition from a monocultural to a multicultural steady state which has been studied in the literature by evaluation of the relative size of the largest cluster. In this article, we propose new measurements based on the concept of activity per agent to study the Axelrod's model on the square lattice. We show that the variance of system activity can be used to indicate the critical points of the transition. Furthermore the frequency distribution of the system activity is able to show a coexistence of phases typical of a first order phase transition. Finally, we verify a power law dependence between cluster activity and cluster size for multicultural steady state configurations at the critical point.

Sulfur Adsorption on the Goethite (110) Surface

NASA Astrophysics Data System (ADS)

Simonetti, S.; Damiani, D.; Brizuela, G.; Juan, A.

The electronic structure of S adsorption on goethite (110) surface has been studied by ASED-MO cluster calculations. For S location, the most exposed surface atoms of goethite surface were selected. The calculations show that the surface offers several places for S adsorption. The most energetically stable system corresponds to S location above H atom. We studied in detail the configurations that correspond to the higher OP values. For these configurations, the H-S and Fe-S computed distances are 2.1 and 3.7 Å, respectively. The H-S and Fe-S are mainly bonding interaction with OP values of 0.156 and 0.034, respectively. The Fe-S interaction mainly involves Fe 3dx2-y2 atomic orbitals with lesser participation of Fe 4py and Fe 3dyz atomic orbitals. The O-S interaction shows the same bonding and antibonding contributions giving a small OP value. The O-S interaction involves O 2p orbitals. There is an electron transfer to the Fe atom from the S atom. On the other hand, there is an electron transfer to S atom from the H and O atoms, respectively.

Hydrogen-vacancy-dislocation interactions in α-Fe

NASA Astrophysics Data System (ADS)

Tehranchi, A.; Zhang, X.; Lu, G.; Curtin, W. A.

2017-02-01

Atomistic simulations of the interactions between dislocations, hydrogen atoms, and vacancies are studied to assess the viability of a recently proposed mechanism for the formation of nanoscale voids in Fe-based steels in the presence of hydrogen. Quantum-mechanics/molecular-mechanics method calculations confirm molecular statics simulations based on embedded atom method (EAM) potential showing that individual vacancies on the compressive side of an edge dislocation can be transported with the dislocation as it glides. Molecular dynamics simulations based on EAM potential then show, however, that vacancy clusters in the glide plane of an approaching dislocation are annihilated or reduced in size by the creation of a double-jog/climb process that is driven by the huge reduction in energy accompanying vacancy annihilation. The effectiveness of annihilation/reduction processes is not reduced by the presence of hydrogen in the vacancy clusters because typical V-H cluster binding energies are much lower than the vacancy formation energy, except at very high hydrogen content in the cluster. Analysis of a range of configurations indicates that hydrogen plays no special role in stabilizing nanovoids against jog formation processes that shrink voids. Experimental observations of nanovoids on the fracture surfaces of steels must be due to as-yet undetermined processes.

Experimental Measurement of RCS Jet Interaction Effects on a Capsule Entry Vehicle

NASA Technical Reports Server (NTRS)

Buck, Gregory M.; Watkins, A. Neal; Danehy, Paul M.; Inman, Jennifer A.; Alderfer, David W.; Dyakonov, Artem A.

2008-01-01

An investigation was made in NASA Langley Research Center s 31-Inch Mach 10 Tunnel to determine the effects of reaction-control system (RCS) jet interactions on the aft-body of a capsule entry vehicle. The test focused on demonstrating and improving advanced measurement techniques that would aid in the rapid measurement and visualization of jet interaction effects for the Orion Crew Exploration Vehicle while providing data useful for developing engineering models or validation of computational tools used to assess actual flight environments. Measurements included global surface imaging with pressure and temperature sensitive paints and three-dimensional flow visualization with a scanning planar laser induced fluorescence technique. The wind tunnel model was fabricated with interchangeable parts for two different aft-body configurations. The first, an Apollo-like configuration, was used to focus primarily on the forward facing roll and yaw jet interactions which are known to have significant aft-body heating augmentation. The second, an early Orion Crew Module configuration (4-cluster jets), was tested blowing only out of the most windward yaw jet, which was expected to have the maximum heating augmentation for that configuration. Jet chamber pressures and tunnel flow conditions were chosen to approximate early Apollo wind tunnel test conditions. Maximum heating augmentation values measured for the Apollo-like configuration (>10 for forward facing roll jet and 4 for yaw jet) using temperature sensitive paint were shown to be similar to earlier experimental results (Jones and Hunt, 1965) using a phase change paint technique, but were acquired with much higher surface resolution. Heating results for the windward yaw jet on the Orion configuration had similar augmentation levels, but affected much less surface area. Numerical modeling for the Apollo-like yaw jet configuration with laminar flow and uniform jet outflow conditions showed similar heating patterns, qualitatively, but also showed significant variation with jet exit divergence angle, with as much as 25 percent variation in heat flux intensity for a 10 degree divergence angle versus parallel outflow. These results along with the fabrication methods and advanced measurement techniques developed will be used in the next phase of testing and evaluation for the updated Orion RCS configuration.

Comparison of the quadratic configuration interaction and coupled cluster approaches to electron correlation including the effect of triple excitations

NASA Technical Reports Server (NTRS)

Taylor, Peter R.; Lee, Timothy J.; Rendell, Alistair P.

1990-01-01

The recently proposed quadratic configuration interaction (QCI) method is compared with the more rigorous coupled cluster (CC) approach for a variety of chemical systems. Some of these systems are well represented by a single-determinant reference function and others are not. The finite order singles and doubles correlation energy, the perturbational triples correlation energy, and a recently devised diagnostic for estimating the importance of multireference effects are considered. The spectroscopic constants of CuH, the equilibrium structure of cis-(NO)2 and the binding energies of Be3, Be4, Mg3, and Mg4 were calculated using both approaches. The diagnostic for estimating multireference character clearly demonstrates that the QCI method becomes less satisfactory than the CC approach as non-dynamical correlation becomes more important, in agreement with a perturbational analysis of the two methods and the numerical estimates of the triple excitation energies they yield. The results for CuH show that the differences between the two methods become more apparent as the chemical systems under investigation becomes more multireference in nature and the QCI results consequently become less reliable. Nonetheless, when the system of interest is dominated by a single reference determinant both QCI and CC give very similar results.

Comparative Study of Multiplet Structures of Mn4+ in K2SiF6, K2GeF6, and K2TiF6 Based on First-Principles Configuration-Interaction Calculations

NASA Astrophysics Data System (ADS)

Novita, Mega; Ogasawara, Kazuyoshi

2012-02-01

We performed first-principles configuration-interaction calculations of multiplet energies for Mn4+ in K2SiF6, K2GeF6, and K2TiF6 crystals. The results indicate that corrections based on a single-electron calculation are effective for the prediction of 4A2 → 4T2 and 4A2 → 4T1a transition energies, while such corrections are not necessary for the prediction of the 4A2 → 2E transition energy. The cluster size dependence of the multiplet energies is small. However, the 4A2 → 2E transition energy is slightly improved by using larger clusters including K ions. The theoretical multiplet energies are improved further by considering the lattice relaxation effect. As a result, the characteristic multiplet energy shifts depending on the host crystal are well reproduced without using any empirical parameters. Although K2GeF6 and K2TiF6 have lower symmetry than K2SiF6, the results indicate that the variation of the multiplet energy is mainly determined by the Mn-F bond length.

Electronic excitation of molecules in solution calculated using the symmetry-adapted cluster–configuration interaction method in the polarizable continuum model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukuda, Ryoichi, E-mail: fukuda@ims.ac.jp; Ehara, Masahiro; Elements Strategy Initiative for Catalysts and Batteries

2015-12-31

The effects from solvent environment are specific to the electronic states; therefore, a computational scheme for solvent effects consistent with the electronic states is necessary to discuss electronic excitation of molecules in solution. The PCM (polarizable continuum model) SAC (symmetry-adapted cluster) and SAC-CI (configuration interaction) methods are developed for such purposes. The PCM SAC-CI adopts the state-specific (SS) solvation scheme where solvent effects are self-consistently considered for every ground and excited states. For efficient computations of many excited states, we develop a perturbative approximation for the PCM SAC-CI method, which is called corrected linear response (cLR) scheme. Our test calculationsmore » show that the cLR PCM SAC-CI is a very good approximation of the SS PCM SAC-CI method for polar and nonpolar solvents.« less

Scientific Cluster Deployment and Recovery - Using puppet to simplify cluster management

NASA Astrophysics Data System (ADS)

Hendrix, Val; Benjamin, Doug; Yao, Yushu

2012-12-01

Deployment, maintenance and recovery of a scientific cluster, which has complex, specialized services, can be a time consuming task requiring the assistance of Linux system administrators, network engineers as well as domain experts. Universities and small institutions that have a part-time FTE with limited time for and knowledge of the administration of such clusters can be strained by such maintenance tasks. This current work is the result of an effort to maintain a data analysis cluster (DAC) with minimal effort by a local system administrator. The realized benefit is the scientist, who is the local system administrator, is able to focus on the data analysis instead of the intricacies of managing a cluster. Our work provides a cluster deployment and recovery process (CDRP) based on the puppet configuration engine allowing a part-time FTE to easily deploy and recover entire clusters with minimal effort. Puppet is a configuration management system (CMS) used widely in computing centers for the automatic management of resources. Domain experts use Puppet's declarative language to define reusable modules for service configuration and deployment. Our CDRP has three actors: domain experts, a cluster designer and a cluster manager. The domain experts first write the puppet modules for the cluster services. A cluster designer would then define a cluster. This includes the creation of cluster roles, mapping the services to those roles and determining the relationships between the services. Finally, a cluster manager would acquire the resources (machines, networking), enter the cluster input parameters (hostnames, IP addresses) and automatically generate deployment scripts used by puppet to configure it to act as a designated role. In the event of a machine failure, the originally generated deployment scripts along with puppet can be used to easily reconfigure a new machine. The cluster definition produced in our CDRP is an integral part of automating cluster deployment in a cloud environment. Our future cloud efforts will further build on this work.

A Data Analytics Approach to Discovering Unique Microstructural Configurations Susceptible to Fatigue

NASA Astrophysics Data System (ADS)

Jha, S. K.; Brockman, R. A.; Hoffman, R. M.; Sinha, V.; Pilchak, A. L.; Porter, W. J.; Buchanan, D. J.; Larsen, J. M.; John, R.

2018-05-01

Principal component analysis and fuzzy c-means clustering algorithms were applied to slip-induced strain and geometric metric data in an attempt to discover unique microstructural configurations and their frequencies of occurrence in statistically representative instantiations of a titanium alloy microstructure. Grain-averaged fatigue indicator parameters were calculated for the same instantiation. The fatigue indicator parameters strongly correlated with the spatial location of the microstructural configurations in the principal components space. The fuzzy c-means clustering method identified clusters of data that varied in terms of their average fatigue indicator parameters. Furthermore, the number of points in each cluster was inversely correlated to the average fatigue indicator parameter. This analysis demonstrates that data-driven methods have significant potential for providing unbiased determination of unique microstructural configurations and their frequencies of occurrence in a given volume from the point of view of strain localization and fatigue crack initiation.

Free energy of singular sticky-sphere clusters.

PubMed

Kallus, Yoav; Holmes-Cerfon, Miranda

2017-02-01

Networks of particles connected by springs model many condensed-matter systems, from colloids interacting with a short-range potential and complex fluids near jamming, to self-assembled lattices and various metamaterials. Under small thermal fluctuations the vibrational entropy of a ground state is given by the harmonic approximation if it has no zero-frequency vibrational modes, yet such singular modes are at the epicenter of many interesting behaviors in the systems above. We consider a system of N spherical particles, and directly account for the singularities that arise in the sticky limit where the pairwise interaction is strong and short ranged. Although the contribution to the partition function from singular clusters diverges in the limit, its asymptotic value can be calculated and depends on only two parameters, characterizing the depth and range of the potential. The result holds for systems that are second-order rigid, a geometric characterization that describes all known ground-state (rigid) sticky clusters. To illustrate the applications of our theory we address the question of emergence: how does crystalline order arise in large systems when it is strongly disfavored in small ones? We calculate the partition functions of all known rigid clusters up to N≤21 and show the cluster landscape is dominated by hyperstatic clusters (those with more than 3N-6 contacts); singular and isostatic clusters are far less frequent, despite their extra vibrational and configurational entropies. Since the most hyperstatic clusters are close to fragments of a close-packed lattice, this underlies the emergence of order in sticky-sphere systems, even those as small as N=10.

Free energy of singular sticky-sphere clusters

NASA Astrophysics Data System (ADS)

Kallus, Yoav; Holmes-Cerfon, Miranda

2017-02-01

Networks of particles connected by springs model many condensed-matter systems, from colloids interacting with a short-range potential and complex fluids near jamming, to self-assembled lattices and various metamaterials. Under small thermal fluctuations the vibrational entropy of a ground state is given by the harmonic approximation if it has no zero-frequency vibrational modes, yet such singular modes are at the epicenter of many interesting behaviors in the systems above. We consider a system of N spherical particles, and directly account for the singularities that arise in the sticky limit where the pairwise interaction is strong and short ranged. Although the contribution to the partition function from singular clusters diverges in the limit, its asymptotic value can be calculated and depends on only two parameters, characterizing the depth and range of the potential. The result holds for systems that are second-order rigid, a geometric characterization that describes all known ground-state (rigid) sticky clusters. To illustrate the applications of our theory we address the question of emergence: how does crystalline order arise in large systems when it is strongly disfavored in small ones? We calculate the partition functions of all known rigid clusters up to N ≤21 and show the cluster landscape is dominated by hyperstatic clusters (those with more than 3 N -6 contacts); singular and isostatic clusters are far less frequent, despite their extra vibrational and configurational entropies. Since the most hyperstatic clusters are close to fragments of a close-packed lattice, this underlies the emergence of order in sticky-sphere systems, even those as small as N =10 .

Adsorption configurations and scanning voltage determined STM images of small hydrogen clusters on bilayer graphene.

PubMed

Cao, Teng Fei; Huang, Liang Feng; Zheng, Xiao Hong; Zhou, Wang Huai; Zeng, Zhi

2013-11-21

By density functional theory calculations, the scanning tunneling microscopy (STM) images of various hydrogen clusters adsorbed on bilayer-graphene are systematically simulated. The hydrogen configurations of the STM images observed in the experiments have been thoroughly figured out. In particular, two kinds of hydrogen dimers (ortho-dimer, para-dimer) and two kinds of tetramers (tetramer-A, -B) are determined to be the hydrogen configurations corresponding to the ellipsoidal-like STM images with different structures and sizes. One particular hexamer (hexamer-B) is the hydrogen configuration generating the star-like STM images. For each hydrogen cluster, the simulated STM images show unique voltage-dependent features, which provides a feasible way to determine hydrogen adsorption states on graphene or graphite surface in the experiments by varying-voltage measurements. Stability analysis proves that the above determined hydrogen configurations are quite stable on graphene, hence they are likely to be detected in the STM experiments. Consequently, through systematic analysis of the STM images and the stability of hydrogen clusters on bilayer graphene, many experimental observations have been consistently explained.

A multi purpose source chamber at the PLEIADES beamline at SOLEIL for spectroscopic studies of isolated species: Cold molecules, clusters, and nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindblad, Andreas; Söderström, Johan; Nicolas, Christophe

2013-11-15

This paper describes the philosophy and design goals regarding the construction of a versatile sample environment: a source capable of producing beams of atoms, molecules, clusters, and nanoparticles in view of studying their interaction with short wavelength (vacuum ultraviolet and x-ray) synchrotron radiation. In the design, specific care has been taken of (a) the use standard components, (b) ensuring modularity, i.e., that swiftly switching between different experimental configurations was possible. To demonstrate the efficiency of the design, proof-of-principle experiments have been conducted by recording x-ray absorption and photoelectron spectra from isolated nanoparticles (SiO{sub 2}) and free mixed clusters (Ar/Xe). Themore » results from those experiments are showcased and briefly discussed.« less

Adsorption of beryllium atoms and clusters both on graphene and in a bilayer of graphite investigated by DFT.

PubMed

Ferro, Yves; Fernandez, Nicolas; Allouche, Alain; Linsmeier, Christian

2013-01-09

We herein investigate the interaction of beryllium with a graphene sheet and in a bilayer of graphite by means of periodic DFT calculations. In all cases, we find the beryllium atoms to be more weakly bonded on graphene than in the bilayer. Be(2) forms both magnetic and non-magnetic structures on graphene depending on the geometrical configuration of adsorption. We find that the stability of the Be/bilayer system increases with the size of the beryllium clusters inserted into the bilayer of graphite. We also find a charge transfer from beryllium to the graphite layers. All these results are analysed in terms of electronic structure.

Multi-cluster processor operating only select number of clusters during each phase based on program statistic monitored at predetermined intervals

DOEpatents

Balasubramonian, Rajeev [Sandy, UT; Dwarkadas, Sandhya [Rochester, NY; Albonesi, David [Ithaca, NY

2009-02-10

In a processor having multiple clusters which operate in parallel, the number of clusters in use can be varied dynamically. At the start of each program phase, the configuration option for an interval is run to determine the optimal configuration, which is used until the next phase change is detected. The optimum instruction interval is determined by starting with a minimum interval and doubling it until a low stability factor is reached.

Thermal and adsorbate effects on the activity and morphology of size-selected Pdn/TiO2 model catalysts

NASA Astrophysics Data System (ADS)

Kaden, William E.; Kunkel, William A.; Roberts, F. Sloan; Kane, Matthew; Anderson, Scott L.

2014-03-01

Model catalysts containing size-selected Pdn (n = 1,2,4,7,10,16,20,25) deposited on rutile TiO2(110) deactivate during repeated CO oxidation temperature-programmed reaction (TPR) cycles, and the deactivation process has been probed using a combination of X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), low-energy ion scattering (ISS), temperature-dependent ion scattering (TD-ISS), annealing experiments, and temperature-programmed desorption following exposure to CO and O2 reactants. Results from such experiments suggest the cluster deactivation proceeds via an alloy-like, strong metal-support interaction (SMSI) effect that chemically modifies the clusters via electronic interactions between the supported metal atoms and Ti from the support. Threshold measurements show that this effect detrimentally affects CO-oxidation activity prior to the formation of an encapsulating overlayer by severely weakening the COPd bond strengths for binding configurations on top of the clusters. Oxidation appears to provide means of partially restoring the clusters to their initial state, but after sufficient exposure to reducing environments and elevated temperatures, all Pdn become covered by an overlayer and begin to electronically and chemically resemble freshly deposited atoms, which are completely inactive towards the probe reaction. In addition, we find evidence of oxygen spillover induced by co-adsorbed CO during TPRs for all active Pdn clusters.

Strong Lensing Analysis of the Galaxy Cluster MACS J1319.9+7003 and the Discovery of a Shell Galaxy

NASA Astrophysics Data System (ADS)

Zitrin, Adi

2017-01-01

We present a strong-lensing (SL) analysis of the galaxy cluster MACS J1319.9+7003 (z = 0.33, also known as Abell 1722), as part of our ongoing effort to analyze massive clusters with archival Hubble Space Telescope (HST) imaging. We spectroscopically measured with Keck/Multi-Object Spectrometer For Infra-Red Exploration (MOSFIRE) two galaxies multiply imaged by the cluster. Our analysis reveals a modest lens, with an effective Einstein radius of {θ }e(z=2)=12+/- 1\\prime\\prime , enclosing 2.1+/- 0.3× {10}13 M⊙. We briefly discuss the SL properties of the cluster, using two different modeling techniques (see the text for details), and make the mass models publicly available (ftp://wise-ftp.tau.ac.il/pub/adiz/MACS1319/). Independently, we identified a noteworthy, young shell galaxy (SG) system forming around two likely interacting cluster members, 20″ north of the brightest cluster galaxy. SGs are rare in galaxy clusters, and indeed, a simple estimate reveals that they are only expected in roughly one in several dozen, to several hundred, massive galaxy clusters (the estimate can easily change by an order of magnitude within a reasonable range of characteristic values relevant for the calculation). Taking advantage of our lens model best-fit, mass-to-light scaling relation for cluster members, we infer that the total mass of the SG system is ˜ 1.3× {10}11 {M}⊙ , with a host-to-companion mass ratio of about 10:1. Despite being rare in high density environments, the SG constitutes an example to how stars of cluster galaxies are efficiently redistributed to the intra-cluster medium. Dedicated numerical simulations for the observed shell configuration, perhaps aided by the mass model, might cast interesting light on the interaction history and properties of the two galaxies. An archival HST search in galaxy cluster images can reveal more such systems.

Cost comparison of centralized and decentralized wastewater management systems using optimization model.

PubMed

Jung, Youngmee Tiffany; Narayanan, N C; Cheng, Yu-Ling

2018-05-01

There is a growing interest in decentralized wastewater management (DWWM) as a potential alternative to centralized wastewater management (CWWM) in developing countries. However, the comparative cost of CWWM and DWWM is not well understood. In this study, the cost of cluster-type DWWM is simulated and compared to the cost of CWWM in Alibag, India. A three-step model is built to simulate a broad range of potential DWWM configurations with varying number and layout of cluster subsystems. The considered DWWM scheme consists of cluster subsystems, that each uses simplified sewer and DEWATS (Decentralized Wastewater Treatment Systems). We consider CWWM that uses conventional sewer and an activated sludge plant. The results show that the cost of DWWM can vary significantly with the number and layout of the comprising cluster subsystems. The cost of DWWM increased nonlinearly with increasing number of comprising clusters, mainly due to the loss in the economies of scale for DEWATS. For configurations with the same number of comprising cluster subsystems, the cost of DWWM varied by ±5% around the mean, depending on the layout of the cluster subsystems. In comparison to CWWM, DWWM was of lower cost than CWWM when configured with fewer than 16 clusters in Alibag, with significantly less operation and maintenance requirement, but with higher capital and land requirement for construction. The study demonstrates that cluster-type DWWM using simplified sewer and DEWATS may be a cost-competitive alternative to CWWM, when carefully configured to lower the cost. Copyright © 2018 Elsevier Ltd. All rights reserved.

Optimized coordinates in vibrational coupled cluster calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomsen, Bo; Christiansen, Ove; Yagi, Kiyoshi

The use of variationally optimized coordinates, which minimize the vibrational self-consistent field (VSCF) ground state energy with respect to orthogonal transformations of the coordinates, has recently been shown to improve the convergence of vibrational configuration interaction (VCI) towards the exact full VCI [K. Yagi, M. Keçeli, and S. Hirata, J. Chem. Phys. 137, 204118 (2012)]. The present paper proposes an incorporation of optimized coordinates into the vibrational coupled cluster (VCC), which has in the past been shown to outperform VCI in approximate calculations where similar restricted state spaces are employed in VCI and VCC. An embarrassingly parallel algorithm for variationalmore » optimization of coordinates for VSCF is implemented and the resulting coordinates and potentials are introduced into a VCC program. The performance of VCC in optimized coordinates (denoted oc-VCC) is examined through pilot applications to water, formaldehyde, and a series of water clusters (dimer, trimer, and hexamer) by comparing the calculated vibrational energy levels with those of the conventional VCC in normal coordinates and VCI in optimized coordinates. For water clusters, in particular, oc-VCC is found to gain orders of magnitude improvement in the accuracy, exemplifying that the combination of optimized coordinates localized to each monomer with the size-extensive VCC wave function provides a supreme description of systems consisting of weakly interacting sub-systems.« less

Highly accurate potential energy surface for the He-H2 dimer

NASA Astrophysics Data System (ADS)

Bakr, Brandon W.; Smith, Daniel G. A.; Patkowski, Konrad

2013-10-01

A new highly accurate interaction potential is constructed for the He-H2 van der Waals complex. This potential is fitted to 1900 ab initio energies computed at the very large-basis coupled-cluster level and augmented by corrections for higher-order excitations (up to full configuration interaction level) and the diagonal Born-Oppenheimer correction. At the vibrationally averaged H-H bond length of 1.448736 bohrs, the well depth of our potential, 15.870 ± 0.065 K, is nearly 1 K larger than the most accurate previous studies have indicated. In addition to constructing our own three-dimensional potential in the van der Waals region, we present a reparameterization of the Boothroyd-Martin-Peterson potential surface [A. I. Boothroyd, P. G. Martin, and M. R. Peterson, J. Chem. Phys. 119, 3187 (2003)] that is suitable for all configurations of the triatomic system. Finally, we use the newly developed potentials to compute the properties of the lone bound states of 4He-H2 and 3He-H2 and the interaction second virial coefficient of the hydrogen-helium mixture.

Configurational coupled cluster approach with applications to magnetic model systems

NASA Astrophysics Data System (ADS)

Wu, Siyuan; Nooijen, Marcel

2018-05-01

A general exponential, coupled cluster like, approach is discussed to extract an effective Hamiltonian in configurational space, as a sum of 1-body, 2-body up to n-body operators. The simplest two-body approach is illustrated by calculations on simple magnetic model systems. A key feature of the approach is that equations up to a certain rank do not depend on higher body cluster operators.

Continuum theory for cluster morphologies of soft colloids.

PubMed

Kosmrlj, A; Pauschenwein, G J; Kahl, G; Ziherl, P

2011-06-09

We introduce a continuum description of the thermodynamics of colloids with a core-corona architecture. In the case of thick coronas, their overlap can be treated approximately by replacing the exact one-particle density distribution by a suitably shaped step profile, which provides a convenient way of modeling the spherical, columnar, lamellar, and inverted cluster morphologies predicted by numerical simulations and the more involved theories. We use the model to study monodisperse particles with the hard-core/square-shoulder pair interaction as the simplest representatives of the core-corona class. We derive approximate analytical expressions for the enthalpies of the cluster morphologies which offer a clear insight into the mechanisms at work, and we calculate the lattice spacing and the cluster size for all morphologies of the phase sequence as well as the phase-transition pressures. By comparing the results with the exact crystalline minimum-enthalpy configurations, we show that the accuracy of the theory increases with shoulder width. We discuss possible extensions of the theory that could account for the finite-temperature effects.

An ab initio-based Er–He interatomic potential in hcp Er

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Li; ye, Yeting; Fan, K. M.

2014-09-01

We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations.more » The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.« less

Effects of applied strain on nanoscale self-interstitial cluster formation in BCC iron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Ning; Setyawan, Wahyu; Kurtz, Richard J.

2017-09-01

The effect of applied strains on the configurational evolution of self-interstitial clusters in BCC iron (Fe) is explored with atomistic simulations. A novel cluster configuration is discovered at low temperatures (<600 K), which consists of <110> dumbbells and <111> crowdions in a specific configuration, resulting in an immobile defect. The stability and diffusion of this cluster at higher temperatures is explored. In addition, an anisotropy distribution factor of a particular [hkl] interstitial loop within the family of loops is calculated as a function of strain. The results show that loop anisotropy is governed by the angle between the stress directionmore » and the orientation of the <111> crowdions in the loop, and directly linked to the stress induced preferred nucleation of self-interstitial atoms.« less

System and method for time synchronization in a wireless network

DOEpatents

Gonia, Patrick S.; Kolavennu, Soumitri N.; Mahasenan, Arun V.; Budampati, Ramakrishna S.

2010-03-30

A system includes multiple wireless nodes forming a cluster in a wireless network, where each wireless node is configured to communicate and exchange data wirelessly based on a clock. One of the wireless nodes is configured to operate as a cluster master. Each of the other wireless nodes is configured to (i) receive time synchronization information from a parent node, (ii) adjust its clock based on the received time synchronization information, and (iii) broadcast time synchronization information based on the time synchronization information received by that wireless node. The time synchronization information received by each of the other wireless nodes is based on time synchronization information provided by the cluster master so that the other wireless nodes substantially synchronize their clocks with the clock of the cluster master.

Configurational Isomerism in Polyoxovanadates.

PubMed

Mahnke, Lisa K; Kondinski, Aleksandar; Warzok, Ulrike; Näther, Christian; van Leusen, Jan; Schalley, Christoph A; Monakhov, Kirill Yu; Kögerler, Paul; Bensch, Wolfgang

2018-03-05

A water-soluble derivative of the polyoxovanadate {V 15 E 6 O 42 } (E=semimetal) archetype enables the study of cluster shell rearrangements driven by supramolecular interactions. A reaction unique to E=Sb, induced exclusively by ligand metathesis in peripheral [Ni(ethylenediamine) 3 ] 2+ counterions, results in the formation of the metastable α 1 * configurational isomer of the {V 14 Sb 8 O 42 } cluster type. Contrary to all other polyoxovanadate shell architectures, this isomer comprises an inward-oriented vanadyl group and is ca. 50 and 12 kJ mol -1 higher in energy than the previously isolated α and β isomers, respectively. We discuss this unexpected reaction in light of supramolecular Sb-O⋅⋅⋅V and Sb-O⋅⋅⋅Sb contacts manifested in {V 14 Sb 8 O 42 } 2 dimers detected in the solid state. ESI MS experiments confirm the stability of these dimers also in solution and in the gas phase. DFT calculations indicate that other, as of yet elusive isomers of {V 14 Sb 8 }, might be accessible as well. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Symmetry adapted cluster-configuration interaction calculation of the photoelectron spectra of famous biological active steroids

NASA Astrophysics Data System (ADS)

Abyar, Fatemeh; Farrokhpour, Hossein

2014-11-01

The photoelectron spectra of some famous steroids, important in biology, were calculated in the gas phase. The selected steroids were 5α-androstane-3,11,17-trione, 4-androstane-3,11,17-trione, cortisol, cortisone, corticosterone, dexamethasone, estradiol and cholesterol. The calculations were performed employing symmetry-adapted cluster/configuration interaction (SAC-CI) method using the 6-311++G(2df,pd) basis set. The population ratios of conformers of each steroid were calculated and used for simulating the photoelectron spectrum of steroid. It was found that more than one conformer contribute to the photoelectron spectra of some steroids. To confirm the calculated photoelectron spectra, they compared with their corresponding experimental spectra. There were no experimental gas phase Hesbnd I photoelectron spectra for some of the steroids of this work in the literature and their calculated spectra can show a part of intrinsic characteristics of this molecules in the gas phase. The canonical molecular orbitals involved in the ionization of each steroid were calculated at the HF/6-311++g(d,p) level of theory. The spectral bands of each steroid were assigned by natural bonding orbital (NBO) calculations. Knowing the electronic structures of steroids helps us to understand their biological activities and find which sites of steroid become active when a modification is performing under a biological pathway.

Modeling Aggregation Processes of Lennard-Jones particles Via Stochastic Networks

NASA Astrophysics Data System (ADS)

Forman, Yakir; Cameron, Maria

2017-07-01

We model an isothermal aggregation process of particles/atoms interacting according to the Lennard-Jones pair potential by mapping the energy landscapes of each cluster size N onto stochastic networks, computing transition probabilities from the network for an N-particle cluster to the one for N+1, and connecting these networks into a single joint network. The attachment rate is a control parameter. The resulting network representing the aggregation of up to 14 particles contains 6427 vertices. It is not only time-irreversible but also reducible. To analyze its transient dynamics, we introduce the sequence of the expected initial and pre-attachment distributions and compute them for a wide range of attachment rates and three values of temperature. As a result, we find the configurations most likely to be observed in the process of aggregation for each cluster size. We examine the attachment process and conduct a structural analysis of the sets of local energy minima for every cluster size. We show that both processes taking place in the network, attachment and relaxation, lead to the dominance of icosahedral packing in small (up to 14 atom) clusters.

Interactive Parallel Data Analysis within Data-Centric Cluster Facilities using the IPython Notebook

NASA Astrophysics Data System (ADS)

Pascoe, S.; Lansdowne, J.; Iwi, A.; Stephens, A.; Kershaw, P.

2012-12-01

The data deluge is making traditional analysis workflows for many researchers obsolete. Support for parallelism within popular tools such as matlab, IDL and NCO is not well developed and rarely used. However parallelism is necessary for processing modern data volumes on a timescale conducive to curiosity-driven analysis. Furthermore, for peta-scale datasets such as the CMIP5 archive, it is no longer practical to bring an entire dataset to a researcher's workstation for analysis, or even to their institutional cluster. Therefore, there is an increasing need to develop new analysis platforms which both enable processing at the point of data storage and which provides parallelism. Such an environment should, where possible, maintain the convenience and familiarity of our current analysis environments to encourage curiosity-driven research. We describe how we are combining the interactive python shell (IPython) with our JASMIN data-cluster infrastructure. IPython has been specifically designed to bridge the gap between the HPC-style parallel workflows and the opportunistic curiosity-driven analysis usually carried out using domain specific languages and scriptable tools. IPython offers a web-based interactive environment, the IPython notebook, and a cluster engine for parallelism all underpinned by the well-respected Python/Scipy scientific programming stack. JASMIN is designed to support the data analysis requirements of the UK and European climate and earth system modeling community. JASMIN, with its sister facility CEMS focusing the earth observation community, has 4.5 PB of fast parallel disk storage alongside over 370 computing cores provide local computation. Through the IPython interface to JASMIN, users can make efficient use of JASMIN's multi-core virtual machines to perform interactive analysis on all cores simultaneously or can configure IPython clusters across multiple VMs. Larger-scale clusters can be provisioned through JASMIN's batch scheduling system. Outputs can be summarised and visualised using the full power of Python's many scientific tools, including Scipy, Matplotlib, Pandas and CDAT. This rich user experience is delivered through the user's web browser; maintaining the interactive feel of a workstation-based environment with the parallel power of a remote data-centric processing facility.

Spectra, composition, and interactions of nuclei with magnet interaction chambers

NASA Astrophysics Data System (ADS)

Parnell, T. A.; Burnett, T. H.; Cherry, M. C.; Dake, S.; Derrickson, J. H.; Fountain, W. F.; Fuki, M.; Gregory, J. C.; Hayashi, T.; Holynski, R.; Iwai, J.; Jurak, A.; Lord, J. J.; Miyamura, O.; Niwa, K.; Oda, H.; Ogata, T.; Roberts, F. E.; Shibata, T.; Strausz, S. C.; Tabuki, T.; Taira, T.; Takahashi, Y.; Tominaga, T.; Watts, J. W.; Wefel, J. P.; Wilczynska, B.; Wilczynski, H.; Wilkes, R. J.; Wolter, W.; Wosiek, T.; Yamamoto, A.; Yokomi, H.; Yuda, T.

1990-03-01

Emulsion chambers will be flown in the Astromag Facility to measure the cosmic ray composition and spectra to 10 exp 15 eV total energy and to definitively study the characteristics of nucleus-nucleus interactions above 10 exp 12 eV/n. Two configurations of emulsion chambers will be flown in the SCIN/MAGIC experiment. One chamber has an emulsion target and a calorimeter similar to those recently flown on balloons for composition and spectra measurements. The other has an identical calorimeter and a low-density target section optimized for performing rigidity measurements on charged particles produced in interactions. The transverse momenta of charged and neutral mesons, direct hadronic pairs from resonance decays and interference effects, and possible charge clustering in high-density states of matter will be studied.

Computational nano-material design of exotic luminescent materials based upon europium doped gallium nitrides

NASA Astrophysics Data System (ADS)

Masago, Akira; Fukushima, Tetsuya; Sato, Kazunori; Katayama-Yoshida, Hiroshi

2015-03-01

Eu-doped GaN has attracted much attention, because the red light luminescence ability provides us with expectations to realize monolithic full-color LEDs, which work on seamless conditions such as substrates, electrodes, and operating bias voltages. Toward implementation of multifunctional activity into the luminescent materials using the spinodal nano-structures, we investigate atomic configurations and magnetic structures of the GaN crystal codoped with Eu, Mg, Si, O, and/or the vacancies using the density functional method (DFT) calculations. Our calculations show that the impurity clusterized distributions are energetically favorable more than the homogeneous distribution. Moreover, analyses of the formation energy and binding energy suggest that the clusterized distributions are spontaneously formed by the nano-spinodal decomposition. Though the host matrix has no magnetic moments, the cluster has finite magnetic moments, where Zener's p-f exchange interaction works between the Eu f-state and the nearby N p-states.

ESTminer: a Web interface for mining EST contig and cluster databases.

PubMed

Huang, Yecheng; Pumphrey, Janie; Gingle, Alan R

2005-03-01

ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are displayed as color-coded tree nodes, where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members, with links to sequence data, GenBank records or user configurable links. Also, the interface allows 'queries within queries' where the result set of a query is further filtered by the subsequent query. ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp agingle@uga.edu.

Spatial Configuration of Drought Disturbance and Forest Gap Creation across Environmental Gradients

PubMed Central

Andrew, Margaret E.; Ruthrof, Katinka X.; Matusick, George; Hardy, Giles E. St. J.

2016-01-01

Climate change is increasing the risk of drought to forested ecosystems. Although drought impacts are often anecdotally noted to occur in discrete patches of high canopy mortality, the landscape effects of drought disturbances have received virtually no study. This study characterized the landscape configuration of drought impact patches and investigated the relationships between patch characteristics, as indicators of drought impact intensity, and environmental gradients related to water availability to determine factors influencing drought vulnerability. Drought impact patches were delineated from aerial surveys following an extreme drought in 2011 in southwestern Australia, which led to patchy canopy dieback of the Northern Jarrah Forest, a Mediterranean forest ecosystem. On average, forest gaps produced by drought-induced dieback were moderate in size (6.6 ± 9.7 ha, max = 85.7 ha), compact in shape, and relatively isolated from each other at the scale of several kilometers. However, there was considerable spatial variation in the size, shape, and clustering of forest gaps. Drought impact patches were larger and more densely clustered in xeric areas, with significant relationships observed with topographic wetness index, meteorological variables, and stand height. Drought impact patch clustering was more strongly associated with the environmental factors assessed (R2 = 0.32) than was patch size (R2 = 0.21); variation in patch shape remained largely unexplained (R2 = 0.02). There is evidence that the xeric areas with more intense drought impacts are ‘chronic disturbance patches’ susceptible to recurrent drought disturbance. The spatial configuration of drought disturbances is likely to influence ecological processes including forest recovery and interacting disturbances such as fire. Regime shifts to an alternate, non-forested ecosystem may occur preferentially in areas with large or clustered drought impact patches. Improved understanding of drought impacts and their patterning in space and time will expand our knowledge of forest ecosystems and landscape processes, informing management of these dynamic systems in an uncertain future. PMID:27275744

Geometric and electronic structures of silicon-sodium binary clusters. I. Ionization energy of SinNam

NASA Astrophysics Data System (ADS)

Kishi, Reiko; Iwata, Suehiro; Nakajima, Atsushi; Kaya, Koji

1997-08-01

Sodium doped silicon clusters (SinNam; 1⩽n⩽14, 1⩽m⩽5) produced by two types of laser vaporization were studied. The adsorption of Na atoms on the Sin clusters leads the substantial lowering of the ionization energy, Ei, of SinNam clusters. Their reactivity toward NO molecules was measured with a fast flow reactor, and the anticorrelation between the Eis and the reactivity was clearly observed; species having low Ei exhibit high reactivity and vice versa. Moreover, the clear parallelism between the Eis of SinNa and the EAs of Sin is found. This is consistent with the fact that the structure of SinNa clusters keeps the frame of the corresponding Sin cluster unchanged and that the electronic structure of SinNa is similar to that of the corresponding negative ion Sin-. In addition to the experimental studies, the geometries, adsorption energies, and vertical ionization energies of SinNa (n=1-7) were investigated with ab initio MO calculations including electron correlation; The Møller-Plesset perturbation theory was used and the configuration interaction (CI) calculation was carried out, particularly for a diatomic molecule, SiNa.

Certification of Completion of Level-2 Milestone 464: Complete Phase 1 Integration of Site-Wide Global Parallel File System (SWGPFS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heidelberg, S T; Fitzgerald, K J; Richmond, G H

2006-01-24

There has been substantial development of the Lustre parallel filesystem prior to the configuration described below for this milestone. The initial Lustre filesystems that were deployed were directly connected to the cluster interconnect, i.e. Quadrics Elan3. That is, the clients (OSSes) and Meta-data Servers (MDS) were all directly connected to the cluster's internal high speed interconnect. This configuration serves a single cluster very well, but does not provide sharing of the filesystem among clusters. LLNL funded the development of high-efficiency ''portals router'' code by CFS (the company that develops Lustre) to enable us to move the Lustre servers to amore » GigE-connected network configuration, thus making it possible to connect to the servers from several clusters. With portals routing available, here is what changes: (1) another storage-only cluster is deployed to front the Lustre storage devices (these become the Lustre OSSes and MDS), (2) this ''Lustre cluster'' is attached via GigE connections to a large GigE switch/router cloud, (3) a small number of compute-cluster nodes are designated as ''gateway'' or ''portal router'' nodes, and (4) the portals router nodes are GigE-connected to the switch/router cloud. The Lustre configuration is then changed to reflect the new network paths. A typical example of this is a compute cluster and a related visualization cluster: the compute cluster produces the data (writes it to the Lustre filesystem), and the visualization cluster consumes some of the data (reads it from the Lustre filesystem). This process can be expanded by aggregating several collections of Lustre backend storage resources into one or more ''centralized'' Lustre filesystems, and then arranging to have several ''client'' clusters mount these centralized filesystems. The ''client clusters'' can be any combination of compute, visualization, archiving, or other types of cluster. This milestone demonstrates the operation and performance of a scaled-down version of such a large, centralized, shared Lustre filesystem concept.« less

Effects of applied strain on nanoscale self-interstitial cluster formation in BCC iron

NASA Astrophysics Data System (ADS)

Gao, Ning; Setyawan, Wahyu; Kurtz, Richard J.; Wang, Zhiguang

2017-09-01

The effect of applied strains on the configurational evolution of self-interstitial clusters in BCC iron (Fe) is explored with atomistic simulations. A novel cluster configuration is discovered at low temperatures (<600 K), which consists of 〈 110 〉 dumbbells and 〈 111 〉 crowdions in a specific configuration, resulting in an immobile defect. The stability and diffusion of this cluster at higher temperatures is explored. In addition, an anisotropy distribution factor of a particular [ hkl ] interstitial loop within the family of 〈 hkl 〉 loops is calculated as a function of strain. The results show that loop anisotropy is governed by the angle between the stress direction and the orientation of the 〈 111 〉 crowdions in the loop, and directly linked to the stress induced preferred nucleation of self-interstitial atoms.

Parallelization of MRCI based on hole-particle symmetry.

PubMed

Suo, Bing; Zhai, Gaohong; Wang, Yubin; Wen, Zhenyi; Hu, Xiangqian; Li, Lemin

2005-01-15

The parallel implementation of multireference configuration interaction program based on the hole-particle symmetry is described. The platform to implement the parallelization is an Intel-Architectural cluster consisting of 12 nodes, each of which is equipped with two 2.4-G XEON processors, 3-GB memory, and 36-GB disk, and are connected by a Gigabit Ethernet Switch. The dependence of speedup on molecular symmetries and task granularities is discussed. Test calculations show that the scaling with the number of nodes is about 1.9 (for C1 and Cs), 1.65 (for C2v), and 1.55 (for D2h) when the number of nodes is doubled. The largest calculation performed on this cluster involves 5.6 x 10(8) CSFs.

Dynamical evolution of dense star clusters in galactic nuclei

NASA Astrophysics Data System (ADS)

Haas, Jaroslav; Šubr, Ladislav

2014-05-01

By means of direct numerical N-body modeling, we investigate the orbital evolution of an initially thin, central mass dominated stellar disk. We include the perturbative gravitational influence of an extended spherically symmetric star cluster and the mutual gravitational interaction of the stars within the disk. Our results show that the two-body relaxation of the disk leads to significant changes of its radial density profile. In particular, the disk naturally evolves, for a variety of initial configurations, a similar broken power-law surface density profile. Hence, it appears that the single power-law surface density profile ∝R -2 suggested by various authors to describe the young stellar disk observed in the Sgr A* region does not match theoretical expectations.

Resonant photoemission study of pyrite-type NiS2, CoS2 and FeS2

NASA Astrophysics Data System (ADS)

Fujimori, A.; Mamiya, K.; Mizokawa, T.; Miyadai, T.; Sekiguchi, T.; Takahashi, H.; Môri, N.; Suga, S.

1996-12-01

The electronic structure of pyrite-type NiS2, CoS2, and FeS2 has been studied by photoemission spectroscopy. From resonant photoemission studies and configuration-interaction cluster-model analysis of the spectra, NiS2 is found to be a charge-transfer-type insulator, the band gap of which is formed between the occupied S 3p and the empty Ni 3d states. Cluster-model calculations indicate that the short Fe-S distance favors the low-spin (S=0) ground state in FeS2 compared to the high-spin FeS. Resonant photoemission results indicate a sign of electron correlation in the nonmagnetic semiconductor FeS2.

Complex magnetic structure of clusters and chains of Ni and Fe on Pt(111)

PubMed Central

Bezerra-Neto, Manoel M.; Ribeiro, Marcelo S.; Sanyal, Biplab; Bergman, Anders; Muniz, Roberto B.; Eriksson, Olle; Klautau, Angela B.

2013-01-01

We present an approach to control the magnetic structure of adatoms adsorbed on a substrate having a high magnetic susceptibility. Using finite Ni-Pt and Fe-Pt nanowires and nanostructures on Pt(111) surfaces, our ab initio results show that it is possible to tune the exchange interaction and magnetic configuration of magnetic adatoms (Fe or Ni) by introducing different numbers of Pt atoms to link them, or by including edge effects. The exchange interaction between Ni (or Fe) adatoms on Pt(111) can be considerably increased by introducing Pt chains to link them. The magnetic ordering can be regulated allowing for ferromagnetic or antiferromagnetic configurations. Noncollinear magnetic alignments can also be stabilized by changing the number of Pt-mediated atoms. An Fe-Pt triangularly-shaped nanostructure adsorbed on Pt(111) shows the most complex magnetic structure of the systems considered here: a spin-spiral type of magnetic order that changes its propagation direction at the triangle vertices. PMID:24165828

Photonuclear reaction as a probe for α -clustering nuclei in the quasi-deuteron region

NASA Astrophysics Data System (ADS)

Huang, B. S.; Ma, Y. G.; He, W. B.

2017-03-01

Photon-nuclear reaction in a transport model frame, namely an extended quantum molecular dynamics model, has been realized at the photon energy of 70-140 MeV in the quasi-deuteron regime. For an important application, we pay a special focus on photonuclear reactions of 12C(γ ,n p )10B where 12C is considered as different configurations including α clustering. Obvious differences for some observables have been observed among different configurations, which can be attributed to spatial-momentum correlation of a neutron-proton pair inside nucleus, and therefore it gives us a sensitive probe to distinguish the different configurations including α clustering with the help of the photonuclear reaction mechanism.

Differential global structural changes in the core particle of yeast and mouse proteasome induced by ligand binding

PubMed Central

Arciniega, Marcelino; Beck, Philipp; Lange, Oliver F.; Groll, Michael; Huber, Robert

2014-01-01

Two clusters of configurations of the main proteolytic subunit β5 were identified by principal component analysis of crystal structures of the yeast proteasome core particle (yCP). The apo-cluster encompasses unliganded species and complexes with nonpeptidic ligands, and the pep-cluster comprises complexes with peptidic ligands. The murine constitutive CP structures conform to the yeast system, with the apo-form settled in the apo-cluster and the PR-957 (a peptidic ligand) complex in the pep-cluster. In striking contrast, the murine immune CP classifies into the pep-cluster in both the apo and the PR-957–liganded species. The two clusters differ essentially by multiple small structural changes and a domain motion enabling enclosure of the peptidic ligand and formation of specific hydrogen bonds in the pep-cluster. The immune CP species is in optimal peptide binding configuration also in its apo form. This favors productive ligand binding and may help to explain the generally increased functional activity of the immunoproteasome. Molecular dynamics simulations of the representative murine species are consistent with the experimentally observed configurations. A comparison of all 28 subunits of the unliganded species with the peptidic liganded forms demonstrates a greatly enhanced plasticity of β5 and suggests specific signaling pathways to other subunits. PMID:24979800

The adsorption of Run (n = 1-4) on γ-Al2O3 Surface: A DFT study

NASA Astrophysics Data System (ADS)

Liu, Zhe; Guo, Yafei; Chen, Yu; Shen, Rong

2018-05-01

The density functional theory (DFT) was adopted to study the adsorption and growth of Run (n = 1-4) clusters on γ-Al2O3 surface, which is of great significances for the design of many important catalysts, especially for carbon dioxide methanation. It is found that both the Rusbnd Ru bond length and adsorption energy Eads of Ru clusters with the surface increase with the Run clusters increasing. The growth ability of the supported Run cluster is weaker than the gas phase Run clusters through comparing their respective growth process, which ascribes to the stabilization of γ-Al2O3 support. An interesting discovery is that the basin structure was supposed to be the most favorable adsorption geometry for Run clusters. Additionally, the distances between Ru atoms in the adsorbed clusters are longer than that in their isolated counterparts. Bader charge analysis was conducted for the most stable configurations of Run (n = 1-4) clusters on γ-Al2O3 surface as well. And the results suggest that Run (n = 1-4) clusters serve as the electron donators. The result of projected density of states (PDOS) shows that strong adsorption of Ru atom on the γ-Al2O3 surface correlates with strong interaction between d orbital of Ru atom and p orbital of Al or O atom of the Al2O3 support.

A stochastic reaction-diffusion model for protein aggregation on DNA

NASA Astrophysics Data System (ADS)

Voulgarakis, Nikolaos K.

Vital functions of DNA, such as transcription and packaging, depend on the proper clustering of proteins on the double strand. The present study investigates how the interplay between DNA allostery and electrostatic interactions affects protein clustering. The statistical analysis of a simple but transparent computational model reveals two major consequences of this interplay. First, depending on the protein and salt concentration, protein filaments exhibit a bimodal DNA stiffening and softening behavior. Second, within a certain domain of the control parameters, electrostatic interactions can cause energetic frustration that forces proteins to assemble in rigid spiral configurations. Such spiral filaments might trigger both positive and negative supercoiling, which can ultimately promote gene compaction and regulate the promoter. It has been experimentally shown that bacterial histone-like proteins assemble in similar spiral patterns and/or exhibit the same bimodal behavior. The proposed model can, thus, provide computational insights into the physical mechanisms used by proteins to control the mechanical properties of the DNA.

Relaxation pathways of photoexcited iodide-methanol clusters: a computational investigation.

PubMed

Mak, Chun C; Peslherbe, Gilles H

2014-06-26

Upon photoexcitation of iodide-methanol clusters, I(-)(CH3OH)n, to a charge-transfer-to-solvent (CTTS) excited state, extensive relaxation was found to occur, accompanied by a convoluted modulation of the stability of the excited electron, which ultimately decreases substantially. In order to develop a molecular-level understanding of the relaxation processes of CTTS excited I(-)(CH3OH)n, high-level quantum chemical calculations are first used to investigate the ground, excited, and ionized states of I(-)(CH3OH)n (n = 2). Because of the relatively small size of I(-)(CH3OH)2, it was possible to characterize the contributions of solvent-solvent interactions to the stability of the CTTS excited cluster relative to dissociation into methanol, iodine, and a free electron, which exhibits a substantial dependence on the cluster geometric configuration. Ab initio molecular dynamics simulations of CTTS excited I(-)(CH3OH)3 are then performed to shed some light onto the nature of the relaxation pathways involved in the modulation of the stability of the excited electron in larger clusters. Simulation results suggest that separation of I and (CH3OH)3(-) accompanied by solvent reorganization in the latter can initially stabilize the excited electron, while gradual cluster fragmentation to I, (CH3OH)2(-), and CH3OH ultimately destabilizes it. This work shows, for the first time, that the inability of small CTTS excited I(-)(CH3OH)n to retain a solvated electron may be attributed to the limited hydrogen-bonding capacity of CH3OH, which increases the propensity for fragmentation to smaller clusters with lower excess-electron binding energies, and highlights the critical role of intricate molecular interactions in the electron solvation process.

Clustering analysis of water distribution systems: identifying critical components and community impacts.

PubMed

Diao, K; Farmani, R; Fu, G; Astaraie-Imani, M; Ward, S; Butler, D

2014-01-01

Large water distribution systems (WDSs) are networks with both topological and behavioural complexity. Thereby, it is usually difficult to identify the key features of the properties of the system, and subsequently all the critical components within the system for a given purpose of design or control. One way is, however, to more explicitly visualize the network structure and interactions between components by dividing a WDS into a number of clusters (subsystems). Accordingly, this paper introduces a clustering strategy that decomposes WDSs into clusters with stronger internal connections than external connections. The detected cluster layout is very similar to the community structure of the served urban area. As WDSs may expand along with urban development in a community-by-community manner, the correspondingly formed distribution clusters may reveal some crucial configurations of WDSs. For verification, the method is applied to identify all the critical links during firefighting for the vulnerability analysis of a real-world WDS. Moreover, both the most critical pipes and clusters are addressed, given the consequences of pipe failure. Compared with the enumeration method, the method used in this study identifies the same group of the most critical components, and provides similar criticality prioritizations of them in a more computationally efficient time.

Size-guided multi-seed heuristic method for geometry optimization of clusters: Application to benzene clusters.

PubMed

Takeuchi, Hiroshi

2018-05-08

Since searching for the global minimum on the potential energy surface of a cluster is very difficult, many geometry optimization methods have been proposed, in which initial geometries are randomly generated and subsequently improved with different algorithms. In this study, a size-guided multi-seed heuristic method is developed and applied to benzene clusters. It produces initial configurations of the cluster with n molecules from the lowest-energy configurations of the cluster with n - 1 molecules (seeds). The initial geometries are further optimized with the geometrical perturbations previously used for molecular clusters. These steps are repeated until the size n satisfies a predefined one. The method locates putative global minima of benzene clusters with up to 65 molecules. The performance of the method is discussed using the computational cost, rates to locate the global minima, and energies of initial geometries. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Trap configuration and spacing influences parameter estimates in spatial capture-recapture models

USGS Publications Warehouse

Sun, Catherine C.; Fuller, Angela K.; Royle, J. Andrew

2014-01-01

An increasing number of studies employ spatial capture-recapture models to estimate population size, but there has been limited research on how different spatial sampling designs and trap configurations influence parameter estimators. Spatial capture-recapture models provide an advantage over non-spatial models by explicitly accounting for heterogeneous detection probabilities among individuals that arise due to the spatial organization of individuals relative to sampling devices. We simulated black bear (Ursus americanus) populations and spatial capture-recapture data to evaluate the influence of trap configuration and trap spacing on estimates of population size and a spatial scale parameter, sigma, that relates to home range size. We varied detection probability and home range size, and considered three trap configurations common to large-mammal mark-recapture studies: regular spacing, clustered, and a temporal sequence of different cluster configurations (i.e., trap relocation). We explored trap spacing and number of traps per cluster by varying the number of traps. The clustered arrangement performed well when detection rates were low, and provides for easier field implementation than the sequential trap arrangement. However, performance differences between trap configurations diminished as home range size increased. Our simulations suggest it is important to consider trap spacing relative to home range sizes, with traps ideally spaced no more than twice the spatial scale parameter. While spatial capture-recapture models can accommodate different sampling designs and still estimate parameters with accuracy and precision, our simulations demonstrate that aspects of sampling design, namely trap configuration and spacing, must consider study area size, ranges of individual movement, and home range sizes in the study population.

Calculating the Motion and Direction of Flux Transfer Events with Cluster

NASA Technical Reports Server (NTRS)

Collado-Vega, Y. M.; Sibeck, D. G.

2012-01-01

For many years now, the interactions of the solar wind plasma with the Earth's magnetosphere has been one of the most important problems for Space Physics. It is very important that we understand these processes because the high-energy particles and also the solar wind energy that cross the magneto sphere could be responsible for serious damage to our technological systems. The solar wind is inherently a dynamic medium, and the particles interaction with the Earth's magnetosphere can be steady or unsteady. Unsteady interaction include transient processes like bursty magnetic reconnection. Flux Transfer Events (FTEs) are magnetopause signatures that usually occur during transient times of reconnection. They exhibit bipolar signatures in the normal component of the magnetic field. We use multi-point timing analysis to determine the orientation and motion of ux transfer events (FTEs) detected by the four Cluster spacecraft on the high-latitude dayside and flank magnetopause during 2002 and 2003. During these years, the distances between the Cluster spacecraft were greater than 1000 km, providing the tetrahedral configuration needed to select events and determine velocities. Each velocity and location will be examined in detail and compared to the velocities and locations determined by the predictions of the component and antiparallel reconnection models for event formation, orientation, motion, and acceleration for a wide range of spacecraft locations and solar wind conditions.

Relativistic many-body calculation of energies, multipole transition rates, and lifetimes in tungsten ions

NASA Astrophysics Data System (ADS)

Safronova, U. I.; Safronova, M. S.; Nakamura, N.

2017-04-01

Atomic properties of Cd-like W26 +, In-like W25 +, and Sn-like W24 + ions are evaluated by using a relativistic CI+all -order approach that combines configuration-interaction and the coupled-cluster methods. The energies, transition rates, and lifetimes of low-lying levels are calculated and compared with available theoretical and experimental values. The magnetic-dipole transition rates are calculated to determine the branching ratios and lifetimes for the 4 f3 states in W25 + and for the 4 f4 states in W24 + ions. Excellent agreement of the CI+all -order values provided a benchmark test of this method for the 4 fn configurations validating the recommended values of tungsten ion properties calculated in this work.

Neutral and charged gallium clusters: structures, physical properties and implications for the melting features

NASA Astrophysics Data System (ADS)

Núñez, Sara; López, José M.; Aguado, Andrés

2012-09-01

We report the putative Global Minimum (GM) structures and electronic properties of GaN+, GaN and GaN- clusters with N = 13-37 atoms, obtained from first-principles density functional theory structural optimizations. The calculations include spin polarization and employ an exchange-correlation functional which accounts for van der Waals dispersion interactions (vdW-DFT). We find a wide diversity of structural motifs within the located GM, including decahedral, polyicosahedral, polytetrahedral and layered structures. The GM structures are also extremely sensitive to the number of electrons in the cluster, so that the structures of neutral and charged clusters differ for most sizes. The main magic numbers (clusters with an enhanced stability) are identified and interpreted in terms of electronic and geometric shell closings. The theoretical results are consistent with experimental abundance mass spectra of GaN+ and with photoelectron spectra of GaN-. The size dependence of the latent heats of melting, the shape of the heat capacity peaks, and the temperature dependence of the collision cross-sections, all measured for GaN+ clusters, are properly interpreted in terms of the calculated cohesive energies, spectra of configurational excitations, and cluster shapes, respectively. The transition from ``non-melter'' to ``magic-melter'' behaviour, experimentally observed between Ga30+ and Ga31+, is traced back to a strong geometry change. Finally, the higher-than-bulk melting temperatures of gallium clusters are correlated with a more typically metallic behaviour of the clusters as compared to the bulk, contrary to previous theoretical claims.We report the putative Global Minimum (GM) structures and electronic properties of GaN+, GaN and GaN- clusters with N = 13-37 atoms, obtained from first-principles density functional theory structural optimizations. The calculations include spin polarization and employ an exchange-correlation functional which accounts for van der Waals dispersion interactions (vdW-DFT). We find a wide diversity of structural motifs within the located GM, including decahedral, polyicosahedral, polytetrahedral and layered structures. The GM structures are also extremely sensitive to the number of electrons in the cluster, so that the structures of neutral and charged clusters differ for most sizes. The main magic numbers (clusters with an enhanced stability) are identified and interpreted in terms of electronic and geometric shell closings. The theoretical results are consistent with experimental abundance mass spectra of GaN+ and with photoelectron spectra of GaN-. The size dependence of the latent heats of melting, the shape of the heat capacity peaks, and the temperature dependence of the collision cross-sections, all measured for GaN+ clusters, are properly interpreted in terms of the calculated cohesive energies, spectra of configurational excitations, and cluster shapes, respectively. The transition from ``non-melter'' to ``magic-melter'' behaviour, experimentally observed between Ga30+ and Ga31+, is traced back to a strong geometry change. Finally, the higher-than-bulk melting temperatures of gallium clusters are correlated with a more typically metallic behaviour of the clusters as compared to the bulk, contrary to previous theoretical claims. Electronic supplementary information (ESI) available: Atomic coordinates (in xyz format and Å units) and point group symmetries for the global minimum structures reported in this paper. See DOI: 10.1039/c2nr31222k

Cluster analysis based on dimensional information with applications to feature selection and classification

NASA Technical Reports Server (NTRS)

Eigen, D. J.; Fromm, F. R.; Northouse, R. A.

1974-01-01

A new clustering algorithm is presented that is based on dimensional information. The algorithm includes an inherent feature selection criterion, which is discussed. Further, a heuristic method for choosing the proper number of intervals for a frequency distribution histogram, a feature necessary for the algorithm, is presented. The algorithm, although usable as a stand-alone clustering technique, is then utilized as a global approximator. Local clustering techniques and configuration of a global-local scheme are discussed, and finally the complete global-local and feature selector configuration is shown in application to a real-time adaptive classification scheme for the analysis of remote sensed multispectral scanner data.

Theoretical investigation of existence of meta-stability in iron and cobalt clusters

NASA Astrophysics Data System (ADS)

Berry, Habte Dulla; Zhang, Qinfang; Wang, Baolin

2018-03-01

Nowadays considerable attention has been given for researches on magnetic properties of transition metal clusters (specifically FeN and CoN). This is because these clusters offer big hopes for the possibility of presenting significant magnetic anisotropy energy which is critical for technological applications. This study intends to find out the causes for the existence of the two states (ground and meta-stable) in Iron and Cobalt clusters. The study also explains the role of valence electrons for the existence of magnetism in the two states by using the concept of ionization potential, electron dipole polarizabilities, chemical hardness and softness of the clusters. Assuming that, when all itinerant electrons are at s-level and also at the d-level (ns = n andns → 0.) the ground state and meta-stable state energies with distinct energy minima are (Egs = l / 2 n +εc n - 2μB hn andEms =εd n - gμB hn) respectively. The findings also showed that polarizability of small cluster of the specified elements are increased compared with the bulk value, which means that there is an effective increase in the cluster radius due to the spilling out of the electronic charge. Furthermore, it is obvious that 4s electrons are more delocalized than the 3d electrons so that they spill out more than the 3d electrons. This leads to the conclusion that 4s electrons are primarily responsible for the enhanced polarizabilities and for shell structure effects. This indicates that polarizability at the meta-stable state is less than that of the ground state i.e. the meta-stable state loses its s electron. Therefore the two minima represent a ground state of configuration 3 d↑5 3 d↓ 2 + δ 4s 2 - δ with energy Egs and meta-stable state of configuration 3 d↑5 3 d↓ 3 + δ 4s 1 - δ with energy Ems for Co clusters and a ground state configuration 3 d↑5 3 d↓ 1 + δ 4s 2 - δ with energy Egs an meta-stable state of configuration 3 d↑5 3 d↓ 2 + δ 4s 1 - δ with energy Ems for Fe clusters. Hence, the existence of the two states (meta-stable & ground state) is due to the large disproportion in electronic configurations of the two clusters at their respective states. Furthermore, the chemical hardness and softness of the clusters also provide evidence for the existence of stability of the two states depending on the cluster size.

Scaling analysis and SE simulation of the tilted cylinder-interface capillary interaction

NASA Astrophysics Data System (ADS)

Gao, S. Q.; Zhang, X. Y.; Zhou, Y. H.

2018-06-01

The capillary interaction induced by a tilted cylinder and interface is the basic configuration of many complex systems, such as micro-pillar arrays clustering, super-hydrophobicity of hairy surface, water-walking insects, and fiber aggregation. We systematically analyzed the scaling laws of tilt angle, contact angle, and cylinder radius on the contact line shape by SE simulation and experiment. The following in-depth analysis of the characteristic parameters (shift, stretch and distortion) of the deformed contact lines reveals the self-similar shape of contact line. Then a general capillary force scaling law is proposed to incredibly grasp all the simulated and experimental data by a quite straightforward ellipse approximation approach.

Cluster model studies of anion and molecular specificities via electrospray ionization photoelectron spectroscopy

DOE PAGES

Wang, Xue -Bin

2017-01-06

Ion specificity, a widely observed macroscopic phenomenon in condensed phases and at interfaces, is essentially a fundamental chemical physical issue. We have been investigating such effects using cluster models in an “atom-by-atom” and “molecule-by-molecule” fashion not possible with condensed-phase methods. We use electrospray ionization (ESI) to generate molecular and ionic clusters to simulate key molecular entities involved in local binding regions, and characterize them employing negative ion photoelectron spectroscopy (NIPES). Inter- and intramolecular interactions and binding configurations are directly obtained as functions of cluster size and composition, providing insightful molecular-level description and characterization over the local active sites that playmore » crucial roles in determining solution chemistry and condensed phase phenomena. Finally, the topics covered in this article are relevant to a wide scope of research fields ranging from ion specific effects in electrolyte solutions, ion selectivity/recognition in normal functioning of life, to molecular specificity in aerosol particle formation, as well as in rational material design and synthesis.« less

MULTIMODE quantum calculations of vibrational energies and IR spectrum of the NO⁺(H₂O) cluster using accurate potential energy and dipole moment surfaces.

PubMed

Homayoon, Zahra

2014-09-28

A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO(+)(H2O) cluster is reported. The PES is based on fitting of roughly 32,000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO(+)(H2O) and NO(+)(D2O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO(+)(H2O) and NO(+)(D2O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO(+)(H2O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water "antisymmetric" stretching mode with the low-frequency intermolecular modes results in intensity borrowing.

MULTIMODE quantum calculations of vibrational energies and IR spectrum of the NO+(H2O) cluster using accurate potential energy and dipole moment surfaces

NASA Astrophysics Data System (ADS)

Homayoon, Zahra

2014-09-01

A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO+(H2O) cluster is reported. The PES is based on fitting of roughly 32 000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO+(H2O) and NO+(D2O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO+(H2O) and NO+(D2O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO+(H2O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water "antisymmetric" stretching mode with the low-frequency intermolecular modes results in intensity borrowing.

Efficient gradient-based Monte Carlo simulation of materials: Applications to amorphous Si and Fe and Ni clusters

NASA Astrophysics Data System (ADS)

Limbu, Dil; Biswas, Parthapratim

We present a simple and efficient Monte-Carlo (MC) simulation of Iron (Fe) and Nickel (Ni) clusters with N =5-100 and amorphous Silicon (a-Si) starting from a random configuration. Using Sutton-Chen and Finnis-Sinclair potentials for Ni (in fcc lattice) and Fe (in bcc lattice), and Stillinger-Weber potential for a-Si, respectively, the total energy of the system is optimized by employing MC moves that include both the stochastic nature of MC simulations and the gradient of the potential function. For both iron and nickel clusters, the energy of the configurations is found to be very close to the values listed in the Cambridge Cluster Database, whereas the maximum force on each cluster is found to be much lower than the corresponding value obtained from the optimized structural configurations reported in the database. An extension of the method to model the amorphous state of Si is presented and the results are compared with experimental data and those obtained from other simulation methods. The work is partially supported by the NSF under Grant Number DMR 1507166.

A DFT study of the stability of SIAs and small SIA clusters in the vicinity of solute atoms in Fe

NASA Astrophysics Data System (ADS)

Becquart, C. S.; Ngayam Happy, R.; Olsson, P.; Domain, C.

2018-03-01

The energetics, defect volume and magnetic properties of single SIAs and small SIA clusters up to size 6 have been calculated by DFT for different configurations like the parallel 〈110〉 dumbbell, the non parallel 〈110〉 dumbbell and the C15 structure. The most stable configurations of each type have been further analyzed to determine the influence on their stability of various solute atoms (Ti, V, Cr, Mn, Co, Ni, Cu, Mo, W, Pd, Al, Si, P), relevant for steels used under irradiation. The results show that the presence of solute atoms does not change the relative stability order among SIA clusters. The small SIA clusters investigated can bind to both undersized and oversized solutes. Several descriptors have been considered to derive interesting trends from results. It appears that the local atomic volume available for the solute is the main physical quantity governing the binding energy evolution, whatever the solute type (undersized or oversized) and the cluster configuration (size and type).

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite.

PubMed

Liu, Jie; Jiang, Xiangang; Cao, Yu; Zhang, Chen; Zhao, Guangyao; Zhao, Maoshuang; Feng, Li

2018-05-07

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.

Ion Beam Characterization of a NEXT Multi-Thruster Array Plume

NASA Technical Reports Server (NTRS)

Pencil, Eric J.; Foster, John E.; Patterson, Michael J.; Diaz, Esther M.; Van Noord, Jonathan L.; McEwen, Heather K.

2006-01-01

Three operational, engineering model, 7-kW ion thrusters and one instrumented, dormant thruster were installed in a cluster array in a large vacuum facility at NASA Glenn Research Center. A series of engineering demonstration tests were performed to evaluate the system performance impacts of operating various multiple-thruster configurations in an array. A suite of diagnostics was installed to investigate multiple-thruster operation impact on thruster performance and life, thermal interactions, and alternative system modes and architectures. The ion beam characterization included measuring ion current density profiles and ion energy distribution with Faraday probes and retarding potential analyzers, respectively. This report focuses on the ion beam characterization during single thruster operation, multiple thruster operation, various neutralizer configurations, and thruster gimbal articulation. Comparison of beam profiles collected during single and multiple thruster operation demonstrated the utility of superimposing single engine beam profiles to predict multi-thruster beam profiles. High energy ions were detected in the region 45 off the thruster axis, independent of thruster power, number of operating thrusters, and facility background pressure, which indicated that the most probable ion energy was not effected by multiple-thruster operation. There were no significant changes to the beam profiles collected during alternate thruster-neutralizer configurations, therefore supporting the viability of alternative system configuration options. Articulation of one thruster shifted its beam profile, whereas the beam profile of a stationary thruster nearby did not change, indicating there were no beam interactions which was consistent with the behavior of a collisionless beam expansion.

Impact of non-uniform correlation structure on sample size and power in multiple-period cluster randomised trials.

PubMed

Kasza, J; Hemming, K; Hooper, R; Matthews, Jns; Forbes, A B

2017-01-01

Stepped wedge and cluster randomised crossover trials are examples of cluster randomised designs conducted over multiple time periods that are being used with increasing frequency in health research. Recent systematic reviews of both of these designs indicate that the within-cluster correlation is typically taken account of in the analysis of data using a random intercept mixed model, implying a constant correlation between any two individuals in the same cluster no matter how far apart in time they are measured: within-period and between-period intra-cluster correlations are assumed to be identical. Recently proposed extensions allow the within- and between-period intra-cluster correlations to differ, although these methods require that all between-period intra-cluster correlations are identical, which may not be appropriate in all situations. Motivated by a proposed intensive care cluster randomised trial, we propose an alternative correlation structure for repeated cross-sectional multiple-period cluster randomised trials in which the between-period intra-cluster correlation is allowed to decay depending on the distance between measurements. We present results for the variance of treatment effect estimators for varying amounts of decay, investigating the consequences of the variation in decay on sample size planning for stepped wedge, cluster crossover and multiple-period parallel-arm cluster randomised trials. We also investigate the impact of assuming constant between-period intra-cluster correlations instead of decaying between-period intra-cluster correlations. Our results indicate that in certain design configurations, including the one corresponding to the proposed trial, a correlation decay can have an important impact on variances of treatment effect estimators, and hence on sample size and power. An R Shiny app allows readers to interactively explore the impact of correlation decay.

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es; Fernández-Perea, Ricardo; Madzharova, Fani

2016-06-28

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet thismore » challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He–Mg pair potentials is also presented, as an improvement of the approximation using isolated He–Mg pairs.« less

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

NASA Astrophysics Data System (ADS)

de Lara-Castells, María Pilar; Fernández-Perea, Ricardo; Madzharova, Fani; Voloshina, Elena

2016-06-01

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet this challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He-Mg pair potentials is also presented, as an improvement of the approximation using isolated He-Mg pairs.

Anomalously slow relaxation of the system of liquid clusters in a disordered nanoporous medium according to the self-organized criticality scenario

NASA Astrophysics Data System (ADS)

Borman, V. D.; Tronin, V. N.; Byrkin, V. A.

2016-04-01

We propose a physical model of a relaxation of states of clusters of nonwetting liquid confined in a random nanoporous medium. The relaxation is occurred by the self-organized criticality (SOC) scenario. Process is characterized by waiting for fluctuation necessary for overcoming of a local energy barrier with the subsequent avalanche hydrodynamic extrusion of the liquid by surface forces of the nonwetting frame. The dependence of the interaction between local configurations on the number of filled pores belonging to the infinite percolation cluster of filled pores serves as an internal feedback initiating the SOC process. The calculations give a power-law time dependence of the relative volume θ of the confined liquid θ ∼t-ν (ν ∼ 0.2) as in the picture of relaxation in the mean field approximation. The model of the relaxation of the porous medium with the nonwetting liquid demonstrates possible mechanisms and scenarios of SOC for relaxation of other disordered systems.

Cluster studies of La[sub 2]CuO[sub 4]: A mapping onto the Pariser--Parr--Pople (PPP) model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, R.L.

1993-06-01

The techniques of [ital ab] [ital initio] electronic structure theory are used to study Cu[sub 2]O[sub 7] and Cu[sub 2]O[sub 11] cluster models of La[sub 2]CuO[sub 4]. Fair agreement is obtained with the experimentally determined spin exchange constant [ital J] (90 meV calculated vs 125 meV measured) at the expense of quite large configuration interactions (CI) expansions. Results for various charge states of the cluster are well described by a single-band'' Pariser--Parr--Pople (PPP) model. As in earlier local-density-functional (LDF) based parameter determinations, the present work suggests these materials fall in the strong coupling regime. However, a significant intersite Coulomb repulsionmore » is found in the present research. It is of sufficient strength [ital V][similar to][ital U]/5 to indicate that charge fluctuations may be more important in these materials than generally believed.« less

Assessing wild bees in perennial bioenergy landscapes: effects of bioenergy crop composition, landscape configuration, and bioenergy crop area

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, John B.; Nassauer, Joan I.; Currie, William S.

Wild bee populations are currently under threat, which has led to recent efforts to increase pollinator habitat in North America. Simultaneously, U.S. federal energy policies are beginning to encourage perennial bioenergy cropping (PBC) systems, which have the potential to support native bees. Our objective was to explore the potentially interactive effects of crop composition, total PBC area, and PBC patches in different landscape configurations. Using a spatially-explicit modeling approach, the Lonsdorf model, we simulated the impacts of three perennial bioenergy crops (PBC: willow, switchgrass, and prairie), three scenarios with different total PBC area (11.7%, 23.5% and 28.8% of agricultural landmore » converted to PBC) and two types of landscape configurations (PBC in clustered landscape patterns that represent realistic future configurations or in dispersed neutral landscape models) on a nest abundance index in an Illinois landscape. Our modeling results suggest that crop composition and PBC area are particularly important for bee nest abundance, whereas landscape configuration is associated with bee nest abundance at the local scale but less so at the regional scale. Moreover, strategies to enhance wild bee habitat should therefore emphasize the crop composition and amount of PBC.« less

Assessing wild bees in perennial bioenergy landscapes: effects of bioenergy crop composition, landscape configuration, and bioenergy crop area

DOE PAGES

Graham, John B.; Nassauer, Joan I.; Currie, William S.; ...

2017-03-25

Wild bee populations are currently under threat, which has led to recent efforts to increase pollinator habitat in North America. Simultaneously, U.S. federal energy policies are beginning to encourage perennial bioenergy cropping (PBC) systems, which have the potential to support native bees. Our objective was to explore the potentially interactive effects of crop composition, total PBC area, and PBC patches in different landscape configurations. Using a spatially-explicit modeling approach, the Lonsdorf model, we simulated the impacts of three perennial bioenergy crops (PBC: willow, switchgrass, and prairie), three scenarios with different total PBC area (11.7%, 23.5% and 28.8% of agricultural landmore » converted to PBC) and two types of landscape configurations (PBC in clustered landscape patterns that represent realistic future configurations or in dispersed neutral landscape models) on a nest abundance index in an Illinois landscape. Our modeling results suggest that crop composition and PBC area are particularly important for bee nest abundance, whereas landscape configuration is associated with bee nest abundance at the local scale but less so at the regional scale. Moreover, strategies to enhance wild bee habitat should therefore emphasize the crop composition and amount of PBC.« less

Potential energy surfaces of the ground and low-lying states of HCCS and NCS: CASSCF, MRCI and CCSD(T) studies

NASA Astrophysics Data System (ADS)

Li, Yumin; Iwata, Suehiro

1997-07-01

For astronomically interesting molecules, HCCS and NCS, the equilibrium geometries and potential energy curves of three states (X 2Π, A 2Π and B 2Σ+) as well as vertical excitation energies are studied using complete active space SCF (CASSCF), multi-reference configuration interaction (MRCI) and coupled cluster (CCSD(T)) methods with cc-pVTZ basis sets. The difference and similarity in the three states of HCCS and NCS are illustrated. The results obtained are in good agreement with available experimental data.

Tidal stripping stellar substructures around four metal-poor globular clusters in the galactic bulge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chun, Sang-Hyun; Kang, Minhee; Jung, DooSeok

2015-01-01

We investigate the spatial density configuration of stars around four metal-poor globular clusters (NGC 6266, NGC 6626, NGC 6642, and NGC 6723) in the Galactic bulge region using wide-field deep J, H, and K imaging data obtained with the Wide Field Camera near-infrared array on the United Kingdom Infrared Telescope. A statistical weighted filtering algorithm for the stars on the color–magnitude diagram is applied in order to sort cluster member candidates from the field star contamination. In two-dimensional isodensity contour maps of the clusters, we find that all four of the globular clusters exhibit strong evidence of tidally stripped stellarmore » features beyond the tidal radius in the form of tidal tails or small density lobes/chunks. The orientations of the extended stellar substructures are likely to be associated with the effect of dynamic interaction with the Galaxy and the cluster's space motion. The observed radial density profiles of the four globular clusters also describe the extended substructures; they depart from theoretical King and Wilson models and have an overdensity feature with a break in the slope of the profile at the outer region of clusters. The observed results could imply that four globular clusters in the Galactic bulge region have experienced strong environmental effects such as tidal forces or bulge/disk shocks of the Galaxy during the dynamical evolution of globular clusters. These observational results provide further details which add to our understanding of the evolution of clusters in the Galactic bulge region as well as the formation of the Galaxy.« less

Atomic scale behavior of oxygen-based radicals in water

NASA Astrophysics Data System (ADS)

Verlackt, C. C. W.; Neyts, E. C.; Bogaerts, A.

2017-03-01

Cold atmospheric pressure plasmas in and in contact with liquids represent a growing field of research for various applications. Understanding the interactions between the plasma generated species and the liquid is crucial. In this work we perform molecular dynamics (MD) simulations based on a quantum mechanical method, i.e. density-functional based tight-binding (DFTB), to examine the interactions of OH radicals and O atoms in bulk water. Our calculations reveal that the transport of OH radicals through water is not only governed by diffusion, but also by an equilibrium reaction of H-abstraction with water molecules. Furthermore, when two OH radicals encounter each other, they either form a stable cluster, or react, resulting in the formation of a new water molecule and an O atom. In addition, the O atoms form either oxywater (when in singlet configuration) or they remain stable in solution (when in triplet configuration), stressing the important role that O atoms can play in aqueous solution, and in contact with biomolecules. Our observations are in line with both experimental and ab initio results from the literature.

Relation between the Dynamics of Glassy Clusters and Characteristic Features of their Energy Landscape

NASA Astrophysics Data System (ADS)

De, Sandip; Schaefer, Bastian; Sadeghi, Ali; Sicher, Michael; Kanhere, D. G.; Goedecker, Stefan

2014-02-01

Based on a recently introduced metric for measuring distances between configurations, we introduce distance-energy (DE) plots to characterize the potential energy surface of clusters. Producing such plots is computationally feasible on the density functional level since it requires only a few hundred stable low energy configurations including the global minimum. By using standard criteria based on disconnectivity graphs and the dynamics of Lennard-Jones clusters, we show that the DE plots convey the necessary information about the character of the potential energy surface and allow us to distinguish between glassy and nonglassy systems. We then apply this analysis to real clusters at the density functional theory level and show that both glassy and nonglassy clusters can be found in simulations. It turns out that among our investigated clusters only those can be synthesized experimentally which exhibit a nonglassy landscape.

Computational Studies on the Anharmonic Dynamics of Molecular Clusters

NASA Astrophysics Data System (ADS)

Mancini, John S.

Molecular nanoclusters present ideal systems to probe the physical forces and dynamics that drive the behavior of larger bulk systems. At the nanocluster limit the first instances of several phenomena can be observed including the breaking of hydrogen and molecular bonds. Advancements in experimental and theoretical techniques have made it possible to explore these phenomena in great detail. The most fruitful of these studies have involved the use of both experimental and theoretical techniques to leverage to strengths of the two approaches. This dissertation seeks to explore several important phenomena of molecular clusters using new and existing theoretical methodologies. Three specific systems are considered, hydrogen chloride clusters, mixed water and hydrogen chloride clusters and the first cluster where hydrogen chloride autoionization occurs. The focus of these studies remain as close as possible to experimentally observable phenomena with the intention of validating, simulating and expanding on experimental work. Specifically, the properties of interested are those related to the vibrational ground and excited state dynamics of these systems. Studies are performed using full and reduced dimensional potential energy surface alongside advanced quantum mechanical methods including diffusion Monte Carlo, vibrational configuration interaction theory and quasi-classical molecular dynamics. The insight gained from these studies are great and varied. A new on-they-fly ab initio method for studying molecular clusters is validated for (HCl)1--6. A landmark study of the dissociation energy and predissociation mechanism of (HCl)3 is reported. The ground states of mixed (HCl)n(H2O)m are found to be highly delocalized across multiple stationary point configurations. Furthermore, it is identified that the consideration of this delocalization is required in vibrational excited state calculations to achieve agreement with experimental measurements. Finally, the theoretical infrared spectra for the first case of HCl ionization in (H 2O)m is reported, H+(H2O) 3Cl--. The calculation indicates that the ionized cluster's spectra is much more complex than any pervious harmonic predictions, with a large number of the system's infrared active peaks resulting from overtones of lower frequency molecular motions.

Monte Carlo simulation of two-component bilayers: DMPC/DSPC mixtures.

PubMed Central

Sugár, I P; Thompson, T E; Biltonen, R L

1999-01-01

In this paper, we describe a relatively simple lattice model of a two-component, two-state phospholipid bilayer. Application of Monte Carlo methods to this model permits simulation of the observed excess heat capacity versus temperature curves of dimyristoylphosphatidylcholine (DMPC)/distearoylphosphatidylcholine (DSPC) mixtures as well as the lateral distributions of the components and properties related to these distributions. The analysis of the bilayer energy distribution functions reveals that the gel-fluid transition is a continuous transition for DMPC, DSPC, and all DMPC/DSPC mixtures. A comparison of the thermodynamic properties of DMPC/DSPC mixtures with the configurational properties shows that the temperatures characteristics of the configurational properties correlate well with the maxima in the excess heat capacity curves rather than with the onset and completion temperatures of the gel-fluid transition. In the gel-fluid coexistence region, we also found excellent agreement between the threshold temperatures at different system compositions detected in fluorescence recovery after photobleaching experiments and the temperatures at which the percolation probability of the gel clusters is 0.36. At every composition, the calculated mole fraction of gel state molecules at the fluorescence recovery after photobleaching threshold is 0.34 and, at the percolation threshold of gel clusters, it is 0.24. The percolation threshold mole fraction of gel or fluid lipid depends on the packing geometry of the molecules and the interchain interactions. However, it is independent of temperature, system composition, and state of the percolating cluster. PMID:10096905

Self-assembly of Carbon Vacancies in Sub-stoichiometric ZrC1−x

PubMed Central

Zhang, Yanhui; Liu, Bin; Wang, Jingyang

2015-01-01

Sub-stoichiometric interstitial compounds, including binary transition metal carbides (MC1−x), maintain structural stability even if they accommodate abundant anion vacancies. This unique character endows them with variable-composition, diverse-configuration and controllable-performance through composition and structure design. Herein, the evolution of carbon vacancy (VC) configuration in sub-stoichiometric ZrC1−x is investigated by combining the cluster expansion method and first-principles calculations. We report the interesting self-assembly of VCs and the fingerprint VC configuration (VC triplet constructed by 3rd nearest neighboring vacancies) in all the low energy structures of ZrC1−x. When VC concentration is higher than the critical value of 0.5 (x > 0.5), the 2nd nearest neighboring VC configurations with strongly repulsive interaction inevitably appear, and meanwhile, the system energy (or formation enthalpy) of ZrC1−x increases sharply which suggests the material may lose phase stability. The present results clarify why ZrC1−x bears a huge amount of VCs, tends towards VC ordering, and retains stability up to a stoichiometry of x = 0.5. PMID:26667083

Impurity and defect interactions during laser thermal annealing in Ge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milazzo, R., E-mail: ruggero.milazzo@unipd.it; De Salvador, D.; Carnera, A.

2016-01-28

The microscopic mechanisms involving dopants, contaminants, and defects in Ge during pulsed melting laser thermal annealing (LTA) are investigated in detail. Samples both un-implanted and implanted with As or B are processed by LTA as well as characterized in terms of chemical (1D and 3D), electrical, and strain profiling. The clustering of As is directly measured by 3D chemical profiling and correlated with its partial electrical activation along with a reduction of the lattice strain induced by As atoms. A semi-quantitative microscopic model involving the interaction with mobile As-vacancy (AsV) complexes is proposed to describe the clustering mechanism. Boron ismore » shown to follow different clustering behavior that changes with depth and marked by completely different strain levels. Oxygen penetrates from the surface into all the samples as a result of LTA and, only in un-implanted Ge, it occupies an interstitial position inducing also positive strain in the lattice. On the contrary, data suggest that the presence of As or B forces O to assume different configurations with negligible strain, through O-V or O-B interactions for the two dopant species, respectively. These data suggest that LTA does not inject a significant amount of vacancies in Ge, at variance with Si, unless As atoms or possibly other n-type dopants are present. These results have to be carefully considered for modeling the LTA process in Ge and its implementation in technology.« less

Stability and change in adolescent spirituality/religiosity: a person-centered approach.

PubMed

Good, Marie; Willoughby, Teena; Busseri, Michael A

2011-03-01

Although there has been a substantial increase over the past decade in studies that have examined the psychosocial correlates of spirituality/religiosity in adolescence, very little is known about spirituality/religiosity as a domain of development in its own right. To address this limitation, the authors identified configurations of multiple dimensions of spirituality/religiosity across 2 time points with an empirical classification procedure (cluster analysis) and assessed development in these configurations at the sample and individual level. Participants included 756 predominately Canadian-born adolescents (53% female, 47% male) from southern Ontario, Canada, who completed a survey in Grade 11 (M age = 16.41 years) and Grade 12 (M age = 17.36 years). Measures included religious activity involvement, enjoyment of religious activities, the Spiritual Transcendence Index, wondering about spiritual issues, frequency of prayer, and frequency of meditation. Sample-level development (structural stability and change) was assessed by examining whether the structural configurations of the clusters were consistent over time. Individual-level development was assessed by examining intraindividual stability and change in cluster membership over time. Results revealed that a five cluster-solution was optimal at both grades. Clusters were identified as aspiritual/irreligious, disconnected wonderers, high institutional and personal, primarily personal, and meditators. With the exception of the high institutional and personal cluster, the cluster structures were stable over time. There also was significant intraindividual stability in all clusters over time; however, a significant proportion of individuals classified as high institutional and personal in Grade 11 moved into the primarily personal cluster in Grade 12. PsycINFO Database Record (c) 2011 APA, all rights reserved.

Structure, Stabilities, Thermodynamic Properties, and IR Spectra of Acetylene Clusters (C2H2)n=2-5.

PubMed

Karthikeyan, S; Lee, Han Myoung; Kim, Kwang S

2010-10-12

There are no clear conclusions over the structures of the acetylene clusters. In this regard, we have carried out high-level calculations for acetylene clusters (C2H2)2-5 using dispersion-corrected density functional theory (DFT-D), Møller-Plesset second-order perturbation theory (MP2); and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] at the complete basis set limit. The lowest energy structure of the acetylene dimer has a T-shaped structure of C2v symmetry, but it is nearly isoenergetic to the displaced stacked structure of C2h symmetry. We find that the structure shows the quantum statistical distribution for configurations between the T-shaped and displaced stacked structures for which the average angle (|θ̃|) between two acetylene molecules would be 53-78°, close to the T-shaped structure. The trimer has a triangular structure of C3h symmetry. The tetramer has two lowest energy isomers of S4 and C2h symmetry in zero-point energy (ZPE)-uncorrected energy (ΔEe), but one lowest energy isomer of C2v symmetry in ZPE-corrected energy (ΔE0). For the pentamer, the global minimum structure is C1 symmetry with eight sets of T-type π-H interactions and a set of π-π interactions. Our high-level ab initio calculations are consistent with available experimental data.

Multiconfiguration pair-density functional theory investigation of the electronic spectrum of MnO4-

NASA Astrophysics Data System (ADS)

Sharma, Prachi; Truhlar, Donald G.; Gagliardi, Laura

2018-03-01

The electronic spectrum of permanganate ions contains various highly multiconfigurational ligand-to-metal charge transfer states and is notorious for being one of the most challenging systems to be treated by quantum-chemical methods. Here we studied the lowest nine vertical excitation energies using restricted active space second-order perturbation theory (RASPT2) and multiconfiguration pair-density functional theory (MC-PDFT) to test and compare these two theories in computing such a challenging spectrum. The results are compared to literature data, including time-dependent density functional theory, completely renormalized equation-of-motion couple-cluster theory with single and double excitations, symmetry-adapted-cluster configuration interaction, and experimental spectra in the gas phase and solution. Our results show that MC-PDFT accurately predicts the spectrum at a significantly reduced cost as compared to RASPT2.

Ab initio multireference study of the BN molecule

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.; Scuseria, Gustavo E.; Taylor, Peter R.

1992-01-01

The lowest 1Sigma(+) and 3Pi states of the BN molecule are studied using multireference configuration interaction (MRCI) and averaged coupled-pair functional (ACPF) methods and large atomic natural orbital (ANO) basis sets, as well as several coupled cluster methods. Our calculations strongly support a 3Pi ground state, but the a1Sigma(+) state lies only 381 +/- 100/cm higher. The a1Sigma(+) state wave function exhibits strong multireference character and, consequently, the predictions of the perturbationally-based single-reference CCSD(T) coupled cluster method are not as reliable in this case as the multireference results. The theoretical predictions for the spectroscopic constants of BN are in good agreement with experiment for the Chi3Pi state, but strongly suggest a misassignment of the fundamental vibrational frequency for the a1Sigma(+) state.

Mixing and demixing of binary mixtures of polar chiral active particles.

PubMed

Ai, Bao-Quan; Shao, Zhi-Gang; Zhong, Wei-Rong

2018-05-17

We study a binary mixture of polar chiral (counterclockwise or clockwise) active particles in a two-dimensional box with periodic boundary conditions. Besides the excluded volume interactions between particles, the particles are also subjected to the polar velocity alignment. From the extensive Brownian dynamics simulations, it is found that the particle configuration (mixing or demixing) is determined by the competition between the chirality difference and the polar velocity alignment. When the chirality difference competes with the polar velocity alignment, the clockwise particles aggregate in one cluster and the counterclockwise particles aggregate in the other cluster; thus, the particles are demixed and can be separated. However, when the chirality difference or the polar velocity alignment is dominant, the particles are mixed. Our findings could be used for the experimental pursuit of the separation of binary mixtures of chiral active particles.

Multiconfiguration pair-density functional theory investigation of the electronic spectrum of MnO4.

PubMed

Sharma, Prachi; Truhlar, Donald G; Gagliardi, Laura

2018-03-28

The electronic spectrum of permanganate ions contains various highly multiconfigurational ligand-to-metal charge transfer states and is notorious for being one of the most challenging systems to be treated by quantum-chemical methods. Here we studied the lowest nine vertical excitation energies using restricted active space second-order perturbation theory (RASPT2) and multiconfiguration pair-density functional theory (MC-PDFT) to test and compare these two theories in computing such a challenging spectrum. The results are compared to literature data, including time-dependent density functional theory, completely renormalized equation-of-motion couple-cluster theory with single and double excitations, symmetry-adapted-cluster configuration interaction, and experimental spectra in the gas phase and solution. Our results show that MC-PDFT accurately predicts the spectrum at a significantly reduced cost as compared to RASPT2.

An {alpha}-cluster model for {sub {Lambda}}{sup 9}Be spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Filikhin, I. N., E-mail: ifilikhin@nccu.edu; Suslov, V. M.; Vlahovic, B.

An {alpha}-cluster model is applied to study low-lying spectrum of the {sub {Lambda}}{sup 9}Be hypernucleus. The three-body {alpha}{alpha}{Lambda} problem is numerically solved by the Faddeev equations in configuration space using phenomenological pair potentials. We found a set of the potentials that reproduces experimental data for the ground state (1/2{sup +}) binding energy and excitation energy of the 5/2{sup +} and 3/2{sup +} states, simultaneously. This set includes the Ali-Bodmer potential of the version 'e' for {alpha}{alpha} and modified Tang-Herndon potential for {alpha}{Lambda} interactions. The spin-orbit {alpha}{Lambda} interaction is given by modified Scheerbaum potential. Low-lying energy levels are evaluated applying amore » variant of the analytical continuation method in the coupling constant. It is shown that the spectral properties of {sub {Lambda}}{sup 9}Be can be classified as an analog of {sup 9}Be spectrum with the exception of several 'genuine hypernuclear states'. This agrees qualitatively with previous studies. The results are compared with experimental data and new interpretation of the spectral structure is discussed.« less

Explicitly correlated coupled cluster calculations for propadienylidene (H(2)CCC).

PubMed

Botschwina, Peter; Oswald, Rainer

2010-09-16

Propadienylidene (H(2)CCC), a reactive carbene of interest to combustion processes and astrochemistry, has been studied by explicitly correlated coupled cluster theory at the CCSD(T)-F12x (x = a, b) level. Vibrational configuration interaction (VCI) has been employed to calculate accurate wavenumbers for the fundamental vibrations of H(2)CCC, D(2)CCC, and HDCCC. The symmetric CH stretching vibration of H(2)CCC is predicted to occur at ν(1) = 2984 cm(-1). Absorptions observed by argon matrix infrared spectroscopy at 3049.5 and 3059.6 cm(-1) are reassigned to the combination tone ν(2) + ν(4), which interacts with ν(1) and is predicted to have a higher intensity than the latter. Furthermore, IR bands detected at 865.4 and 868.8 cm(-1) are assigned to ν(6)(HDCCC), and those observed at 904.0 and 909.8 cm(-1) are assigned to the out-of-plane bending vibration ν(8)(HDCCC). An accurate value of 79.8 +/- 0.2 kJ mol(-1) is recommended for the zero-point vibrational energy of H(2)CCC.

Structural and electronic properties of Aun-xPtx (n = 2-14; x ⩽ n) clusters: The density functional theory investigation

NASA Astrophysics Data System (ADS)

Yuan, H. K.; Kuang, A. L.; Tian, C. L.; Chen, H.

2014-03-01

The structural evolutions and electronic properties of bimetallic Aun-xPtx (n = 2-14; x ⩽ n) clusters are investigated by using the density functional theory (DFT) with the generalized gradient approximation (GGA). The monatomic doping Aun-1Pt clusters are emphasized and compared with the corresponding pristine Aun clusters. The results reveal that the planar configurations are favored for both Aun-1Pt and Aun clusters with size up to n = 13, and the former often employ the substitution patterns based on the structures of the latter. The most stable clusters are Au6 and Au6Pt, which adopt regular planar triangle (D3h) and hexagon-ring (D6h) structures and can be regarded as the preferential building units in designing large clusters. For Pt-rich bimetallic clusters, their structures can be obtained from the substitution of Pt atoms by Au atoms from the Ptn structures, where Pt atoms assemble together and occupy the center yet Au atoms prefer the apex positions showing a segregation effect. With respect to pristine Au clusters, AunPt clusters exhibit somewhat weaker and less pronounced odd-even oscillations in the highest occupied and lowest unoccupied molecular-orbital gaps (HOMO-LUMO gap), electron affinity (EA), and ionization potential (IP) due to the partially released electron pairing effect. The analyses of electronic structure indicate that Pt atoms in AuPt clusters would delocalize their one 6s and one 5d electrons to contribute the electronic shell closure. The sp-d hybridizations as well as the d-d interactions between the host Au and dopant Pt atoms result in the enhanced stabilities of AuPt clusters.

Tensor contraction engine: Abstraction and automated parallel implementation of configuration-interaction, coupled-cluster, and many-body perturbation theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirata, So

2003-11-20

We develop a symbolic manipulation program and program generator (Tensor Contraction Engine or TCE) that automatically derives the working equations of a well-defined model of second-quantized many-electron theories and synthesizes efficient parallel computer programs on the basis of these equations. Provided an ansatz of a many-electron theory model, TCE performs valid contractions of creation and annihilation operators according to Wick's theorem, consolidates identical terms, and reduces the expressions into the form of multiple tensor contractions acted by permutation operators. Subsequently, it determines the binary contraction order for each multiple tensor contraction with the minimal operation and memory cost, factorizes commonmore » binary contractions (defines intermediate tensors), and identifies reusable intermediates. The resulting ordered list of binary tensor contractions, additions, and index permutations is translated into an optimized program that is combined with the NWChem and UTChem computational chemistry software packages. The programs synthesized by TCE take advantage of spin symmetry, Abelian point-group symmetry, and index permutation symmetry at every stage of calculations to minimize the number of arithmetic operations and storage requirement, adjust the peak local memory usage by index range tiling, and support parallel I/O interfaces and dynamic load balancing for parallel executions. We demonstrate the utility of TCE through automatic derivation and implementation of parallel programs for various models of configuration-interaction theory (CISD, CISDT, CISDTQ), many-body perturbation theory [MBPT(2), MBPT(3), MBPT(4)], and coupled-cluster theory (LCCD, CCD, LCCSD, CCSD, QCISD, CCSDT, and CCSDTQ).« less

Interaction between bosonic dark matter and stars

NASA Astrophysics Data System (ADS)

Brito, Richard; Cardoso, Vitor; Macedo, Caio F. B.; Okawa, Hirotada; Palenzuela, Carlos

2016-02-01

We provide a detailed analysis of how bosonic dark matter "condensates" interact with compact stars, extending significantly the results of a recent Letter [1]. We focus on bosonic fields with mass mB , such as axions, axion-like candidates and hidden photons. Self-gravitating bosonic fields generically form "breathing" configurations, where both the spacetime geometry and the field oscillate, and can interact and cluster at the center of stars. We construct stellar configurations formed by a perfect fluid and a bosonic condensate, and which may describe the late stages of dark matter accretion onto stars, in dark-matter-rich environments. These composite stars oscillate at a frequency which is a multiple of f =2.5 ×1014(mBc2/eV ) Hz . Using perturbative analysis and numerical relativity techniques, we show that these stars are generically stable, and we provide criteria for instability. Our results also indicate that the growth of the dark matter core is halted close to the Chandrasekhar limit. We thus dispel a myth concerning dark matter accretion by stars: dark matter accretion does not necessarily lead to the destruction of the star, nor to collapse to a black hole. Finally, we argue that stars with long-lived bosonic cores may also develop in other theories with effective mass couplings, such as (massless) scalar-tensor theories.

A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization

NASA Astrophysics Data System (ADS)

Hamprecht, Fred A.; Peter, Christine; Daura, Xavier; Thiel, Walter; van Gunsteren, Wilfred F.

2001-02-01

We propose an approach for summarizing the output of long simulations of complex systems, affording a rapid overview and interpretation. First, multidimensional scaling techniques are used in conjunction with dimension reduction methods to obtain a low-dimensional representation of the configuration space explored by the system. A nonparametric estimate of the density of states in this subspace is then obtained using kernel methods. The free energy surface is calculated from that density, and the configurations produced in the simulation are then clustered according to the topography of that surface, such that all configurations belonging to one local free energy minimum form one class. This topographical cluster analysis is performed using basin spanning trees which we introduce as subgraphs of Delaunay triangulations. Free energy surfaces obtained in dimensions lower than four can be visualized directly using iso-contours and -surfaces. Basin spanning trees also afford a glimpse of higher-dimensional topographies. The procedure is illustrated using molecular dynamics simulations on the reversible folding of peptide analoga. Finally, we emphasize the intimate relation of density estimation techniques to modern enhanced sampling algorithms.

New Theoretical Developments in Exploring Electronically Excited States: Including Localized Configuration Interaction Singles and Application to Large Helium Clusters

NASA Astrophysics Data System (ADS)

Closser, Kristina Danielle

This thesis presents new developments in excited state electronic structure theory. Contrasted with the ground state, the electronically excited states of atoms and molecules often are unstable and have short lifetimes, exhibit a greater diversity of character and are generally less well understood. The very unusual excited states of helium clusters motivated much of this work. These clusters consist of large numbers of atoms (experimentally 103--109 atoms) and bands of nearly degenerate excited states. For an isolated atom the lowest energy excitation energies are from 1s → 2s and 1s → 2 p transitions, and in clusters describing the lowest energy band minimally requires four states per atom. In the ground state the clusters are weakly bound by van der Waals interactions, however in the excited state they can form well-defined covalent bonds. The computational cost of quantum chemical calculations rapidly becomes prohibitive as the size of the systems increase. Standard excited-state methods such as configuration interaction singles (CIS) and time-dependent density functional theory (TD-DFT) can be used with ≈100 atoms, and are optimized to treat only a few states. Thus, one of our primary aims is to develop a method which can treat these large systems with large numbers of nearly degenerate excited states. Additionally, excited states are generally formed far from their equilibrium structures. Vertical excitations from the ground state induce dynamics in the excited states. Thus, another focus of this work is to explore the results of these forces and the fate of the excited states. Very little was known about helium cluster excited states when this work began, thus we first investigated the excitations in small helium clusters consisting of 7 or 25 atoms using CIS. The character of these excited states was determined using attachment/detachment density analysis and we found that in the n = 2 manifold the excitations could generally be interpreted as superpositions of atomic states with surface states appearing close to the atomic excitation energies and interior states being blue shifted by up to ≈2 eV. The dynamics resulting from excitation of He_7 were subsequently explored using ab initio molecular dynamics (AIMD). These simulations were performed with classical adiabatic dynamics coupled to a new state-following algorithm on CIS potential energy surfaces. Most clusters were found to completely dissociate and resulted in a single excited atomic state (90%), however, some trajectories formed bound, He*2 (3%), and a few yielded excited trimers (<0.5%). Comparisons were made with available experimental information on much larger clusters. Various applications of this state following algorithm are also presented. In addition to AIMD, these include excited-state geometry optimization and minimal energy path finding via the growing string method. When using state following we demonstrate that more physical results can be obtained with AIMD calculations. Also, the optimized geometries of three excited states of cytosine, two of which were not found without state following, and the minimal energy path between the lowest two singlet excited states of protonated formaldimine are offered as example applications. Finally, to address large clusters, a local variation of CIS was developed. This method exploits the properties of absolutely localized molecular orbitals (ALMOs) to limit the total number of excitations to scaling only linearly with cluster size, which results in formal scaling with the third power of the system size. The derivation of the equations and design of the algorithm are discussed in detail, and computational timings as well as a pilot application to the size dependence of the helium cluster spectrum are presented.

Merging symmetry projection methods with coupled cluster theory: Lessons from the Lipkin model Hamiltonian

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wahlen-Strothman, J. M.; Henderson, T. H.; Hermes, M. R.

Coupled cluster and symmetry projected Hartree-Fock are two central paradigms in electronic structure theory. However, they are very different. Single reference coupled cluster is highly successful for treating weakly correlated systems, but fails under strong correlation unless one sacrifices good quantum numbers and works with broken-symmetry wave functions, which is unphysical for finite systems. Symmetry projection is effective for the treatment of strong correlation at the mean-field level through multireference non-orthogonal configuration interaction wavefunctions, but unlike coupled cluster, it is neither size extensive nor ideal for treating dynamic correlation. We here examine different scenarios for merging these two dissimilar theories.more » We carry out this exercise over the integrable Lipkin model Hamiltonian, which despite its simplicity, encompasses non-trivial physics for degenerate systems and can be solved via diagonalization for a very large number of particles. We show how symmetry projection and coupled cluster doubles individually fail in different correlation limits, whereas models that merge these two theories are highly successful over the entire phase diagram. Despite the simplicity of the Lipkin Hamiltonian, the lessons learned in this work will be useful for building an ab initio symmetry projected coupled cluster theory that we expect to be accurate in the weakly and strongly correlated limits, as well as the recoupling regime.« less

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

DOE PAGES

Faria, José P.; Davis, James J.; Edirisinghe, Janaka N.; ...

2016-11-24

Understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. A multitude of technologies, abstractions, and interpretive frameworks have emerged to answer the challenges presented by genome function and regulatory network inference. Here, we propose a new approach for producing biologically meaningful clusters of coexpressed genes, called Atomic Regulons (ARs), based on expression data, gene context, and functional relationships. We demonstrate this new approach by computing ARs for Escherichia coli, which we compare with the coexpressed gene clusters predicted by two prevalent existing methods: hierarchical clustering and k-meansmore » clustering. We test the consistency of ARs predicted by all methods against expected interactions predicted by the Context Likelihood of Relatedness (CLR) mutual information based method, finding that the ARs produced by our approach show better agreement with CLR interactions. We then apply our method to compute ARs for four other genomes: Shewanella oneidensis, Pseudomonas aeruginosa, Thermus thermophilus, and Staphylococcus aureus. We compare the AR clusters from all genomes to study the similarity of coexpression among a phylogenetically diverse set of species, identifying subsystems that show remarkable similarity over wide phylogenetic distances. We also study the sensitivity of our method for computing ARs to the expression data used in the computation, showing that our new approach requires less data than competing approaches to converge to a near final configuration of ARs. We go on to use our sensitivity analysis to identify the specific experiments that lead most rapidly to the final set of ARs for E. coli. As a result, this analysis produces insights into improving the design of gene expression experiments.« less

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faria, José P.; Davis, James J.; Edirisinghe, Janaka N.

Understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. A multitude of technologies, abstractions, and interpretive frameworks have emerged to answer the challenges presented by genome function and regulatory network inference. Here, we propose a new approach for producing biologically meaningful clusters of coexpressed genes, called Atomic Regulons (ARs), based on expression data, gene context, and functional relationships. We demonstrate this new approach by computing ARs for Escherichia coli, which we compare with the coexpressed gene clusters predicted by two prevalent existing methods: hierarchical clustering and k-meansmore » clustering. We test the consistency of ARs predicted by all methods against expected interactions predicted by the Context Likelihood of Relatedness (CLR) mutual information based method, finding that the ARs produced by our approach show better agreement with CLR interactions. We then apply our method to compute ARs for four other genomes: Shewanella oneidensis, Pseudomonas aeruginosa, Thermus thermophilus, and Staphylococcus aureus. We compare the AR clusters from all genomes to study the similarity of coexpression among a phylogenetically diverse set of species, identifying subsystems that show remarkable similarity over wide phylogenetic distances. We also study the sensitivity of our method for computing ARs to the expression data used in the computation, showing that our new approach requires less data than competing approaches to converge to a near final configuration of ARs. We go on to use our sensitivity analysis to identify the specific experiments that lead most rapidly to the final set of ARs for E. coli. As a result, this analysis produces insights into improving the design of gene expression experiments.« less

All possible tripartitions of {}(236) 236U isotope in collinear configuration

NASA Astrophysics Data System (ADS)

Santhosh, K. P.; Krishnan, Sreejith; Joseph, Jayesh George

2018-07-01

Using the recently proposed unified ternary fission model (UTFM), the tripartition of ^{236}U isotope was studied for all possible fragmentations, in which the interacting potential barrier is taken as the sum of the Coulomb and proximity potentials with fragments in collinear configuration. The highest yield is obtained for the fragmentation ^{48}Ca{+}^{58}Ti{+}^{130}Sn and next highest yield is found for ^{58}Cr{+}^{46}Ar{+}^{132}Sn, which stress the importance of doubly magic or near doubly magic nuclei in the tripartition of ^{236}U isotope. The formation of ^{68}Ni and ^{70}Ni as the edge fragments linking the doubly magic nucleus ^{132}Sn by the isotope of Si is in good agreement with experimental and theoretical studies, in the collinear cluster tripartition of ^{236}U isotope which reveals the reliability of our model (UTFM) in ternary fission.

A comparison of human performance in figural and navigational versions of the traveling salesman problem.

PubMed

Blaser, R E; Wilber, Julie

2013-11-01

Performance on a typical pen-and-paper (figural) version of the Traveling Salesman Problem was compared to performance on a room-sized navigational version of the same task. Nine configurations were designed to examine the use of the nearest-neighbor (NN), cluster approach, and convex-hull strategies. Performance decreased with an increasing number of nodes internal to the hull, and improved when the NN strategy produced the optimal path. There was no overall difference in performance between figural and navigational task modalities. However, there was an interaction between modality and configuration, with evidence that participants relied more heavily on the NN strategy in the figural condition. Our results suggest that participants employed similar, but not identical, strategies when solving figural and navigational versions of the problem. Surprisingly, there was no evidence that participants favored global strategies in the figural version and local strategies in the navigational version.

Interhemispheric differences in ionospheric convection: Cluster EDI observations revisited

NASA Astrophysics Data System (ADS)

Förster, M.; Haaland, S.

2015-07-01

The interaction between the interplanetary magnetic field and the geomagnetic field sets up a large-scale circulation in the magnetosphere. This circulation is also reflected in the magnetically connected ionosphere. In this paper, we present a study of ionospheric convection based on Cluster Electron Drift Instrument (EDI) satellite measurements covering both hemispheres and obtained over a full solar cycle. The results from this study show that average flow patterns and polar cap potentials for a given orientation of the interplanetary magnetic field can be very different in the two hemispheres. In particular during southward directed interplanetary magnetic field conditions, and thus enhanced energy input from the solar wind, the measurements show that the southern polar cap has a higher cross polar cap potential. There are persistent north-south asymmetries, which cannot easily be explained by the influence of external drivers. These persistent asymmetries are primarily a result of the significant differences in the strength and configuration of the geomagnetic field between the Northern and Southern Hemispheres. Since the ionosphere is magnetically connected to the magnetosphere, this difference will also be reflected in the magnetosphere in the form of different feedback from the two hemispheres. Consequently, local ionospheric conditions and the geomagnetic field configuration are important for north-south asymmetries in large regions of geospace.

A Strategic Interaction Model of Punishment Favoring Contagion of Honest Behavior

PubMed Central

Cremene, Marcel; Dumitrescu, D.; Cremene, Ligia

2014-01-01

The punishment effect on social behavior is analyzed within the strategic interaction framework of Cellular Automata and computational Evolutionary Game Theory. A new game, called Social Honesty (SH), is proposed. The SH game is analyzed in spatial configurations. Probabilistic punishment is used as a dishonesty deterrence mechanism. In order to capture the intrinsic uncertainty of social environments, payoffs are described as random variables. New dynamics, with a new relation between punishment probability and punishment severity, are revealed. Punishment probability proves to be more important than punishment severity in guiding convergence towards honesty as predominant behavior. This result is confirmed by empirical evidence and reported experiments. Critical values and transition intervals for punishment probability and severity are identified and analyzed. Clusters of honest or dishonest players emerge spontaneously from the very first rounds of interaction and are determinant for the future dynamics and outcomes. PMID:24489917

Naver: a PC-cluster-based VR system

NASA Astrophysics Data System (ADS)

Park, ChangHoon; Ko, HeeDong; Kim, TaiYun

2003-04-01

In this paper, we present a new framework NAVER for virtual reality application. The NAVER is based on a cluster of low-cost personal computers. The goal of NAVER is to provide flexible, extensible, scalable and re-configurable framework for the virtual environments defined as the integration of 3D virtual space and external modules. External modules are various input or output devices and applications on the remote hosts. From the view of system, personal computers are divided into three servers according to its specific functions: Render Server, Device Server and Control Server. While Device Server contains external modules requiring event-based communication for the integration, Control Server contains external modules requiring synchronous communication every frame. And, the Render Server consists of 5 managers: Scenario Manager, Event Manager, Command Manager, Interaction Manager and Sync Manager. These managers support the declaration and operation of virtual environment and the integration with external modules on remote servers.

Dark matter dynamics in Abell 3827: new data consistent with standard cold dark matter

NASA Astrophysics Data System (ADS)

Massey, Richard; Harvey, David; Liesenborgs, Jori; Richard, Johan; Stach, Stuart; Swinbank, Mark; Taylor, Peter; Williams, Liliya; Clowe, Douglas; Courbin, Frédéric; Edge, Alastair; Israel, Holger; Jauzac, Mathilde; Joseph, Rémy; Jullo, Eric; Kitching, Thomas D.; Leonard, Adrienne; Merten, Julian; Nagai, Daisuke; Nightingale, James; Robertson, Andrew; Romualdez, Luis Javier; Saha, Prasenjit; Smit, Renske; Tam, Sut-Ieng; Tittley, Eric

2018-06-01

We present integral field spectroscopy of galaxy cluster Abell 3827, using Atacama Large Millimetre Array (ALMA) and Very Large Telescope/Multi-Unit Spectroscopic Explorer. It reveals an unusual configuration of strong gravitational lensing in the cluster core, with at least seven lensed images of a single background spiral galaxy. Lens modelling based on Hubble Space Telescope imaging had suggested that the dark matter associated with one of the cluster's central galaxies may be offset. The new spectroscopic data enable better subtraction of foreground light, and better identification of multiple background images. The inferred distribution of dark matter is consistent with being centred on the galaxies, as expected by Λ cold dark matter. Each galaxy's dark matter also appears to be symmetric. Whilst, we do not find an offset between mass and light (suggestive of self-interacting dark matter) as previously reported, the numerical simulations that have been performed to calibrate Abell 3827 indicate that offsets and asymmetry are still worth looking for in collisions with particular geometries. Meanwhile, ALMA proves exceptionally useful for strong lens image identifications.

The effect of clustering on perceived quantity in humans (Homo sapiens) and in chicks (Gallus gallus).

PubMed

Bertamini, Marco; Guest, Martin; Vallortigara, Giorgio; Rugani, Rosa; Regolin, Lucia

2018-04-30

Animals can perceive the numerosity of sets of visual elements. Qualitative and quantitative similarities in different species suggest the existence of a shared system (approximate number system). Biases associated with sensory properties are informative about the underlying mechanisms. In humans, regular spacing increases perceived numerosity (regular-random numerosity illusion). This has led to a model that predicts numerosity based on occupancy (a measure that decreases when elements are close together). We used a procedure in which observers selected one of two stimuli and were given feedback with respect to whether the choice was correct. One configuration had 20 elements and the other 40, randomly placed inside a circular region. Participants had to discover the rule based on feedback. Because density and clustering covaried with numerosity, different dimensions could be used. After reaching a criterion, test trials presented two types of configurations with 30 elements. One type had a larger interelement distance than the other (high or low clustering). If observers had adopted a numerosity strategy, they would choose low clustering (if reinforced with 40) and high clustering (if reinforced with 20). A clustering or density strategy predicts the opposite. Human adults used a numerosity strategy. Chicks were tested using a similar procedure. There were two behavioral measures: first approach response and final circumnavigation (walking behind the screen). The prediction based on numerosity was confirmed by the first approach data. For chicks, one clear pattern from both responses was a preference for the configurations with higher clustering. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Cooperative peer-to-peer multiagent-based systems

NASA Astrophysics Data System (ADS)

Caram, L. F.; Caiafa, C. F.; Ausloos, M.; Proto, A. N.

2015-08-01

A multiagent based model for a system of cooperative agents aiming at growth is proposed. This is based on a set of generalized Verhulst-Lotka-Volterra differential equations. In this study, strong cooperation is allowed among agents having similar sizes, and weak cooperation if agents have markedly different "sizes", thus establishing a peer-to-peer modulated interaction scheme. A rigorous analysis of the stable configurations is presented first examining the fixed points of the system, next determining their stability as a function of the model parameters. It is found that the agents are self-organizing into clusters. Furthermore, it is demonstrated that, depending on parameter values, multiple stable configurations can coexist. It occurs that only one of them always emerges with probability close to one, because its associated attractor dominates over the rest. This is shown through numerical integrations and simulations, after analytic developments. In contrast to the competitive case, agents are able to increase their capacity beyond the no-interaction case limit. In other words, when some collaborative partnership among a relatively small number of partners takes place, all agents act in good faith prioritizing the common good, when receiving a mutual benefit allowing them to surpass their capacity.

Cooperative peer-to-peer multiagent-based systems.

PubMed

Caram, L F; Caiafa, C F; Ausloos, M; Proto, A N

2015-08-01

A multiagent based model for a system of cooperative agents aiming at growth is proposed. This is based on a set of generalized Verhulst-Lotka-Volterra differential equations. In this study, strong cooperation is allowed among agents having similar sizes, and weak cooperation if agents have markedly different "sizes", thus establishing a peer-to-peer modulated interaction scheme. A rigorous analysis of the stable configurations is presented first examining the fixed points of the system, next determining their stability as a function of the model parameters. It is found that the agents are self-organizing into clusters. Furthermore, it is demonstrated that, depending on parameter values, multiple stable configurations can coexist. It occurs that only one of them always emerges with probability close to one, because its associated attractor dominates over the rest. This is shown through numerical integrations and simulations, after analytic developments. In contrast to the competitive case, agents are able to increase their capacity beyond the no-interaction case limit. In other words, when some collaborative partnership among a relatively small number of partners takes place, all agents act in good faith prioritizing the common good, when receiving a mutual benefit allowing them to surpass their capacity.

Energy decomposition analysis for exciplexes using absolutely localized molecular orbitals

NASA Astrophysics Data System (ADS)

Ge, Qinghui; Mao, Yuezhi; Head-Gordon, Martin

2018-02-01

An energy decomposition analysis (EDA) scheme is developed for understanding the intermolecular interaction involving molecules in their excited states. The EDA utilizes absolutely localized molecular orbitals to define intermediate states and is compatible with excited state methods based on linear response theory such as configuration interaction singles and time-dependent density functional theory. The shift in excitation energy when an excited molecule interacts with the environment is decomposed into frozen, polarization, and charge transfer contributions, and the frozen term can be further separated into Pauli repulsion and electrostatics. These terms can be added to their counterparts obtained from the ground state EDA to form a decomposition of the total interaction energy. The EDA scheme is applied to study a variety of systems, including some model systems to demonstrate the correct behavior of all the proposed energy components as well as more realistic systems such as hydrogen-bonding complexes (e.g., formamide-water, pyridine/pyrimidine-water) and halide (F-, Cl-)-water clusters that involve charge-transfer-to-solvent excitations.

Environment overwhelms both nature and nurture in a model spin glass

NASA Astrophysics Data System (ADS)

Middleton, A. Alan; Yang, Jie

We are interested in exploring what information determines the particular history of the glassy long term dynamics in a disordered material. We study the effect of initial configurations and the realization of stochastic dynamics on the long time evolution of configurations in a two-dimensional Ising spin glass model. The evolution of nearest neighbor correlations is computed using patchwork dynamics, a coarse-grained numerical heuristic for temporal evolution. The dependence of the nearest neighbor spin correlations at long time on both initial spin configurations and noise histories are studied through cross-correlations of long-time configurations and the spin correlations are found to be independent of both. We investigate how effectively rigid bond clusters coarsen. Scaling laws are used to study the convergence of configurations and the distribution of sizes of nearly rigid clusters. The implications of the computational results on simulations and phenomenological models of spin glasses are discussed. We acknowledge NSF support under DMR-1410937 (CMMT program).

Nuclear structure studies performed using the (18O,16O) two-neutron transfer reactions

NASA Astrophysics Data System (ADS)

Carbone, D.; Agodi, C.; Cappuzzello, F.; Cavallaro, M.; Ferreira, J. L.; Foti, A.; Gargano, A.; Lenzi, S. M.; Linares, R.; Lubian, J.; Santagati, G.

2018-02-01

Excitation energy spectra and absolute cross section angular distributions were measured for the 13C(18O,16O)15C two-neutron transfer reaction at 84 MeV incident energy. This reaction selectively populates two-neutron configurations in the states of the residual nucleus. Exact finite-range coupled reaction channel calculations are used to analyse the data. Two approaches are discussed: the extreme cluster and the newly introduced microscopic cluster. The latter makes use of spectroscopic amplitudes in the centre of mass reference frame, derived from shell-model calculations using the Moshinsky transformation brackets. The results describe well the experimental cross section and highlight cluster configurations in the involved wave functions.

Intermolecular configurations dominated by quadrupole-quadrupole electrostatic interactions: explicit correlation treatment of the five-dimensional potential energy surface and infrared spectra for the CO-N2 complex.

PubMed

Liu, Jing-Min; Zhai, Yu; Zhang, Xiao-Long; Li, Hui

2018-01-17

A thorough understanding of the intermolecular configurations of van der Waals complexes is a great challenge due to their weak interactions, floppiness and anharmonic nature. Although high-resolution microwave or infrared spectroscopy provides one of the most direct and precise pieces of experimental evidence, the origin and key role in determining such intermolecular configurations of a van der Waals system strongly depend on its highly accurate potential energy surface (PES) and a detailed analysis of its ro-vibrational wavefunctions. Here, a new five-dimensional potential energy surface for the van der Waals complex of CO-N 2 which explicitly incorporates the dependence on the stretch coordinate of the CO monomer is generated using the explicitly correlated couple cluster (CCSD(T)-F12) method in conjunction with a large basis set. Analytic four-dimensional PESs are obtained by the least-squares fitting of vibrationally averaged interaction energies for v = 0 and v = 1 to the Morse/Long-Range potential mode (V MLR ). These fits to 7966 points have root-mean-square deviations (RMSD) of 0.131 cm -1 and 0.129 cm -1 for v = 0 and v = 1, respectively, with only 315 parameters. Energy decomposition analysis is carried out, and it reveals that the dominant factor in controlling intermolecular configurations is quadrupole-quadrupole electrostatic interactions. Moreover, the rovibrational levels and wave functions are obtained for the first time. The predicted infrared transitions and intensities for the ortho-N 2 -CO complex as well as the calculated energy levels for para-N 2 -CO are in good agreement with the available experimental data with RMSD discrepancies smaller than 0.068 cm -1 . The calculated infrared band origin shift associated with the fundamental band frequency of CO is -0.721 cm -1 for ortho-N 2 -CO which is in excellent agreement with the experimental value of -0.739 cm -1 . The agreement with experimental values validates the high quality of the PESs and enhances our confidence to explain the observed mystery lines around 2163 cm -1 .

Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer.

PubMed

Zhai, Yingteng; Laio, Alessandro; Tosatti, Erio; Gong, Xin-Gao

2011-03-02

We introduce an approach for the accurate calculation of thermal properties of classical nanoclusters. On the basis of a recently developed enhanced sampling technique, replica exchange metadynamics, the method yields the true free energy of each relevant cluster structure, directly sampling its basin and measuring its occupancy in full equilibrium. All entropy sources, whether vibrational, rotational anharmonic, or especially configurational, the latter often forgotten in many cluster studies, are automatically included. For the present demonstration, we choose the water nonamer (H(2)O)(9), an extremely simple cluster, which nonetheless displays a sufficient complexity and interesting physics in its relevant structure spectrum. Within a standard TIP4P potential description of water, we find that the nonamer second relevant structure possesses a higher configurational entropy than the first, so that the two free energies surprisingly cross for increasing temperature.

Finite Temperature Properties of Clusters by Replica Exchange Metadynamics: The Water Nonamer

NASA Astrophysics Data System (ADS)

Zhai, Yingteng; Laio, Alessandro; Tosatti, Erio; Gong, Xingao

2012-02-01

We introduce an approach for the accurate calculation of thermal properties of classical nanoclusters. Based on a recently developed enhanced sampling technique, replica exchange metadynamics, the method yields the true free energy of each relevant cluster structure, directly sampling its basin and measuring its occupancy in full equilibrium. All entropy sources, whether vibrational, rotational anharmonic and especially configurational -- the latter often forgotten in many cluster studies -- are automatically included. For the present demonstration we choose the water nonamer (H2O)9, an extremely simple cluster which nonetheless displays a sufficient complexity and interesting physics in its relevant structure spectrum. Within a standard TIP4P potential description of water, we find that the nonamer second relevant structure possesses a higher configurational entropy than the first, so that the two free energies surprisingly cross for increasing temperature.

Electronic excitation spectra of molecules in solution calculated using the symmetry-adapted cluster-configuration interaction method in the polarizable continuum model with perturbative approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukuda, Ryoichi, E-mail: fukuda@ims.ac.jp; Ehara, Masahiro; Elements Strategy Initiative for Catalysts and Batteries

A perturbative approximation of the state specific polarizable continuum model (PCM) symmetry-adapted cluster-configuration interaction (SAC-CI) method is proposed for efficient calculations of the electronic excitations and absorption spectra of molecules in solutions. This first-order PCM SAC-CI method considers the solvent effects on the energies of excited states up to the first-order with using the zeroth-order wavefunctions. This method can avoid the costly iterative procedure of the self-consistent reaction field calculations. The first-order PCM SAC-CI calculations well reproduce the results obtained by the iterative method for various types of excitations of molecules in polar and nonpolar solvents. The first-order contribution ismore » significant for the excitation energies. The results obtained by the zeroth-order PCM SAC-CI, which considers the fixed ground-state reaction field for the excited-state calculations, are deviated from the results by the iterative method about 0.1 eV, and the zeroth-order PCM SAC-CI cannot predict even the direction of solvent shifts in n-hexane for many cases. The first-order PCM SAC-CI is applied to studying the solvatochromisms of (2,2{sup ′}-bipyridine)tetracarbonyltungsten [W(CO){sub 4}(bpy), bpy = 2,2{sup ′}-bipyridine] and bis(pentacarbonyltungsten)pyrazine [(OC){sub 5}W(pyz)W(CO){sub 5}, pyz = pyrazine]. The SAC-CI calculations reveal the detailed character of the excited states and the mechanisms of solvent shifts. The energies of metal to ligand charge transfer states are significantly sensitive to solvents. The first-order PCM SAC-CI well reproduces the observed absorption spectra of the tungsten carbonyl complexes in several solvents.« less

Effects of different set configurations on barbell velocity and displacement during a clean pull.

PubMed

Haff, G Gregory; Whitley, Adrian; McCoy, Lora B; O'Bryant, Harold S; Kilgore, J Lon; Haff, Erin E; Pierce, Kyle; Stone, Michael H

2003-02-01

The effects of 3 types of set configurations (cluster, traditional, and undulating) on barbell kinematics were investigated in the present study. Thirteen men (track and field = 8; Olympic weightlifters = 5) (mean +/- SEM age, 23.4 +/- 1.1 years; height, 181.3 +/- 2.1 cm; body mass, 89.8 +/- 4.2 kg) performed 1 set of 5 repetitions in a cluster, traditional, and undulating fashion at 90 and 120% of their 1 repetition maximum (1RM) power clean (119.0 +/- 4.3 kg). All data were collected at 50 Hz and analyzed with a V-Scope Weightlifting Analysis System. Peak velocity (PV) and peak displacement (PD) were analyzed for each repetition and averaged for each set type. Results indicated that a significantly (p < 0.016) higher PV occurred during the cluster set when compared with the traditional sets at both intensities. PD was significantly higher than traditional sets at the 120% intensity. The present study suggests set configuration can affect PV and PD during clean pulls.

Analysis of factors that influence the maximum number of repetitions in two upper-body resistance exercises: curl biceps and bench press.

PubMed

Iglesias, Eliseo; Boullosa, Daniel A; Dopico, Xurxo; Carballeira, Eduardo

2010-06-01

The purpose of this study was to analyze the influence of exercise type, set configuration, and relative intensity load on relationship between 1 repetition maximum (1RM) and maximum number of repetitions (MNR). Thirteen male subjects, experienced in resistance training, were tested in bench press and biceps curl for 1RM, MNR at 90% of 1RM with cluster set configuration (rest of 30s between repetitions) and MNR at 70% of 1RM with traditional set configuration (no rest between repetitions). A lineal encoder was used for measuring displacement of load. Analysis of variance analysis revealed a significant effect of load (p<0.01) and a tendency in exercise factor (p=0.096), whereas the interaction effect was not significant. MNR at 70% of 1RM was lower for biceps curl (16.31+/-2.59 vs. 8.77+/-3 in bench press and biceps curl, respectively; p<0.05) and at 90% of 1RM (21.85+/-11.06 vs. 18.54+/-12.84 in bench press and biceps curl, respectively; p>0.05). Correlation between 1RM and MNR was significant for medium-intensity in biceps curl (r=-0.574; p<0.05) and between MNR and 1RM/body mass (r=-0.574; p<0.05). Neither 1RM nor 1RM/body mass correlated with velocity along set, so velocity seems to be similar at a same relative intensity for subjects with differences in maximum strength levels. From our results, we suggest the employment of MNR rather than % of 1RM for training monitoring. Furthermore, we suggest the introduction of cluster set configuration for upper-body assessment of MNR and for upper-body muscular endurance training at high-intensity loads, as it seems an efficient approach in looking for sessions with greater training volumes. This could be an interesting approach for such sports as wrestling or weightlifting.

Reexamining organizational configurations: an update, validation, and expansion of the taxonomy of health networks and systems.

PubMed

Dubbs, Nicole L; Bazzoli, Gloria J; Shortell, Stephen M; Kralovec, Peter D

2004-02-01

To (a) assess how the original cluster categories of hospital-led health networks and systems have changed over time; (b) identify any new patterns of cluster configurations; and (c) demonstrate how additional data can be used to refine and enhance the taxonomy measures. DATA SOURCES; 1994 and 1998 American Hospital Association (AHA) Annual Survey of Hospitals. As in the original taxonomy, separate cluster solutions are identified for health networks and health systems by applying three strategic/structural dimensions (differentiation, integration, and centralization) to three components of the health service/product continuum (hospital services, physician arrangements, and provider-based insurance activities). Factor, cluster, and discriminant analyses are used to analyze the 1998 data. Descriptive and comparative methods are used to analyze the updated 1998 taxonomy relative to the original 1994 version. The 1998 cluster categories are similar to the original taxonomy, however, they reveal some new organizational configurations. For the health networks, centralization of product/service lines is occurring more selectively than in the past. For the health systems, participation has grown in and dispersed across a more diverse set of decentralized organizational forms. For both networks and systems, the definition of centralization has changed over time. In its updated form, the taxonomy continues to provide policymakers and practitioners with a descriptive and contextual framework against which to assess organizational programs and policies. There is a need to continue to revisit the taxonomy from time to time because of the persistent evolution of the U.S. health care industry and the consequent shifting of organizational configurations in this arena. There is also value in continuing to move the taxonomy in the direction of refinement/expansion as new opportunities become available.

Spectroscopic accuracy directly from quantum chemistry: application to ground and excited states of beryllium dimer.

PubMed

Sharma, Sandeep; Yanai, Takeshi; Booth, George H; Umrigar, C J; Chan, Garnet Kin-Lic

2014-03-14

We combine explicit correlation via the canonical transcorrelation approach with the density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods to compute a near-exact beryllium dimer curve, without the use of composite methods. In particular, our direct density matrix renormalization group calculations produce a well-depth of D(e) = 931.2 cm(-1) which agrees very well with recent experimentally derived estimates D(e) = 929.7±2 cm(-1) [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)] and D(e) = 934.6 cm(-1) [K. Patkowski, V. Špirko, and K. Szalewicz, Science 326, 1382 (2009)], as well the best composite theoretical estimates, D(e) = 938±15 cm(-1) [K. Patkowski, R. Podeszwa, and K. Szalewicz, J. Phys. Chem. A 111, 12822 (2007)] and D(e) = 935.1±10 cm(-1) [J. Koput, Phys. Chem. Chem. Phys. 13, 20311 (2011)]. Our results suggest possible inaccuracies in the functional form of the potential used at shorter bond lengths to fit the experimental data [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)]. With the density matrix renormalization group we also compute near-exact vertical excitation energies at the equilibrium geometry. These provide non-trivial benchmarks for quantum chemical methods for excited states, and illustrate the surprisingly large error that remains for 1 ¹Σ(g)⁻ state with approximate multi-reference configuration interaction and equation-of-motion coupled cluster methods. Overall, we demonstrate that explicitly correlated density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods allow us to fully converge to the basis set and correlation limit of the non-relativistic Schrödinger equation in small molecules.

Exhaustive comparison and classification of ligand-binding surfaces in proteins

PubMed Central

Murakami, Yoichi; Kinoshita, Kengo; Kinjo, Akira R; Nakamura, Haruki

2013-01-01

Many proteins function by interacting with other small molecules (ligands). Identification of ligand-binding sites (LBS) in proteins can therefore help to infer their molecular functions. A comprehensive comparison among local structures of LBSs was previously performed, in order to understand their relationships and to classify their structural motifs. However, similar exhaustive comparison among local surfaces of LBSs (patches) has never been performed, due to computational complexity. To enhance our understanding of LBSs, it is worth performing such comparisons among patches and classifying them based on similarities of their surface configurations and electrostatic potentials. In this study, we first developed a rapid method to compare two patches. We then clustered patches corresponding to the same PDB chemical component identifier for a ligand, and selected a representative patch from each cluster. We subsequently exhaustively as compared the representative patches and clustered them using similarity score, PatSim. Finally, the resultant PatSim scores were compared with similarities of atomic structures of the LBSs and those of the ligand-binding protein sequences and functions. Consequently, we classified the patches into ∼2000 well-characterized clusters. We found that about 63% of these clusters are used in identical protein folds, although about 25% of the clusters are conserved in distantly related proteins and even in proteins with cross-fold similarity. Furthermore, we showed that patches with higher PatSim score have potential to be involved in similar biological processes. PMID:23934772

Accurate bond energies of hydrocarbons from complete basis set extrapolated multi-reference singles and doubles configuration interaction.

PubMed

Oyeyemi, Victor B; Pavone, Michele; Carter, Emily A

2011-12-09

Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: 1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; 2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and 3) DFT-B3LYP calculations of minimum-energy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of CC and CH bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations.

PubMed

Balatti, Galo E; Ambroggio, Ernesto E; Fidelio, Gerardo D; Martini, M Florencia; Pickholz, Mónica

2017-10-20

In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG) model within the MARTINI force field; we simulated the peptide-lipid system from three different initial configurations: (a) peptides in water in the presence of a pre-equilibrated lipid bilayer; (b) peptides inside the hydrophobic core of the membrane; and (c) random configurations that allow self-assembled molecular structures. This last approach allowed us to sample the structural space of the systems and consider cooperative effects. The peptides used in our simulations are aurein 1.2 and maculatin 1.1; two well-known antimicrobial peptides from the Australian tree frogs; and molecules that present different membrane-perturbing behaviors. Our results showed differential behaviors for each type of peptide seen in a different organization that could guide a molecular interpretation of the experimental data. While both peptides are capable of forming membrane aggregates; the aurein 1.2 ones have a pore-like structure and exhibit a higher level of organization than those conformed by maculatin 1.1. Furthermore; maculatin 1.1 has a strong tendency to form clusters and induce curvature at low peptide-lipid ratios. The exploration of the possible lipid-peptide structures; as the one carried out here; could be a good tool for recognizing specific configurations that should be further studied with more sophisticated methodologies.

The spherical-harmonics representation for the interaction between diatomic molecules: The general case and applications to COsbnd CO and COsbnd HF

NASA Astrophysics Data System (ADS)

Barreto, Patricia R. P.; Cruz, Ana Claudia P. S.; Barreto, Rodrigo L. P.; Palazzetti, Federico; Albernaz, Alessandra F.; Lombardi, Andrea; Maciel, Glauciete S.; Aquilanti, Vincenzo

2017-07-01

The spherical-harmonics expansion is a mathematically rigorous procedure and a powerful tool for the representation of potential energy surfaces of interacting molecular systems, determining their spectroscopic and dynamical properties, specifically in van der Waals clusters, with applications also to classical and quantum molecular dynamics simulations. The technique consists in the construction (by ab initio or semiempirical methods) of the expanded potential interaction up to terms that provide the generation of a number of leading configurations sufficient to account for faithful geometrical representations. This paper reports the full general description of the method of the spherical-harmonics expansion as applied to diatomic-molecule - diatomic-molecule systems of increasing complexity: the presentation of the mathematical background is given for providing both the application to the prototypical cases considered previously (O2sbnd O2, N2sbnd N2, and N2sbnd O2 systems) and the generalization to: (i) the COsbnd CO system, where a characteristic feature is the lower symmetry order with respect to the cases studied before, requiring a larger number of expansion terms necessary to adequately represent the potential energy surface; and (ii) the COsbnd HF system, which exhibits the lowest order of symmetry among this class of aggregates and therefore the highest number of leading configurations.

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Pairwise additivity in the nuclear magnetic resonance interactions of atomic xenon.

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2009-04-14

Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.

Formation and Levitation of Unconfined Droplet Clusters

NASA Technical Reports Server (NTRS)

Liu, S.; Ruff, G. A.

1999-01-01

Combustion experiments using arrays of droplets seek to provide a link between single droplet combustion phenomena and the behavior of complex spray combustion systems. Both single droplet and droplet array studies have been conducted in microgravity to better isolate the droplet interaction phenomena and eliminate or reduce the confounding effects of buoyancy-induced convection. In most experiments involving droplet arrays, the droplets are supported on fibers to keep them stationary and close together before the combustion event. The presence of the fiber, however, disturbs the combustion process by introducing a source of heat transfer and asymmetry into the configuration. As the number of drops in a droplet array increases, supporting the drops on fibers becomes less practical because of the cumulative effect of the fibers on the combustion process. The overall objective of this research is to study the combustion of well-characterized drop clusters in a microgravity environment. Direct experimental observations and measurements of the combustion of droplet clusters would fill a large gap in our current understanding of droplet and spray combustion and provide unique experimental data for the verification and improvement of spray combustion models. This paper describes current work on the design and performance of an apparatus to generate and stabilize droplet clusters using acoustic and electrostatic forces.

A general ansatz for constructing quasi-diabatic states in electronically excited aggregated systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Wenlan; Köhn, Andreas; InnovationLab GmbH, Speyerer St. 4, D-69115 Heidelberg

2015-08-28

We present a general method for analyzing the character of singly excited states in terms of charge transfer (CT) and locally excited (LE) configurations. The analysis is formulated for configuration interaction singles (CIS) singly excited wave functions of aggregate systems. It also approximately works for the second-order approximate coupled cluster singles and doubles and the second-order algebraic-diagrammatic construction methods [CC2 and ADC(2)]. The analysis method not only generates a weight of each character for an excited state, but also allows to define the related quasi-diabatic states and corresponding coupling matrix elements. In the character analysis approach, we divide the targetmore » system into domains and use a modified Pipek-Mezey algorithm to localize the canonical MOs on each domain, respectively. The CIS wavefunction is then transformed into the localized basis, which allows us to partition the wavefunction into LE configurations within domains and CT configuration between pairs of different domains. Quasi-diabatic states are then obtained by mixing excited states subject to the condition of maximizing the weight of one single LE or CT configuration (localization in configuration space). Different aims of such a procedure are discussed, either the construction of pure LE and CT states for analysis purposes (by including a large number of excited states) or the construction of effective models for dynamics calculations (by including a restricted number of excited states). Applications are given to LE/CT mixing in π-stacked systems, charge-recombination matrix elements in a hetero-dimer, and excitonic couplings in multi-chromophoric systems.« less

Interaction Heterogeneity can Favorably Impact Colloidal Crystal Nucleation

NASA Astrophysics Data System (ADS)

Jenkins, Ian C.; Crocker, John C.; Sinno, Talid

2017-10-01

Colloidal particles with short-ranged attractions, e.g., micron-scale spheres functionalized with single-stranded DNA oligomers, are susceptible to becoming trapped in disordered configurations even when a crystalline arrangement is the ground state. Moreover, for reasons that are not well understood, seemingly minor variations in the particle formulation can lead to dramatic changes in the crystallization outcome. We demonstrate, using a combination of equilibrium and nonequilibrium computer simulations, that interaction heterogeneity—variations in the energetic interactions among different particle pairs in the population—may favorably impact crystal nucleation. Specifically, interaction heterogeneity is found to lower the free energy barrier to nucleation via the formation of clusters comprised preferentially of strong-binding particle pairs. Moreover, gelation is inhibited by "spreading out over time" the nucleation process, resulting in a reduced density of stable nuclei, allowing each to grow unhindered and larger. Our results suggest a simple and robust approach for enhancing colloidal crystallization near the "sticky sphere" limit, and support the notion that differing extents of interaction heterogeneity arising from various particle functionalization protocols may contribute to the otherwise unexplained variations in crystallization outcomes reported in the literature.

Collective orientational dynamics of pinned chemically-propelled nanorotors

NASA Astrophysics Data System (ADS)

Robertson, Bryan; Stark, Holger; Kapral, Raymond

2018-04-01

Collections of chemically propelled nanomotors free to move in solution can form dynamic clusters with diverse properties as a result of interactions through hydrodynamic flow and concentration fields, as well as direct intermolecular interactions between motors. Here, we study the collective rotational behavior of pinned sphere-dimer motors where direct motor-motor interactions play no role. Since the centers of mass of the motors are pinned, they cannot execute directed translational motion, but they can pump fluid and rotate; thus, the rotors remain coupled through hydrodynamic and chemical fields. Using a microscopic simulation method that accounts for coupling through both these fields, we show that different rotor configurations with a high degree of correlation exist and their forms depend on the nature of the fluid-rotor interactions. The correlations are greatly reduced or completely destroyed when the chemical interactions are removed, indicating that hydrodynamic coupling, while present, plays a lesser role in determining the collective rotor dynamics. These conclusions are supported by Langevin dynamics simulations that neglect hydrodynamics and include an approximate form of coupling through chemical fields.

Baikal-GVD

NASA Astrophysics Data System (ADS)

Avrorin, A. D.; Avrorin, A. V.; Aynutdinov, V. M.; Bannash, R.; Belolaptikov, I. A.; Brudanin, V. B.; Budnev, N. M.; Danilchenko, I. A.; Demidov, S. V.; Domogatsky, G. V.; Doroshenko, A. A.; Dvornicky, R.; Dyachok, A. N.; Dzhilkibaev, Zh.-A. M.; Fajt, L.; Fialkovsky, S. V.; Gafarov, A. R.; Gaponenko, O. N.; Golubkov, K. V.; Gress, T. I.; Honz, Z.; Kebkal, K. G.; Kebkal, O. G.; Konischev, K. V.; Korobchenko, A. V.; Koshechkin, A. P.; Koshel, F. K.; Kozhin, A. V.; Kulepov, V. F.; Kuleshov, D. A.; Milenin, M. B.; Mirgazov, R. A.; Osipova, E. R.; Panfilov, A. I.; Pan'kov, L. V.; Pliskovsky, E. N.; Rozanov, M. I.; Rjabov, E. V.; Shamakhov, F. A.; Shaybonov, B. A.; Sheifler, A. A.; Shelepov, M. D.; Simkovic, F.; Skurihin, A. V.; Smagina, A. A.; Stekl, I.; Suvorova, O. V.; Tabolenko, V. A.; Tarashansky, B. A.; Yakovlev, S. A.; Zagorodnikov, A. V.; Zurbanov, V. L.

2017-03-01

We present the status of the Gigaton Volume Detector in Lake Baikal (Baikal-GVD) designed for the detection of high energy neutrinos of astrophysical origin. The telescope consists of functionally independent clusters, sub-arrays of optical modules (OMs), which are connected to shore by individual electro-optical cables. During 2015 the GVD demonstration cluster, comprising 192 OMs, has been successfully operated in Lake Baikal. In 2016 this array was upgraded to baseline configuration of GVD cluster with 288 OMs arranged on eight vertical strings. Thus the instrumented water volume has been increased up to about 5.9 Mtons. The array was commissioned in early April 2016 and takes data since then. We describe the configuration and design of the 2016 array. Preliminary results obtained with data recorded in 2015 are also discussed.

Circular dichroism spectra of uridine derivatives: ChiraSac study.

PubMed

Miyahara, Tomoo; Nakatsuji, Hiroshi; Wada, Takehiko

2014-04-24

The experimental circular dichroism (CD) spectra of uridine and NH2-uridine that were different in the intensity and shape were studied in the light of the ChiraSac method. The theoretical CD spectra at several different conformations using the symmetry-adapted-cluster configuration-interaction (SAC-CI) theory largely depended on the conformational angle, but those of the anti-conformers and the Boltzmann average reproduced the experimentally obtained CD spectra of both uridine and NH2-uridine. The differences in the CD spectra between the two uridine derivatives were analyzed by using the angle θ between the electric transition dipole moment (ETDM) and the magnetic transition dipole moment (MTDM).

Emergence of the mass discrepancy-acceleration relation from dark matter-baryon interactions

NASA Astrophysics Data System (ADS)

Famaey, Benoit; Khoury, Justin; Penco, Riccardo

2018-03-01

The observed tightness of the mass discrepancy-acceleration relation (MDAR) poses a fine-tuning challenge to current models of galaxy formation. We propose that this relation could arise from collisional interactions between baryons and dark matter (DM) particles, without the need for modification of gravity or ad hoc feedback processes. We assume that these interactions satisfy the following three conditions: (i) the relaxation time of DM particles is comparable to the dynamical time in disk galaxies; (ii) DM exchanges energy with baryons due to elastic collisions; (iii) the product between the baryon-DM cross section and the typical energy exchanged in a collision is inversely proportional to the DM number density. As a proof of principle, we present an example of a particle physics model that gives a DM-baryon cross section with the desired density and velocity dependence. For consistency with direct detection constraints, our DM particles must be either very light (m ll mb) or very heavy (mgg mb), corresponding respectively to heating and cooling of DM by baryons. In both cases, our mechanism applies and an equilibrium configuration can in principle be reached. In this exploratory paper, we focus on the heavy DM/cooling case because it is technically simpler, since the average energy exchanged turns out to be approximately constant throughout galaxies. Under these assumptions, we find that rotationally-supported disk galaxies could naturally settle to equilibrium configurations satisfying a MDAR at all radii without invoking finely tuned feedback processes. We also discuss issues related to the small scale clumpiness of baryons, as well as predictions for pressure-supported systems. We argue in particular that galaxy clusters do not follow the MDAR despite being DM-dominated because they have not reached their equilibrium configuration. Finally, we revisit existing phenomenological, astrophysical and cosmological constraints on baryon-DM interactions in light of the unusual density dependence of the cross section of DM particles.

Measurement of entanglement entropy in the two-dimensional Potts model using wavelet analysis.

PubMed

Tomita, Yusuke

2018-05-01

A method is introduced to measure the entanglement entropy using a wavelet analysis. Using this method, the two-dimensional Haar wavelet transform of a configuration of Fortuin-Kasteleyn (FK) clusters is performed. The configuration represents a direct snapshot of spin-spin correlations since spin degrees of freedom are traced out in FK representation. A snapshot of FK clusters loses image information at each coarse-graining process by the wavelet transform. It is shown that the loss of image information measures the entanglement entropy in the Potts model.

Correlation Functions in Two-Dimensional Critical Systems with Conformal Symmetry

NASA Astrophysics Data System (ADS)

Flores, Steven Miguel

This thesis presents a study of certain conformal field theory (CFT) correlation functions that describe physical observables in conform ally invariant two-dimensional critical systems. These are typically continuum limits of critical lattice models in a domain within the complex plane and with a boundary. Certain clusters, called boundary clusters, anchor to the boundary of the domain, and many of their features are governed by a conformally invariant probability measure. For example, percolaion is an example of a critical lattice model, and when it is confined to a domain with a boundary, connected clusters of activated bonds that touch that boundary are the boundary clusters. This thesis is concerned with how the boundary clusters interact with each other according to that measure. One question that it considers are "how likely are these clusters to repel each other or to connect with one another in a certain topological configuration?" Chapter one non-rigorously derives an already well-known elliptic system of differential equations closely tied to this matter by using standard techniques of CFT, chapters two and three rigorously infer certain properties concerning the solution space of this system, and chapter four uses some of those results to predict an answer to this question. This thesis also considers local variations of this question such as "what regions of the domain do the perimeters of the boundary clusters explore," and "how often will several boundary clusters connect at just a single, specified point in the domain?" Chapter five predicts precise answers to these questions. All of these answers are quantitative predictions that we verify via high-precision computer simulation. Chapters four and five also present these simulation results. Further material that supplements chapter one is included in two appendices.

Dynamical theory of dense groups of galaxies

NASA Technical Reports Server (NTRS)

Mamon, Gary A.

1990-01-01

It is well known that galaxies associate in groups and clusters. Perhaps 40% of all galaxies are found in groups of 4 to 20 galaxies (e.g., Tully 1987). Although most groups appear to be so loose that the galaxy interactions within them ought to be insignificant, the apparently densest groups, known as compact groups appear so dense when seen in projection onto the plane of the sky that their members often overlap. These groups thus appear as dense as the cores of rich clusters. The most popular catalog of compact groups, compiled by Hickson (1982), includes isolation among its selection critera. Therefore, in comparison with the cores of rich clusters, Hickson's compact groups (HCGs) appear to be the densest isolated regions in the Universe (in galaxies per unit volume), and thus provide in principle a clean laboratory for studying the competition of very strong gravitational interactions. The $64,000 question here is then: Are compact groups really bound systems as dense as they appear? If dense groups indeed exist, then one expects that each of the dynamical processes leading to the interaction of their member galaxies should be greatly enhanced. This leads us to the questions: How stable are dense groups? How do they form? And the related question, fascinating to any theorist: What dynamical processes predominate in dense groups of galaxies? If HCGs are not bound dense systems, but instead 1D change alignments (Mamon 1986, 1987; Walke & Mamon 1989) or 3D transient cores (Rose 1979) within larger looser systems of galaxies, then the relevant question is: How frequent are chance configurations within loose groups? Here, the author answers these last four questions after comparing in some detail the methods used and the results obtained in the different studies of dense groups.

Crystalline embryos at ice-vapor interfaces

NASA Technical Reports Server (NTRS)

Bartley, D. L.

1976-01-01

The nucleation of small monolayer ice-like clusters at the basal and prism ice-vapor interfaces is considered. It is found that the basal surfaces prefer triangular embryos with an orientation that reverses from layer to layer, whereas the most stable clusters on the prism surfaces are rectangular in configuration. At any given saturation ratio, the preferred prism clusters are found to have a critical energy of formation significantly lower than that of the basal clusters, basically because of differences in cluster corner free energies.

Cluster structures influenced by interaction with a surface.

PubMed

Witt, Christopher; Dieterich, Johannes M; Hartke, Bernd

2018-05-30

Clusters on surfaces are vitally important for nanotechnological applications. Clearly, cluster-surface interactions heavily influence the preferred cluster structures, compared to clusters in vacuum. Nevertheless, systematic explorations and an in-depth understanding of these interactions and how they determine the cluster structures are still lacking. Here we present an extension of our well-established non-deterministic global optimization package OGOLEM from isolated clusters to clusters on surfaces. Applying this approach to intentionally simple Lennard-Jones test systems, we produce a first systematic exploration that relates changes in cluster-surface interactions to resulting changes in adsorbed cluster structures.

Investigation on structure, electronic and magnetic properties of Cr doped (ZnO)12 clusters: First-principles calculations

NASA Astrophysics Data System (ADS)

Liu, Huan; Zhang, Jian-Min

2018-05-01

The structural, electronic, and magnetic properties of (ZnO)12 clusters doped with Cr atoms have been investigated by using spin-polarized first-principles calculations. The exohedral a3 isomer is favorable than endohedral a2 isomer. The isomer a1 and a5 respectively have the narrowest and biggest gap between highest unoccupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO) of 0.473 and 1.291 eV among these five monodoped isomers. The magnetic moment may be related to the local environment around the Cr atom that the a2 isomer whose total magnetic moment is 6 μB while the other monodoped isomers which all isomers have nearly total magnetic moments 4 μB . For Cr-doped (ZnO)12 on a1 or a3 isomer, the DOS of spin-up channel cross the Fermi level EF showing a finite magnitude near the Fermi level which might be useful for half metallic character. For the bidoped cases, the exohedral isomers are found to be most favorable. Including all bipoed isomers of substitutional, exohedral and endohedral bidoped clusters, the total magnetic moment of the ferromagnetic (antiferromagnetic) state is 8 (0) μB and the HOMO-LUMO gap of antiferromagnetic state is slightly larger than that of ferromagnetic state. The magnetic coupling between the Cr atoms in bidoped configurations is mainly governed by the competition between direct Cr and Cr atoms antiferromagnetic interaction and the ferromagnetic interaction between two Cr atoms via O atom due to strong p-d hybridization. Most importantly, we show that the exohedral bidoped (ZnO)12 clusters favor the ferromagnetic state, which may have the future applications in spin-dependent magneto-optical and magneto-electrical devices.

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turi, László, E-mail: turi@chem.elte.hu

2016-04-21

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions withmore » n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.« less

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

NASA Astrophysics Data System (ADS)

Turi, László

2016-04-01

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

Operational Dynamic Configuration Analysis

NASA Technical Reports Server (NTRS)

Lai, Chok Fung; Zelinski, Shannon

2010-01-01

Sectors may combine or split within areas of specialization in response to changing traffic patterns. This method of managing capacity and controller workload could be made more flexible by dynamically modifying sector boundaries. Much work has been done on methods for dynamically creating new sector boundaries [1-5]. Many assessments of dynamic configuration methods assume the current day baseline configuration remains fixed [6-7]. A challenging question is how to select a dynamic configuration baseline to assess potential benefits of proposed dynamic configuration concepts. Bloem used operational sector reconfigurations as a baseline [8]. The main difficulty is that operational reconfiguration data is noisy. Reconfigurations often occur frequently to accommodate staff training or breaks, or to complete a more complicated reconfiguration through a rapid sequence of simpler reconfigurations. Gupta quantified a few aspects of airspace boundary changes from this data [9]. Most of these metrics are unique to sector combining operations and not applicable to more flexible dynamic configuration concepts. To better understand what sort of reconfigurations are acceptable or beneficial, more configuration change metrics should be developed and their distribution in current practice should be computed. This paper proposes a method to select a simple sequence of configurations among operational configurations to serve as a dynamic configuration baseline for future dynamic configuration concept assessments. New configuration change metrics are applied to the operational data to establish current day thresholds for these metrics. These thresholds are then corroborated, refined, or dismissed based on airspace practitioner feedback. The dynamic configuration baseline selection method uses a k-means clustering algorithm to select the sequence of configurations and trigger times from a given day of operational sector combination data. The clustering algorithm selects a simplified schedule containing k configurations based on stability score of the sector combinations among the raw operational configurations. In addition, the number of the selected configurations is determined based on balance between accuracy and assessment complexity.

StarBooster Demonstrator Cluster Configuration Analysis/Verification Program

NASA Technical Reports Server (NTRS)

DeTurris, Dianne J.

2003-01-01

In order to study the flight dynamics of the cluster configuration of two first stage boosters and upper-stage, flight-testing of subsonic sub-scale models has been undertaken using two glideback boosters launched on a center upper-stage. Three high power rockets clustered together were built and flown to demonstrate vertical launch, separation and horizontal recovery of the boosters. Although the boosters fly to conventional aircraft landing, the centerstage comes down separately under its own parachute. The goal of the project has been to collect data during separation and flight for comparison with a six degree of freedom simulation. The configuration for the delta wing canard boosters comes from a design by Starcraft Boosters, Inc. The subscale rockets were constructed of foam covered in carbon or fiberglass and were launched with commercially available solid rocket motors. The first set of boosters built were 3-ft tall with a 4-ft tall centerstage, and two additional sets of boosters were made that were each over 5-ft tall with a 7.5 ft centerstage. The rocket cluster is launched vertically, then after motor bum out the boosters are separated and flown to a horizontal landing under radio-control. An on-board data acquisition system recorded data during both the launch and glide phases of flight.

Dynamical pattern formation in a low-concentration magnetorheological fluid under two orthogonal sinusoidal fields

NASA Astrophysics Data System (ADS)

Yépez, L. D.; Carrillo, J. L.; Donado, F.; Sausedo-Solorio, J. M.; Miranda-Romagnoli, P.

2016-06-01

The dynamical pattern formation of clusters of magnetic particles in a low-concentration magnetorheological fluid, under the influence of a superposition of two perpendicular sinusoidal fields, is studied experimentally. By varying the frequency and phase shift of the perpendicular fields, this configuration enables us to experimentally analyze a wide range of field configurations, including the case of a pure rotating field and the case of an oscillating unidirectional field. The fields are applied parallel to the horizontal plane where the fluid lies or in the vertical plane. For fields applied in the horizontal plane, we observed that, when the ratio of the frequencies increases, the average cluster size exhibits a kind of periodic resonances. When the phase shift between the fields is varied, the average chain length reaches maximal values for the cases of the rotating field and the unidirectional case. We analyze and discuss these results in terms of a weighted average of the time-dependent Mason number. In the case of a rotating field on the vertical plane, we also observe that the competition between the magnetic and the viscous forces determines the average cluster size. We show that this configuration generates a series of physically meaningful self-organization of clusters and transport phenomena.

Simulating complex atomistic processes: On-the-fly kinetic Monte Carlo scheme with selective active volumes

NASA Astrophysics Data System (ADS)

Xu, Haixuan; Osetsky, Yury N.; Stoller, Roger E.

2011-10-01

An accelerated atomistic kinetic Monte Carlo (KMC) approach for evolving complex atomistic structures has been developed. The method incorporates on-the-fly calculations of transition states (TSs) with a scheme for defining active volumes (AVs) in an off-lattice (relaxed) system. In contrast to conventional KMC models that require all reactions to be predetermined, this approach is self-evolving and any physically relevant motion or reaction may occur. Application of this self-evolving atomistic kinetic Monte Carlo (SEAK-MC) approach is illustrated by predicting the evolution of a complex defect configuration obtained in a molecular dynamics (MD) simulation of a displacement cascade in Fe. Over much longer times, it was shown that interstitial clusters interacting with other defects may change their structure, e.g., from glissile to sessile configuration. The direct comparison with MD modeling confirms the atomistic fidelity of the approach, while the longer time simulation demonstrates the unique capability of the model.

Can nonadditive dispersion forces explain chain formation of nanoparticles?

NASA Astrophysics Data System (ADS)

Kwaadgras, Bas W.; Verdult, Maarten W. J.; Dijkstra, Marjolein; van Roij, René

2013-03-01

We study to what extent dielectric nanoparticles prefer to self-assemble into linear chains or into more compact structures. To calculate the Van der Waals (VdW) attraction between the clusters we use the Coupled Dipole Method (CDM), which treats each atom in the nanoparticle as an inducible oscillating point dipole. The VdW attraction then results from the full many-body interactions between the dipoles. For non-capped nanoparticles, we calculate in which configuration the VdW attraction is maximal. We find that in virtually all cases we studied, many-body effects only result in local potential minima at the linear configuration, as opposed to global ones, and that these metastable minima are in most cases rather shallow compared to the thermal energy. In this work, we also compare the CDM results with those from Hamaker-de Boer and Axilrod-Teller theory to investigate the influence of the many-body effects and the accuracy of these two approximate methods.

H 2 Adsorbed Site-to-Site Electronic Delocalization within IRMOF-1: Understanding Non-Negligible Interactions at High Pressure

DOE PAGES

Wu, Jian; Kucukkal, Mustafa U.; Clark, Aurora E.

2016-07-15

Isoreticular metal organic frameworks (IRMOFs) have shown high uptake capabilities for storage of H 2 (11.5 wt % at 77 K and 170 bar). A significant literature has employed fragment models and a single adsorbed H 2 to identify adsorption sites within IRMOFs, as well as the necessary adsorbate–adsorbent interactions needed to reach sufficient adsorption enthalpy for practical usage, however at high pressures it remains to be seen if H 2···H 2 intermolecular interactions may influence the energetics. This study focuses upon IRMOF-1 (also known as MOF-5), and examines the individual H 2 stabilization energies at different sites using Möller–Plessetmore » perturbation theory and density functional theory alongside chemical models that consist of isolated fragment models and a cubic super cell cluster consisting of both the face- and edge-cube’s of IRMOF-1. Optimization of twenty stable configurations of singly adsorbed H 2 in the super-cell cluster is observed to be essential to obtain energy ordering of the five primary sites consistent with experiment and prior benchmark calculations (α >> β > γ > δ ≈ ε). To examine site-to-site interactions that may occur in the high-pressure regime, 64 co-adsorbed H2 within a super-cell cluster have been studied (a theoretical maximum of all adsorption sites, 14 wt %). There, delocalization and/or charge transfer of electrons is observed from the σ orbitals of the H 2 bound at the γ positions into the σ* orbitals of H 2 bound at the α sites leads to stabilization of the interaction of H 2 at the γ, by 1.4 kJ/mol, respectively (using M06-2X/LANL2DZ). Furthermore, this effect has been confirmed to be charge transfer, and not a manifestation of enhanced dispersion at high loading, through natural bond order (NBO) analysis and by comparisons of the square of off-diagonal NBO Fock matrix elements for both density functionals that account for dispersion interactions and Hartree–Fock calculations that ignore dispersion.« less

Structural, electronic and vibrational properties of small GaxNy (x+y = 2 5) nanoclusters: a B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Yadav, P. S.; Yadav, R. K.; Agrawal, B. K.

2007-02-01

An ab initio study of the stability, structural and electronic properties has been made for 49 gallium nitride nanoclusters, GaxNy (x+y = 2-5). Among the various configurations corresponding to a fixed x+y = n value, the configuration possessing the maximum value of binding energy (BE) is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize the geometries of the nanoclusters fully. The binding energies (BEs), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps and the bond lengths have been obtained for all the clusters. We have considered the zero-point energy (ZPE) corrections ignored by the earlier workers. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have been investigated for the most stable structures. The configurations containing the N atoms in majority are seen to be the most stable structures. The strong N-N bond has an important role in stabilizing the clusters. For clusters containing one Ga atom and all the others as N atoms, the BE increases monotonically with the number of the N atoms. The HOMO-LUMO gap and IP fluctuate with the cluster size n, having larger values for the clusters containing odd number of N atoms. On the other hand, the EA decreases with the cluster size up to n = 3, and shows slow fluctuations thereafter for the larger clusters. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA) because of the lower energies of the most stable ground state of the cationic (anionic) clusters. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in experiments.

Static force fields simulations of reduced CeO2 (110) surface: Structure and adsorption of H2O molecule

NASA Astrophysics Data System (ADS)

Vives, Serge; Meunier, Cathy

2018-02-01

The CeO2(110) surface properties are largely involved in the catalysis, energy and biological phenomenon. The Static Force Fields simulations are able to describe large atomic systems surface even if no information on the electronic structure can be obtained. We employ those simulations to study the formation of the neutral 2 CeCe‧ VO•• cluster. We focus on seven different cluster configurations and find that the defect formation energy is the lower for the 1N-2N configurations. Two geometries are possible, as it is the case for the ab initio studies, the in plane and the more stable bridging one. We evidence the modifications of the surface energy and the Potential Energy Surface due to the presence of the 2 CeCe‧ VO•• defect. The physical adsorption of a water molecule is calculated and the geometry described for all the cluster configurations. The H2O molecule physisorption stabilizes the Ce(110) surface and the presence of the 2 CeCe‧ VO•• defect increases this effect.

Automatic provisioning, deployment and orchestration for load-balancing THREDDS instances

NASA Astrophysics Data System (ADS)

Cofino, A. S.; Fernández-Tejería, S.; Kershaw, P.; Cimadevilla, E.; Petri, R.; Pryor, M.; Stephens, A.; Herrera, S.

2017-12-01

THREDDS is a widely used web server to provide to different scientific communities with data access and discovery. Due to THREDDS's lack of horizontal scalability and automatic configuration management and deployment, this service usually deals with service downtimes and time consuming configuration tasks, mainly when an intensive use is done as is usual within the scientific community (e.g. climate). Instead of the typical installation and configuration of a single or multiple independent THREDDS servers, manually configured, this work presents an automatic provisioning, deployment and orchestration cluster of THREDDS servers. This solution it's based on Ansible playbooks, used to control automatically the deployment and configuration setup on a infrastructure and to manage the datasets available in THREDDS instances. The playbooks are based on modules (or roles) of different backends and frontends load-balancing setups and solutions. The frontend load-balancing system enables horizontal scalability by delegating requests to backend workers, consisting in a variable number of instances for the THREDDS server. This implementation allows to configure different infrastructure and deployment scenario setups, as more workers are easily added to the cluster by simply declaring them as Ansible variables and executing the playbooks, and also provides fault-tolerance and better reliability since if any of the workers fail another instance of the cluster can take over it. In order to test the solution proposed, two real scenarios are analyzed in this contribution: The JASMIN Group Workspaces at CEDA and the User Data Gateway (UDG) at the Data Climate Service from the University of Cantabria. On the one hand, the proposed configuration has provided CEDA with a higher level and more scalable Group Workspaces (GWS) service than the previous one based on Unix permissions, improving also the data discovery and data access experience. On the other hand, the UDG has improved its scalability by allowing requests to be distributed to the backend workers instead of being served by a unique THREDDS worker. As a conclusion the proposed configuration supposes a significant improvement with respect to configurations based on non-collaborative THREDDS' instances.

Equalizer: a scalable parallel rendering framework.

PubMed

Eilemann, Stefan; Makhinya, Maxim; Pajarola, Renato

2009-01-01

Continuing improvements in CPU and GPU performances as well as increasing multi-core processor and cluster-based parallelism demand for flexible and scalable parallel rendering solutions that can exploit multipipe hardware accelerated graphics. In fact, to achieve interactive visualization, scalable rendering systems are essential to cope with the rapid growth of data sets. However, parallel rendering systems are non-trivial to develop and often only application specific implementations have been proposed. The task of developing a scalable parallel rendering framework is even more difficult if it should be generic to support various types of data and visualization applications, and at the same time work efficiently on a cluster with distributed graphics cards. In this paper we introduce a novel system called Equalizer, a toolkit for scalable parallel rendering based on OpenGL which provides an application programming interface (API) to develop scalable graphics applications for a wide range of systems ranging from large distributed visualization clusters and multi-processor multipipe graphics systems to single-processor single-pipe desktop machines. We describe the system architecture, the basic API, discuss its advantages over previous approaches, present example configurations and usage scenarios as well as scalability results.

The stabilities and electron structures of Al-Mg clusters with 18 and 20 valence electrons

NASA Astrophysics Data System (ADS)

Yang, Huihui; Chen, Hongshan

2017-07-01

The spherical jellium model predicts that metal clusters having 18 and 20 valence electrons correspond to the magic numbers and will show specific stabilities. We explore in detail the geometric structures, stabilities and electronic structures of Al-Mg clusters containing 18 and 20 valence electrons by using genetic algorithm combined with density functional theories. The stabilities of the clusters are governed by the electronic configurations and Mg/Al ratios. The clusters with lower Mg/Al ratios are more stable. The molecular orbitals accord with the shell structures predicted by the jellium model but the 2S level interweaves with the 1D levels and the 2S and 1D orbitals form a subgroup. The clusters having 20 valence electrons form closed 1S21P61D102S2 shells and show enhanced stability. The Al-Mg clusters with a valence electron count of 18 do not form closed shells because one 1D orbital is unoccupied. The ionization potential and electron affinity are closely related to the electronic configurations; their values are determined by the subgroups the HOMO or LUMO belong to. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80042-9

Close packing of rods on spherical surfaces

NASA Astrophysics Data System (ADS)

Smallenburg, Frank; Löwen, Hartmut

2016-04-01

We study the optimal packing of short, hard spherocylinders confined to lie tangential to a spherical surface, using simulated annealing and molecular dynamics simulations. For clusters of up to twelve particles, we map out the changes in the geometry of the closest-packed configuration as a function of the aspect ratio L/D, where L is the cylinder length and D the diameter of the rods. We find a rich variety of cluster structures. For larger clusters, we find that the best-packed configurations up to around 100 particles are highly dependent on the exact number of particles and aspect ratio. For even larger clusters, we find largely disordered clusters for very short rods (L/D = 0.25), while slightly longer rods (L/D = 0.5 or 1) prefer a global baseball-like geometry of smectic-like domains, similar to the behavior of large-scale nematic shells. Intriguingly, we observe that when compared to their optimal flat-plane packing, short rods adapt to the spherical geometry more efficiently than both spheres and longer rods. Our results provide predictions for experimentally realizable systems of colloidal rods trapped at the interface of emulsion droplets.

Low-lying excited states of model proteins: Performances of the CC2 method versus multireference methods

NASA Astrophysics Data System (ADS)

Ben Amor, Nadia; Hoyau, Sophie; Maynau, Daniel; Brenner, Valérie

2018-05-01

A benchmark set of relevant geometries of a model protein, the N-acetylphenylalanylamide, is presented to assess the validity of the approximate second-order coupled cluster (CC2) method in studying low-lying excited states of such bio-relevant systems. The studies comprise investigations of basis-set dependence as well as comparison with two multireference methods, the multistate complete active space 2nd order perturbation theory (MS-CASPT2) and the multireference difference dedicated configuration interaction (DDCI) methods. First of all, the applicability and the accuracy of the quasi-linear multireference difference dedicated configuration interaction method have been demonstrated on bio-relevant systems by comparison with the results obtained by the standard MS-CASPT2. Second, both the nature and excitation energy of the first low-lying excited state obtained at the CC2 level are very close to the Davidson corrected CAS+DDCI ones, the mean absolute deviation on the excitation energy being equal to 0.1 eV with a maximum of less than 0.2 eV. Finally, for the following low-lying excited states, if the nature is always well reproduced at the CC2 level, the differences on excitation energies become more important and can depend on the geometry.

Low-lying excited states of model proteins: Performances of the CC2 method versus multireference methods.

PubMed

Ben Amor, Nadia; Hoyau, Sophie; Maynau, Daniel; Brenner, Valérie

2018-05-14

A benchmark set of relevant geometries of a model protein, the N-acetylphenylalanylamide, is presented to assess the validity of the approximate second-order coupled cluster (CC2) method in studying low-lying excited states of such bio-relevant systems. The studies comprise investigations of basis-set dependence as well as comparison with two multireference methods, the multistate complete active space 2nd order perturbation theory (MS-CASPT2) and the multireference difference dedicated configuration interaction (DDCI) methods. First of all, the applicability and the accuracy of the quasi-linear multireference difference dedicated configuration interaction method have been demonstrated on bio-relevant systems by comparison with the results obtained by the standard MS-CASPT2. Second, both the nature and excitation energy of the first low-lying excited state obtained at the CC2 level are very close to the Davidson corrected CAS+DDCI ones, the mean absolute deviation on the excitation energy being equal to 0.1 eV with a maximum of less than 0.2 eV. Finally, for the following low-lying excited states, if the nature is always well reproduced at the CC2 level, the differences on excitation energies become more important and can depend on the geometry.

Magnetic anisotropy and chirality of frustrated Cr nanostructures on Au(1 1 1)

NASA Astrophysics Data System (ADS)

Balogh, L.; Udvardi, L.; Szunyogh, L.

2014-10-01

By using a fully relativistic embedded cluster Green's function technique we investigated the magnetic anisotropy properties of four different compact Cr trimers (equilateral triangles) and Cr mono-layers deposited on the Au(1 1 1) surface in both fcc and hcp stackings. For all trimers the magnetic ground state was found to be a frustrated 120° Néel configuration. Applying global spin rotations to the magnetic ground state, predictions of an appropriate second order spin Hamiltonian were reproduced with high accuracy by first principles calculations. For the Cr trimers with adjacent Au atoms in similar geometry, we obtained similar values for the in-plane and out-of-plane anisotropy parameters, however, the Dzyaloshinskii-Moriya (DM) interactions appeared to differ remarkably. For two kinds of trimers we found an unconventional magnetic ground state showing 90° in-the-plane rotation with respect to the high symmetry directions. Due to higher symmetry, the in-plane anisotropy term was missing for the mono-layers and distinctly different DM interactions were obtained for the different stackings. The chiral degeneracy of the Néel configurations was lifted by an energy less than 2 meV for the trimers, while this value increased up to about 15 meV per 3 Cr atoms for the hcp packed mono-layer.

A diagnostic for determining the quality of single-reference electron correlation methods

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Taylor, Peter R.

1989-01-01

It was recently proposed that the Euclidian norm of the t(sub 1) vector of the coupled cluster wave function (normalized by the number of electrons included in the correlation procedure) could be used to determine whether a single-reference-based electron correlation procedure is appopriate. This diagnostic, T(sub 1) is defined for use with self-consistent-field molecular orbitals and is invariant to the same orbital rotations as the coupled cluster energy. T(sub 1) is investigated for several different chemical systems which exhibit a range of multireference behavior, and is shown to be an excellent measure of the importance of non-dynamical electron correlation and is far superior to C(sub 0) from a singles and doubles configuration interaction wave function. It is further suggested that when the aim is to recover a large fraction of the dynamical electron correlation energy, a large T(sub 1) (i.e., greater than 0.02) probably indicates the need for a multireference electron correlation procedure.

A diagnostic for determining the quality of single-reference electron correlation methods

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Taylor, Peter R.

1989-01-01

It was recently proposed that the Euclidian norm of the t sub 1 vector of the coupled cluster wave function (normalized by the number of electrons included in the correlation procedure) could be used to determine whether a single-reference-based electron correlation procedure is appropriate. This diagnostic, T sub 1, is defined for use with self consistent field molecular orbitals and is invariant to the same orbital rotations as the coupled cluster energy. T sub 1 is investigated for several different chemical systems which exhibit a range of multireference behavior, and is shown to be an excellent measure of the importance of nondynamical electron correlation and is far superior to C sub 0 from a singles and doubles configuration interaction wave function. It is further suggested that when the aim is to recover a large fraction of the dynamical electron correlation energy, a large T sub 1 (i.e., greater than 0.02) probably indicates the need for a multireference electron correlation procedure.

Water-chromophore electron transfer determines the photochemistry of cytosine and cytidine.

PubMed

Szabla, Rafał; Kruse, Holger; Šponer, Jiří; Góra, Robert W

2017-07-21

Many of the UV-induced phenomena observed experimentally for aqueous cytidine were lacking the mechanistic interpretation for decades. These processes include the substantial population of the puzzling long-lived dark state, photohydration, cytidine to uridine conversion and oxazolidinone formation. Here, we present quantum-chemical simulations of excited-state spectra and potential energy surfaces of N1-methylcytosine clustered with two water molecules using the second-order approximate coupled cluster (CC2), complete active space with second-order perturbation theory (CASPT2), and multireference configuration interaction with single and double excitation (MR-CISD) methods. We argue that the assignment of the long-lived dark state to a singlet nπ* excitation involving water-chromophore electron transfer might serve as an explanation for the numerous experimental observations. While our simulated spectra for the state are in excellent agreement with experimentally acquired data, the electron-driven proton transfer process occurring on the surface may initiate the subsequent damage in the vibrationally hot ground state of the chromophore.

Universal state-selective corrections to multireference coupled-cluster theories with single and double excitations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brabec, Jiri; van Dam, Hubertus JJ; Pittner, Jiri

2012-03-28

The recently proposed Universal State-Selective (USS) corrections [K. Kowalski, J. Chem. Phys. 134, 194107 (2011)] to approximate Multi-Reference Coupled Cluster (MRCC) energies can be commonly applied to any type of MRCC theory based on the Jeziorski-Monkhorst [B. Jeziorski, H.J. Monkhorst, Phys. Rev. A 24, 1668 (1981)] exponential Ansatz. In this letter we report on the performance of a simple USS correction to the Brillouin-Wigner MRCC (BW-MRCC) formalism employing single and double excitations (BW-MRCCSD). It is shown that the resulting formalism (USS-BW-MRCCSD), which uses the manifold of single and double excitations to construct the correction, can be related to a posteriorimore » corrections utilized in routine BW-MRCCSD calculations. In several benchmark calculations we compare the results of the USS-BW-MRCCSD method with results of the BW-MRCCSD approach employing a posteriori corrections and with results obtained with the Full Configuration Interaction (FCI) method.« less

Supramolecular clusters and chains of 2,6-dimethylpyridine on Cu(110): Observation of dynamic configuration change with real-space surface science techniques and DFT calculations

DOE PAGES

Lee, Junseok; Sorescu, Dan C.; Lee, Jae -Gook; ...

2016-02-02

Here, the adsorption of 2,6-dimethylpyridine (2,6-DMP) on Cu(110) has been studied using low temperature scanning tunneling microscopy (LT-STM), time-of-flight electron stimulated desorption ion angular distribution (TOF-ESDIAD), and density functional theory (DFT) calculations. At low temperatures (T < ~ 150 K), the 2,6-DMP adsorbs in a flat configuration on Cu(110) producing clusters and extended domains via weak hydrogen bonding (C—H···N) with the molecular symmetry axis aligned along the < 001 > surface direction.

Energy levels and exchange interactions of spin clusters

NASA Astrophysics Data System (ADS)

Belorizky, E.

1993-02-01

We first describe a simple method for diagonalizing the isotropic exchange Hamiltonian of a cluster of N spins in the most general case where all the exchange constants are different. The technique, based on the rotation invariance of the system, leads to a considerable reduction of the total matrix. Simple expressions of the magnetization and susceptibility are provided and an example of the determination of the exchange constants of a complex with five Cu^{2+} ions is given. It is also shown that for a large variety of spin configurations occuring in metal complexes, it is possible to diagonalize the dominant isotropic exchange spin hamiltonian in a straightforward way by using recoupling techniques. This allows to solve problems up to a nine spin cluster with spins having different g values. This survey is pursued by the theoretical approach of the magnetic properties of interacting spins on a finite ring with a detailed study of an oligonuclear metal nitroxide complex formed by six Mn^{2+}(S = 5/2) and six free radicals (s = 1/2). The temperature behaviour of the susceptibility is interpreted with a semi-classical model of a cyclic alternate finite chain. Finally we give a procedure for determining the three exchange constants of three spin 1/2 coupled by isotropic exchange constants in the unsolved case where these constants are all dilferent. Nous décrivons d'abord une méthode simple pour diagonaliser l'Hamiltonien d'échange isotrope d'un cluster de N spins dans le cas le plus général où toutes les constantes d'échange sont différentes. La technique, basée sur l'invariance rotationnelle du système, conduit à une réduction considérable de la matrice totale. On donne des expressions simples de l'aimantation et de la susceptibilité et la méthode est appliquée à la détermination des interactions d'échange d'un complexe comprenant cinq ions Cu^{2+}. On montre également que pour une assez grande variété de configurations de spins présentes dans les complexes métalliques, on peut résoudre l'Hamiltonien de spin d'échange isotrope dominant de manière directe par des techniques de recouplage. Ceci permet de traiter des clusters jusqu'à neuf spins, ces derniers pouvant avoir des facteurs g différents. Nous poursuivons cette revue par une étude théorique des propriétés magnétiques de spins en interaction sur un anneau avec une étude détaillée d'un complexe oligonucléaire métal-nitroxyde formé de six ions Mn^{2+}(S = 5/2) et de six radicaux libres (s = 1/2). Le comportement en fonction de la température de la susceptibilité est interprété à l'aide d'un modèle semi-classique de chaine alternée cyclique. Enfin, nous donnons un procédé pour déterminer les trois constantes d'échange d'un système de trois spins 1/2 couplés par échange isotrope dans le cas non résolu où ces trois constantes sont toutes différentes.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

CO2 adsorption on gas-phase Cu4-xPtx (x = 0-4) clusters: a DFT study.

PubMed

Gálvez-González, Luis E; Juárez-Sánchez, J Octavio; Pacheco-Contreras, Rafael; Garzón, Ignacio L; Paz-Borbón, Lauro Oliver; Posada-Amarillas, Alvaro

2018-06-13

Transition and noble metal clusters have proven to be critical novel materials, potentially offering major advantages over conventional catalysts in a range of value-added catalytic processess such as carbon dioxide transformation to methanol. In this work, a systematic computational study of CO2 adsorption on gas-phase Cu4-xPtx (x = 0-4) clusters is performed. An exhaustive potential energy surface exploration is initially performed using our recent density functional theory basin-hopping global optimization implementation. Ground-state and low-lying energy isomers are identified for Cu4-xPtx clusters. Secondly, a CO2 molecule adsorption process is analyzed on the ground-state Cu4-xPtx configurations, as a function of cluster composition. Our results show that the gas-phase linear CO2 molecule is deformed upon adsorption, with its bend angle varying from about 132° to 139°. Cu4-xPtx cluster geometries remain unchanged after CO2 adsorption, with the exception of Cu3Pt1 and Pt4 clusters. For these particular cases, a structural conversion between the ground-state geometry and the corresponding first isomer configurations is found to be assisted by the CO2 adsorption. For all clusters, the energy barriers between the ground-state and first isomer structures are explored. Our calculated CO2 adsorption energies are found to be larger for Pt-rich clusters, exhibiting a volcano-type plot. The overall effect of a hybrid functional including dispersion forces is also discussed.

Measuring the B(E2) of the 1/2- ->3/2- transition in 7 Be

NASA Astrophysics Data System (ADS)

Henderson, S. L.; Ahn, T.; Caprio, M. A.; Constantinou, Ch.; Simon, A.; Twinsol Collaboration

2017-09-01

Ab-initio methods have been successful in describing the structure of light nuclei using realistic nucleon-nucleon interactions, but more experimental data is needed for light unstable nuclei. Recent no-core configuration interaction calculations have made predictions for the ratio of E2 transition strengths for the first excited state transition in 7 Be and 7 Li . Additional calculations that include clustering effects show a significant difference in the 7 Be and 7 Li B(E2) value. The E2 transition strength of the 7 Be first excited state has never been measured, which provides an interesting opportunity to investigate the accuracy of these calculations. To measure this E2 transition strength, a Coulomb Excitation experiment was performed at the University of Notre Dame. 7 Be was produced and separated using TwinSol. A beam of 7 Be ions were scattered off a gold target and the gamma rays from the inelastically scattered ions were detected using six clover Ge detectors. The most recent results for the E2 transition strength and its comparison to the no-core configuration interaction approach will be shown. In addition, new systematic checks on the experiment will be presented including the first stages of a Geant4 simulation to help account for beam anisotropies. This work has been supported by US NSF Grant No. PHY 14-19765 and DOE Grant Number DE-FG02-95ER-40934.

METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Giorgino, Toni; Laio, Alessandro; Rodriguez, Alex

2017-08-01

Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective variables (CVs) along which the dynamics of the system is projected. We developed a graphical user interface (GUI) for facilitating the interactive choice of the appropriate CVs. The GUI allows: defining interactively new CVs; partitioning the configurations into microstates characterized by similar values of the CVs; calculating the free energies of the microstates for both unbiased and biased (metadynamics) simulations; clustering the microstates in kinetic basins; visualizing the free energy landscape as a function of a subset of the CVs used for the analysis. A simple mouse click allows one to quickly inspect structures corresponding to specific points in the landscape.

Calculation of the exchange coupling constants of copper binuclear systems based on spin-flip constricted variational density functional theory.

PubMed

Zhekova, Hristina R; Seth, Michael; Ziegler, Tom

2011-11-14

We have recently developed a methodology for the calculation of exchange coupling constants J in weakly interacting polynuclear metal clusters. The method is based on unrestricted and restricted second order spin-flip constricted variational density functional theory (SF-CV(2)-DFT) and is here applied to eight binuclear copper systems. Comparison of the SF-CV(2)-DFT results with experiment and with results obtained from other DFT and wave function based methods has been made. Restricted SF-CV(2)-DFT with the BH&HLYP functional yields consistently J values in excellent agreement with experiment. The results acquired from this scheme are comparable in quality to those obtained by accurate multi-reference wave function methodologies such as difference dedicated configuration interaction and the complete active space with second-order perturbation theory. © 2011 American Institute of Physics

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

PubMed

Smith, Daniel G A; Burns, Lori A; Sirianni, Dominic A; Nascimento, Daniel R; Kumar, Ashutosh; James, Andrew M; Schriber, Jeffrey B; Zhang, Tianyuan; Zhang, Boyi; Abbott, Adam S; Berquist, Eric J; Lechner, Marvin H; Cunha, Leonardo A; Heide, Alexander G; Waldrop, Jonathan M; Takeshita, Tyler Y; Alenaizan, Asem; Neuhauser, Daniel; King, Rollin A; Simmonett, Andrew C; Turney, Justin M; Schaefer, Henry F; Evangelista, Francesco A; DePrince, A Eugene; Crawford, T Daniel; Patkowski, Konrad; Sherrill, C David

2018-06-11

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

Large-scale atomistic calculations of clusters in intense x-ray pulses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, Phay J.; Knight, Chris

Here, we present the methodology of our recently developed Monte-Carlo/ Molecular-Dynamics method for studying the fundamental ultrafast dynamics induced by high-fluence, high-intensity x-ray free electron laser (XFEL) pulses in clusters. The quantum nature of the initiating ionization process is accounted for by a Monte Carlo method to calculate probabilities of electronic transitions, including photo absorption, inner-shell relaxation, photon scattering, electron collision and recombination dynamics, and thus track the transient electronic configurations explicitly. The freed electrons and ions are followed by classical particle trajectories using a molecular dynamics algorithm. These calculations reveal the surprising role of electron-ion recombination processes that leadmore » to the development of nonuniform spatial charge density profiles in x-ray excited clusters over femtosecond timescales. In the high-intensity limit, it is important to include the recombination dynamics in the calculated scattering response even for a 2- fs pulse. We also demonstrate that our numerical codes and algorithms can make e!cient use of the computational power of massively parallel supercomputers to investigate the intense-field dynamics in systems with increasing complexity and size at the ultrafast timescale and in non-linear x-ray interaction regimes. In particular, picosecond trajectories of XFEL clusters with attosecond time resolution containing millions of particles can be e!ciently computed on upwards of 262,144 processes.« less

Large-scale atomistic calculations of clusters in intense x-ray pulses

DOE PAGES

Ho, Phay J.; Knight, Chris

2017-04-28

Here, we present the methodology of our recently developed Monte-Carlo/ Molecular-Dynamics method for studying the fundamental ultrafast dynamics induced by high-fluence, high-intensity x-ray free electron laser (XFEL) pulses in clusters. The quantum nature of the initiating ionization process is accounted for by a Monte Carlo method to calculate probabilities of electronic transitions, including photo absorption, inner-shell relaxation, photon scattering, electron collision and recombination dynamics, and thus track the transient electronic configurations explicitly. The freed electrons and ions are followed by classical particle trajectories using a molecular dynamics algorithm. These calculations reveal the surprising role of electron-ion recombination processes that leadmore » to the development of nonuniform spatial charge density profiles in x-ray excited clusters over femtosecond timescales. In the high-intensity limit, it is important to include the recombination dynamics in the calculated scattering response even for a 2- fs pulse. We also demonstrate that our numerical codes and algorithms can make e!cient use of the computational power of massively parallel supercomputers to investigate the intense-field dynamics in systems with increasing complexity and size at the ultrafast timescale and in non-linear x-ray interaction regimes. In particular, picosecond trajectories of XFEL clusters with attosecond time resolution containing millions of particles can be e!ciently computed on upwards of 262,144 processes.« less

Molecular dynamics simulation of metal nanoislands growth

NASA Astrophysics Data System (ADS)

Kapralov, N. V.; Babich, E. S.; Redkov, A. V.

2017-11-01

We present the atomistic model and the simulation of a self-assembled growth of a silver nanoisland film and small groups of nanoislands on a glass substrate after thermal poling of the glass with a profiled electrode. The calculations were performed in molecular dynamics simulator LAMMPS taking into account the diffusion of the metal atoms towards and along the glass surface and their clustering. Lennard-Jones potential was used to describe metal-metal and metal-glass interaction. The potential parameters were determined to provide qualitative coincidence of the simulated configurations of the metal nanostructures and the experimental ones, such as an isolated nanoisland, a pair and a set of three nanoislands and a “plasmonic molecule”.

Monte Carlo simulation of Hamaker nanospheres coated with dipolar particles

NASA Astrophysics Data System (ADS)

Meyra, Ariel G.; Zarragoicoechea, Guillermo J.; Kuz, Victor A.

2012-01-01

Parallel tempering Monte Carlo simulation is carried out in systems of N attractive Hamaker spheres dressed with n dipolar particles, able to move on the surface of the spheres. Different cluster configurations emerge for given values of the control parameters. Energy per sphere, pair distribution functions of spheres and dipoles as function of temperature, density, external electric field, and/or the angular orientation of dipoles are used to analyse the state of aggregation of the system. As a consequence of the non-central interaction, the model predicts complex structures like self-assembly of spheres by a double crown of dipoles. This interesting result could be of help in understanding some recent experiments in colloidal science and biology.

Continuous Security and Configuration Monitoring of HPC Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia-Lomeli, H. D.; Bertsch, A. D.; Fox, D. M.

Continuous security and configuration monitoring of information systems has been a time consuming and laborious task for system administrators at the High Performance Computing (HPC) center. Prior to this project, system administrators had to manually check the settings of thousands of nodes, which required a significant number of hours rendering the old process ineffective and inefficient. This paper explains the application of Splunk Enterprise, a software agent, and a reporting tool in the development of a user application interface to track and report on critical system updates and security compliance status of HPC Clusters. In conjunction with other configuration managementmore » systems, the reporting tool is to provide continuous situational awareness to system administrators of the compliance state of information systems. Our approach consisted of the development, testing, and deployment of an agent to collect any arbitrary information across a massively distributed computing center, and organize that information into a human-readable format. Using Splunk Enterprise, this raw data was then gathered into a central repository and indexed for search, analysis, and correlation. Following acquisition and accumulation, the reporting tool generated and presented actionable information by filtering the data according to command line parameters passed at run time. Preliminary data showed results for over six thousand nodes. Further research and expansion of this tool could lead to the development of a series of agents to gather and report critical system parameters. However, in order to make use of the flexibility and resourcefulness of the reporting tool the agent must conform to specifications set forth in this paper. This project has simplified the way system administrators gather, analyze, and report on the configuration and security state of HPC clusters, maintaining ongoing situational awareness. Rather than querying each cluster independently, compliance checking can be managed from one central location.« less

Critical percolation clusters in seven dimensions and on a complete graph

NASA Astrophysics Data System (ADS)

Huang, Wei; Hou, Pengcheng; Wang, Junfeng; Ziff, Robert M.; Deng, Youjin

2018-02-01

We study critical bond percolation on a seven-dimensional hypercubic lattice with periodic boundary conditions (7D) and on the complete graph (CG) of finite volume (number of vertices) V . We numerically confirm that for both cases, the critical number density n (s ,V ) of clusters of size s obeys a scaling form n (s ,V ) ˜s-τn ˜(s /Vdf*) with identical volume fractal dimension df*=2 /3 and exponent τ =1 +1 /df*=5 /2 . We then classify occupied bonds into bridge bonds, which includes branch and junction bonds, and nonbridge bonds; a bridge bond is a branch bond if and only if its deletion produces at least one tree. Deleting branch bonds from percolation configurations produces leaf-free configurations, whereas deleting all bridge bonds leads to bridge-free configurations composed of blobs. It is shown that the fraction of nonbridge (biconnected) bonds vanishes, ρn ,CG→0 , for large CGs, but converges to a finite value, ρn ,7 D=0.006 193 1 (7 ) , for the 7D hypercube. Further, we observe that while the bridge-free dimension dbf*=1 /3 holds for both the CG and 7D cases, the volume fractal dimensions of the leaf-free clusters are different: dlf,7 D *=0.669 (9 ) ≈2 /3 and dlf,CG *=0.3337 (17 ) ≈1 /3 . On the CG and in 7D, the whole, leaf-free, and bridge-free clusters all have the shortest-path volume fractal dimension dmin*≈1 /3 , characterizing their graph diameters. We also study the behavior of the number and the size distribution of leaf-free and bridge-free clusters. For the number of clusters, we numerically find the number of leaf-free and bridge-free clusters on the CG scale as ˜lnV , while for 7D they scale as ˜V . For the size distribution, we find the behavior on the CG is governed by a modified Fisher exponent τ'=1 , while for leaf-free clusters in 7D, it is governed by Fisher exponent τ =5 /2 . The size distribution of bridge-free clusters in 7D displays two-scaling behavior with exponents τ =4 and τ'=1 . The probability distribution P (C1,V ) d C1 of the largest cluster of size C1 for whole percolation configurations is observed to follow a single-variable function P ¯(x ) d x , with x ≡C1/Vdf* for both CG and 7D. Up to a rescaling factor for the variable x , the probability functions for CG and 7D collapse on top of each other within the entire range of x . The analytical expressions in the x →0 and x →∞ limits are further confirmed. Our work demonstrates that the geometric structure of high-dimensional percolation clusters cannot be fully accounted for by their complete-graph counterparts.

Charge dynamics of 57Fe probe atoms in La2Li0.5Cu0.5O4

NASA Astrophysics Data System (ADS)

Presniakov, I. A.; Sobolev, A. V.; Rusakov, V. S.; Moskvin, A. S.; Baranov, A. V.

2018-06-01

The objective of this study is to characterize the electronic state and local surrounding of 57Fe Mössbauer probe atoms within iron-doped layered perovskite La2Li0.5Cu0.5O4 containing transition metal in unusual formal oxidation states "+3". An approach based on the qualitative energy diagrams analysis and the calculations within the cluster configuration interaction method have been developed. It was shown that a large amount of charge is transferred via Cu-O bonds from the O: 2p bands to the Cu: 3d orbitals and the ground state is dominated by the d9L configuration ("Cu2+-O-" state). The dominant d9L ground state for the (CuO6) sublattice induces in the environment of the 57Fe probe cations a charge transfer Fe3+ + O-(L) → Fe4+ + O2-, which transforms "Fe3+" into "Fe4+" state. The experimental spectra in the entire temperature range 77-300 K were described with the use of the stochastic two-level model based on the assumption of dynamic equilibrium between two Fe3+↔Fe4+ valence states related to the iron atom in the [Fe(1)O4]4- center. The relaxation frequencies and activation energies of the corresponding charge fluctuations were estimated based on Mössbauer data. The results are discussed assuming a temperature-induced change in the electronic state of the [CuO4]5- clusters in the layered perovskite.

Role of the magnetosheath in the interaction of magnetic clouds with the Earth's magnetosphere

NASA Astrophysics Data System (ADS)

Fontaine, Dominique; Turc, Lucile; Savoini, Philippe; Modolo, Ronan

2016-04-01

Magnetic clouds are among the most geoeffective solar events capable to trigger strong magnetic storms in the terrestrial magnetosphere. However, their characteristics and those of the surrounding media are not always capable to explain their high level of geoeffectivity. From observations and simulations, we investigate here the role of the bow shock and of the magnetosheath. Conjugated observations upstream (ACE) and downstream (CLUSTER) of the bow shock show that the magnetic clouds' magnetic structure in the magnetosheath can strongly depart from their pristine structure upstream of the bow shock. This modification depends on the shock configuration (quasi-perpendicular, quasi-parallel). We also discuss this question from hybrid simulations of the interaction of magnetic clouds with the bow shock. We show that this interaction may produce unexpected characteristics in the magnetosheath, such as asymmetric distributions of magnetic field, density, temperature, velocity. They thus lead to interactions with the magnetosphere which were not expected from the pristine characteristics of the magnetic clouds in the solar wind upstream of bow shock. We here discuss the effects of such an asymmetric magnetosheath on key parameters for the interaction with the magnetopause (reconnection, instabilities), responsible in turn for the development of geomagnetic activity inside the magnetosphere.

Fast Atom Ionization in Strong Electromagnetic Radiation

NASA Astrophysics Data System (ADS)

Apostol, M.

2018-05-01

The Goeppert-Mayer and Kramers-Henneberger transformations are examined for bound charges placed in electromagnetic radiation in the non-relativistic approximation. The consistent inclusion of the interaction with the radiation field provides the time evolution of the wavefunction with both structural interaction (which ensures the bound state) and electromagnetic interaction. It is shown that in a short time after switching on the high-intensity radiation the bound charges are set free. In these conditions, a statistical criterion is used to estimate the rate of atom ionization. The results correspond to a sudden application of the electromagnetic interaction, in contrast with the well-known ionization probability obtained by quasi-classical tunneling through classically unavailable non-stationary states, or other equivalent methods, where the interaction is introduced adiabatically. For low-intensity radiation the charges oscillate and emit higher-order harmonics, the charge configuration is re-arranged and the process is resumed. Tunneling ionization may appear in these circumstances. Extension of the approach to other applications involving radiation-induced charge emission from bound states is discussed, like ionization of molecules, atomic clusters or proton emission from atomic nuclei. Also, results for a static electric field are included.

Estimate of the neutron fields in ATLAS based on ATLAS-MPX detectors data

NASA Astrophysics Data System (ADS)

Bouchami, J.; Dallaire, F.; Gutiérrez, A.; Idarraga, J.; Král, V.; Leroy, C.; Picard, S.; Pospíšil, S.; Scallon, O.; Solc, J.; Suk, M.; Turecek, D.; Vykydal, Z.; Žemlièka, J.

2011-01-01

The ATLAS-MPX detectors are based on Medipix2 silicon devices designed by CERN for the detection of different types of radiation. These detectors are covered with converting layers of 6LiF and polyethylene (PE) to increase their sensitivity to thermal and fast neutrons, respectively. These devices allow the measurement of the composition and spectroscopic characteristics of the radiation field in ATLAS, particularly of neutrons. These detectors can operate in low or high preset energy threshold mode. The signature of particles interacting in a ATLAS-MPX detector at low threshold are clusters of adjacent pixels with different size and form depending on their type, energy and incidence angle. The classification of particles into different categories can be done using the geometrical parameters of these clusters. The Medipix analysis framework (MAFalda) — based on the ROOT application — allows the recognition of particle tracks left in ATLAS-MPX devices located at various positions in the ATLAS detector and cavern. The pattern recognition obtained from the application of MAFalda was configured to distinguish the response of neutrons from other radiation. The neutron response at low threshold is characterized by clusters of adjoining pixels (heavy tracks and heavy blobs) left by protons and heavy ions resulting from neutron interactions in the converting layers of the ATLAS-MPX devices. The neutron detection efficiency of ATLAS-MPX devices has been determined by the exposure of two detectors of reference to radionuclide sources of neutrons (252Cf and 241AmBe). With these results, an estimate of the neutrons fields produced at the devices locations during ATLAS operation was done.

A proximity-based graph clustering method for the identification and application of transcription factor clusters.

PubMed

Spadafore, Maxwell; Najarian, Kayvan; Boyle, Alan P

2017-11-29

Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, these methods provide no information describing how TFs interact with one another when they do bind. TFs tend to bind the genome in clusters, and current methods to identify these clusters are either limited in scope, unable to detect relationships beyond motif similarity, or not applied to TF-TF interactions. Here, we present a proximity-based graph clustering approach to identify TF clusters using either ChIP-seq or motif search data. We use TF co-occurrence to construct a filtered, normalized adjacency matrix and use the Markov Clustering Algorithm to partition the graph while maintaining TF-cluster and cluster-cluster interactions. We then apply our graph structure beyond clustering, using it to increase the accuracy of motif-based TFBS searching for an example TF. We show that our method produces small, manageable clusters that encapsulate many known, experimentally validated transcription factor interactions and that our method is capable of capturing interactions that motif similarity methods might miss. Our graph structure is able to significantly increase the accuracy of motif TFBS searching, demonstrating that the TF-TF connections within the graph correlate with biological TF-TF interactions. The interactions identified by our method correspond to biological reality and allow for fast exploration of TF clustering and regulatory dynamics.

Restricted random search method based on taboo search in the multiple minima problem

NASA Astrophysics Data System (ADS)

Hong, Seung Do; Jhon, Mu Shik

1997-03-01

The restricted random search method is proposed as a simple Monte Carlo sampling method to search minima fast in the multiple minima problem. This method is based on taboo search applied recently to continuous test functions. The concept of the taboo region instead of the taboo list is used and therefore the sampling of a region near an old configuration is restricted in this method. This method is applied to 2-dimensional test functions and the argon clusters. This method is found to be a practical and efficient method to search near-global configurations of test functions and the argon clusters.

Effect of sharp maximum in ion diffusivity for liquid xenon

NASA Astrophysics Data System (ADS)

Lankin, A. V.; Orekhov, M. A.

2016-11-01

Ion diffusion in a liquid usually could be treated as a movement of an ion cluster in a viscous media. For small ions this leads to a special feature: diffusion coefficient is either independent of the ion size or increases with it. We find a different behavior for small ions in liquid xenon. Calculation of the dependence of an ion diffusion coefficient in liquid xenon on the ion size is carried out. Classical molecular dynamics method is applied. Calculated dependence of the ion diffusion coefficient on its radius has sharp maximums at the ion radiuses 1.75 and 2 Å. Every maximum is placed between two regions with different stable ion cluster configurations. This leads to the instability of these configurations in a small region between them. Consequently ion with radius near 1.75 or 2 Å could jump from one configuration to another. This increases the speed of the diffusion. A simple qualitative model for this effect is suggested. The decomposition of the ion movement into continuous and jump diffusion shows that continuous part of the diffusion is the same as for the ion cluster in the stable region.

Multiconfiguration resonating-group theory of the seven-nucleon system with realistic cluster wave functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujiwara, Y.; Tang, Y.C.

1985-02-01

The properties of the seven-nucleon system are examined with a multiconfiguration and multi- channel resonating-group calculation. The cluster internal functions employed explain the charge-form-factor data over a wide range of q/sup 2/ and satisfy the variational stability condition quite well. The model space used is spanned by /sup 3/H+..cap alpha.., n+ /sup 6/Li, n+ /sup 6/Li(, and d+ /sup 5/He cluster configurations. The result shows that the specific distortion of the /sup 3/H+..cap alpha.. system is quite significant. With our multiconfiguration calculation, the ground-state energy is improved by more than 1 MeV. The calculated level spectrum agrees well with themore » level spectrum empirically determined. The energy positions of both natural-parity and unnatural-parity levels are reasonably explained. In addition, we find that, because of centrifugal-barrier effects, the aligned configuration generally makes the most sig- nificant contribution. The characteristics of nucleon-exchange terms are also briefly examined. Here it is found that, at sufficiently high energies where sharp resonance levels do not exist, the essential properties of these terms can already be learned by performing relatively simple single-configuration calculations.« less

Ab initio coupled-cluster and multi-reference configuration interaction studies of the low-lying electronic states of 1,2,3,4-cyclobutanetetraone

DOE PAGES

Hansen, Jared A.; Bauman, Nicholas P.; Shen, Jun; ...

2015-12-09

In this paper, the four, closely spaced, lowest energy electronic states of the challenging, D 4h-symmetric, 1,2,3,4-cyclobutanetetraone (C 4O 4) molecule have been investigated using high-level ab initio methods. The calculated states include the closed-shell singlet 8π( 1A 1g) state, the singlet 10π( 1A 1g) state, in which the π-type lowest unoccupied molecular orbital (LUMO) of the 8π( 1A 1g) reference is doubly occupied and the σ-type highest occupied molecular orbital (HOMO) is empty, and the open-shell singlet and triplet states, designated as 9π( 1B 2u) and 9π( 3B 2u), respectively, originating from single occupancy of the HOMO and LUMO.more » Our focus is on single-reference coupled-cluster (CC) approaches capable of handling electronic near-degeneracies in diradicals, especially the completely renormalised CR-CC(2,3) and active-space CCSDt methods, along with their CCSD and EOMCCSD counterparts. The internally contracted multi-reference configuration interaction calculations with a quasi-degenerate Davidson correction are performed as well. Our computations demonstrate that the state ordering is 9π( 3B 2u) < 8π( 1A 1g) < 9π( 1B 2u) < 10π( 1A 1g) and that the 8π( 1A 1g) - 9π( 3B 2u) gap is in the 7–11 kJ/mol range, in reasonable agreement with the negative ion photoelectron spectroscopy measurements, which give 6.27 ± 0.5 kJ/mol. Finally, in addition to the theory level used, geometry relaxation and basis set play a significant role in determining the state ordering and energy spacings. In particular, it is unsafe to use lower level, non-CC geometries and smaller basis sets.« less

Near-infrared absorption in symmetric squarylium and croconate dyes: a comparative study using symmetry-adapted cluster-configuration interaction methods.

PubMed

Prabhakar, Ch; Yesudas, K; Krishna Chaitanya, G; Sitha, Sanyasi; Bhanuprakash, K; Rao, V Jayathirtha

2005-09-29

Symmetric croconate (CR) and squarylium dyes (SQ) are well-known near-infrared (NIR) dyes and, in general, are considered to be donor-acceptor-donor type molecules. It is established in the literature that CR dyes absorb in a longer wavelength region than the corresponding SQ dyes. This has been attributed to the CR ring being a better acceptor than the SQ ring. Thus increasing the donor capacity should lead to a bathochromic shift in both SQ and CR. On the other hand, some experiments reported in the literature have revealed that increasing the conjugation in the donor part of the SQ molecule leads first to red shift, which upon a further increase of the conjugation changes to a blue shift. Hence, to understand the role of the central ring and the substitutions in the absorption of these dyes, we carried out high-level symmetry-adapted cluster-configuration interaction (SAC-CI) calculations of some substituted SQ and CR dyes and compare the absorption energy with the existing experimental data. We found that there is very good agreement. We also carried out SAC-CI calculations of some smaller model molecules, which contain the main oxyallyl substructure. We varied the geometry (angle) of the oxyallyl subgroup and the substitution in these model molecules to establish a correlation with the bathochromic shift. We found that the charge transfer is very small and does not play the key role in the red shift, but on the other hand, the perturbation of the HOMO-LUMO gap (HLG) from both the geometry and substitution seems to be responsible for this shift. We suggest as a design principle that increasing the donor capacity of the groups may not help in the red shift, but introducing groups which perturb the HLG and decrease it without changing the MO character should lead to a larger bathochromic shift.

Interpersonal Competence Configurations and Peer Relations in Early Elementary Classrooms: Perceived Popular and Unpopular Aggressive Subtypes

ERIC Educational Resources Information Center

Robertson, Dylan L.; Farmer, Thomas W.; Fraser, Mark W.; Day, Steven H.; Duncan, Tisha; Crowther, Amity; Dadisman, Kimberly A.

2010-01-01

Social relations of second grade students (247 boys, 290 girls) were examined in rural elementary classrooms. Cluster analysis of teacher ratings was used to identify interpersonal competence configurations including perceived unpopular-aggressive (i.e., "Troubled") and perceived popular-aggressive (i.e., "Tough") subtypes for…

Structure and Electronic Properties of Ionized PAH Clusters

NASA Astrophysics Data System (ADS)

Joblin, Christine; Kokkin, Damian L.; Sabbah, Hassan; Bonnamy, Anthony; Dontot, Leo; Rapacioli, Mathias; Simon, Aude; Spiegelman, Fernand; Parneix, Pascal; Pino, Thomas; Pirali, Olivier; Falvo, Cyril; Gamboa, Antonio; Brechignac, Philippe; Garcia, Gustavo A.; Nahon, Laurent

2014-06-01

Polycyclic aromatic hydrocarbon (PAH) clusters have been proposed as candidates for evaporating very small grains that are revealed by their mid-IR emission at the surface of UV-irradiated clouds in interstellar space. This suggestion is a motivation for further characterization of the properties of these clusters in particular when they are ionized. We have used a molecular beam coupled to the photoelectron-photoion coincidence spectrometer DELICIOUS II/ III at the VUV beamline DESIRS of the synchrotron SOLEIL to characterize the electronic properties of cationic coronene (C24H12) and pyrene (C16H10) clusters up to the pentamer and heptamer, respectively. These experimental results are analysed in the light of electronic structure calculations. Simulations of the properties of ionized PAH clusters are faced with the difficulty of describing charge delocalization in these large systems. We will show that recent developments combining a Density Functional Tight Binding method with Configuration Interaction scheme is successful in simulating the ionization potential, which gives strong confidence into the predicted structures for these PAH clusters. We will also present current effort to study charge transfer states by performing complementary measurements with the PIRENEA ion trap set-up. Joint ANR project GASPARIM, ANR-10-BLAN-501 M. Rapacioli, C. Joblin and P. Boissel Astron. & Astrophys., 429 (2005), 193-204. G. Garcia, H. Soldi-Lose and L. Nahon Rev. Sci. Instrum., 80 (2009), 023102; G. Garcia, B. Cunha de Miranda, M. Tia, S. Daly, L. Nahon, Rev. Sci. Instrum., 84 (2013), 053112 M. Rapacioli, A. Simon, L. Dontot and F. Spiegelman Phys. Status Solidi B, 249 (2) (2012), 245-258; L. Dontot, M. Rapacioli and F. Spiegelman (2014) submitted

A Density Functional Theory Investigation of Nin , Pdn , and Ptn Clusters (n=1-4) Adsorbed on Buckminsterfullerene.

PubMed

Pham, Nguyet N T; Le, Hung M

2017-05-19

In this study, we examine the adsorptions of Ni, Pd, and Pt clusters on C 60 by using a computational approach. Our calculation results show that the base structure of C 60 can host Ni n /Pd n /Pt n (n=1-4) clusters with good adsorption stability and the complexes establish either two or no unpaired electrons. The binding energy of Pd and Pt clusters increases as the number of metal atoms increases, implying that the coverage of C 60 with Pd or Pt preferentially establishes a large-size metal cluster. A single metal atom favorably occupies the C-C bridge site. For dimer clusters, the three metals of interest share a similar binding fashion, in which two metal atoms establish direct interactions with the C-C bridge sites. For trimer adsorptions, the formation of linear and triangular structures is observed. Both Pt 3 and Ni 3 preferably constitute isosceles triangles on C 60 , whilst Pd 3 favorably establishes a linear shape. Finally, for each of the Ni 4 and Pd 4 adsorption cases, we observed three stable binding configurations: rhombus, tetrahedron, and Y-form. Whereas Ni 4 establishes a tetrahedral form, Pd 4 attains the most stable form with the Y-shape geometry on C 60 . Overall, we observe that the trend of Pd binding to C 60 tends to go beyond the fashion of Ni and Pt. In terms of magnetic alignment, the Pd n -C 60 systems seem to be non-magnetic in most cases, unlike the Ni and Pt cases, the structures of which possess magnetic moments of 2 μB in their most stable forms. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unified method of knowledge representation in the evolutionary artificial intelligence systems

NASA Astrophysics Data System (ADS)

Bykov, Nickolay M.; Bykova, Katherina N.

2003-03-01

The evolution of artificial intelligence systems called by complicating of their operation topics and science perfecting has resulted in a diversification of the methods both the algorithms of knowledge representation and usage in these systems. Often by this reason it is very difficult to design the effective methods of knowledge discovering and operation for such systems. In the given activity the authors offer a method of unitized representation of the systems knowledge about objects of an external world by rank transformation of their descriptions, made in the different features spaces: deterministic, probabilistic, fuzzy and other. The proof of a sufficiency of the information about the rank configuration of the object states in the features space for decision making is presented. It is shown that the geometrical and combinatorial model of the rank configurations set introduce their by group of some system of incidence, that allows to store the information on them in a convolute kind. The method of the rank configuration description by the DRP - code (distance rank preserving code) is offered. The problems of its completeness, information capacity, noise immunity and privacy are reviewed. It is shown, that the capacity of a transmission channel for such submission of the information is more than unit, as the code words contain the information both about the object states, and about the distance ranks between them. The effective algorithm of the data clustering for the object states identification, founded on the given code usage, is described. The knowledge representation with the help of the rank configurations allows to unitize and to simplify algorithms of the decision making by fulfillment of logic operations above the DRP - code words. Examples of the proposed clustering techniques operation on the given samples set, the rank configuration of resulted clusters and its DRP-codes are presented.

A neural-network potential through charge equilibration for WS2: From clusters to sheets

NASA Astrophysics Data System (ADS)

Hafizi, Roohollah; Ghasemi, S. Alireza; Hashemifar, S. Javad; Akbarzadeh, Hadi

2017-12-01

In the present work, we use a machine learning method to construct a high-dimensional potential for tungsten disulfide using a charge equilibration neural-network technique. A training set of stoichiometric WS2 clusters is prepared in the framework of density functional theory. After training the neural-network potential, the reliability and transferability of the potential are verified by performing a crystal structure search on bulk phases of WS2 and by plotting energy-area curves of two different monolayers. Then, we use the potential to investigate various triangular nano-clusters and nanotubes of WS2. In the case of nano-structures, we argue that 2H atomic configurations with sulfur rich edges are thermodynamically more stable than the other investigated configurations. We also studied a number of WS2 nanotubes which revealed that 1T tubes with armchair chirality exhibit lower bending stiffness.

Equation-of-motion coupled-cluster method for ionised states with spin-orbit coupling using open-shell reference wavefunction

NASA Astrophysics Data System (ADS)

Wang, Zhifan; Wang, Fan

2018-04-01

The equation-of-motion coupled-cluster method for ionised states at the singles and doubles level (EOM-IP-CCSD) with spin-orbit coupling (SOC) included in post-Hartree-Fock (HF) steps is extended to spatially non-degenerate open-shell systems such as high spin states of s1, p3, σ1 or π2 configuration in this work. Pseudopotentials are employed to treat relativistic effects and spin-unrestricted scalar relativistic HF determinant is adopted as reference in calculations. Symmetry is not exploited in the implementation since both time-reversal and spatial symmetry is broken due to SOC. IPs with the EOM-IP-CCSD approach are those from the 3Σ1- states for high spin state of π2 configuration, while the ground state is the 3Σ0- state. When removing an electron from the high spin state of p3 configuration, only the 3P2 state can be reached. The open-shell EOM-IP-CCSD approach with SOC was employed in calculating IPs of some open-shell atoms with s1 configuration, diatomic molecules with π2 configuration and SOC splitting of the ionised π1 state, as well as IPs of VA atoms with p3 configuration. Our results demonstrate that this approach can be applied to ionised states of spatially non-degenerate open-shell states containing heavy elements with reasonable accuracy.

Density functional study of hypophosphite adsorption on Ni (1 1 1) and Cu (1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Zeng, Yue; Liu, Shubin; Ou, Lihui; Yi, Jianlong; Yu, Shanci; Wang, Huixian; Xiao, Xiaoming

2006-02-01

Surface structures and electronic properties of hypophosphite, H 2PO 2-, molecularly adsorbed on Ni(1 1 1) and Cu(1 1 1) surfaces are investigated in this work by density functional theory at B3LYP/6-31++g(d, p) level. We employ a four-metal-atom cluster as the simplified model for the surface and have fully optimized the geometry and orientation of H 2PO 2- on the metal cluster. Six stable orientations have been discovered on both Ni (1 1 1) and Cu (1 1 1) surfaces. The most stable orientation of H 2PO 2- was found to have its two oxygen atoms interact the surface with two P sbnd O bonds pointing downward. Results of the Mulliken population analysis showed that the back donation from 3d orbitals of the transition metal substrate to the unfilled 3d orbital of the phosphorus atom in H 2PO 2- and 4s orbital's acceptance of electron donation from one lone pair of the oxygen atom in H 2PO 2- play very important roles in the H 2PO 2- adsorption on the transition metals. The averaged electron configuration of Ni in Ni 4 cluster is 4s 0.634p 0.023d 9.35 and that of Cu in Cu 4 cluster is 4s 1.004p 0.033d 9.97. Because of this subtle difference of electron configuration, the adsorption energy is larger on the Ni surface than on the Cu surface. The amount of charge transfers due to above two donations is larger from H 2PO 2- to the Ni surface than to the Cu surface, leading to a more positively charged P atom in Ni nH 2PO 2- than in Cu nH 2PO 2-. These results indicate that the phosphorus atom in Ni nH 2PO 2- complex is easier to be attacked by a nucleophile such as OH - and subsequent oxidation of H 2PO 2- can take place more favorably on Ni substrate than on Cu substrate.

A Wide-Field Photometric Survey for Extratidal Tails Around Five Metal-Poor Globular Clusters in the Galactic Halo

NASA Astrophysics Data System (ADS)

Chun, Sang-Hyun; Kim, Jae-Woo; Sohn, Sangmo T.; Park, Jang-Hyun; Han, Wonyong; Kim, Ho-Il; Lee, Young-Wook; Lee, Myung Gyoon; Lee, Sang-Gak; Sohn, Young-Jong

2010-02-01

Wide-field deep g'r'i' images obtained with the Megacam of the Canada-France-Hawaii Telescope are used to investigate the spatial configuration of stars around five metal-poor globular clusters M15, M30, M53, NGC 5053, and NGC 5466, in a field-of-view ~3°. Applying a mask filtering algorithm to the color-magnitude diagrams of the observed stars, we sorted cluster's member star candidates that are used to examine the characteristics of the spatial stellar distribution surrounding the target clusters. The smoothed surface density maps and the overlaid isodensity contours indicate that all of the five metal-poor globular clusters exhibit strong evidence of extratidal overdensity features over their tidal radii, in the form of extended tidal tails around the clusters. The orientations of the observed extratidal features show signatures of tidal tails tracing the clusters' orbits, inferred from their proper motions, and effects of dynamical interactions with the Galaxy. Our findings include detections of a tidal bridge-like feature and an envelope structure around the pair of globular clusters M53 and NGC 5053. The observed radial surface density profiles of target clusters have a deviation from theoretical King models, for which the profiles show a break at 0.5-0.7rt , extending the overdensity features out to 1.5-2rt . Both radial surface density profiles for different angular sections and azimuthal number density profiles confirm the overdensity features of tidal tails around the five metal-poor globular clusters. Our results add further observational evidence that the observed metal-poor halo globular clusters originate from an accreted satellite system, indicative of the merging scenario of the formation of the Galactic halo. Based on observations carried out at the Canada-France-Hawaii Telescope, operated by the National Research Council of Canada, the Centre National de la Recherche Scientifique de France, and the University of Hawaii. This is part of the Searching for the Galactic Halo project using the CFHT, organized by the Korea Astronomy and Space Science Institute.

Propulsion and airframe aerodynamic interactions of supersonic V/STOL configurations, phase 1

NASA Technical Reports Server (NTRS)

Mraz, M. R.; Hiley, P. E.

1985-01-01

A wind tunnel model of a supersonic V/STOL fighter configuration has been tested to measure the aerodynamic interaction effects which can result from geometrically close-coupled propulsion system/airframe components. The approach was to configure the model to present two different test techniques. One was a coventional test technique composed of two test modes. In the Flow-Through mode, absolute configuration aerodynamics are measured, including inlet/airframe interactions. In the Jet-Effects mode, incremental nozzle/airframe interactions are measured. The other test technique is a propulsion simulator approach, where a subscale, externally powered engine is mounted in the model. This allows proper measurement of inlet/airframe and nozzle/airframe interactions simultaneously.

Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability.

PubMed

Parrish, Robert M; Burns, Lori A; Smith, Daniel G A; Simmonett, Andrew C; DePrince, A Eugene; Hohenstein, Edward G; Bozkaya, Uğur; Sokolov, Alexander Yu; Di Remigio, Roberto; Richard, Ryan M; Gonthier, Jérôme F; James, Andrew M; McAlexander, Harley R; Kumar, Ashutosh; Saitow, Masaaki; Wang, Xiao; Pritchard, Benjamin P; Verma, Prakash; Schaefer, Henry F; Patkowski, Konrad; King, Rollin A; Valeev, Edward F; Evangelista, Francesco A; Turney, Justin M; Crawford, T Daniel; Sherrill, C David

2017-07-11

Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements.

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

Configuration and Management of a Cluster Computing Facility in Undergraduate Student Computer Laboratories

ERIC Educational Resources Information Center

Cornforth, David; Atkinson, John; Spennemann, Dirk H. R.

2006-01-01

Purpose: Many researchers require access to computer facilities beyond those offered by desktop workstations. Traditionally, these are offered either through partnerships, to share the cost of supercomputing facilities, or through purpose-built cluster facilities. However, funds are not always available to satisfy either of these options, and…

Photodissociation spectroscopy of the dysprosium monochloride molecular ion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunning, Alexander, E-mail: alexander.dunning@gmail.com; Schowalter, Steven J.; Puri, Prateek

2015-09-28

We have performed a combined experimental and theoretical study of the photodissociation cross section of the molecular ion DyCl{sup +}. The photodissociation cross section for the photon energy range 35 500 cm{sup −1} to 47 500 cm{sup −1} is measured using an integrated ion trap and time-of-flight mass spectrometer; we observe a broad, asymmetric profile that is peaked near 43 000 cm{sup −1}. The theoretical cross section is determined from electronic potentials and transition dipole moments calculated using the relativistic configuration-interaction valence-bond and coupled-cluster methods. The electronic structure of DyCl{sup +} is extremely complex due to the presence of multiple open electronic shells,more » including the 4f{sup 10} configuration. The molecule has nine attractive potentials with ionically bonded electrons and 99 repulsive potentials dissociating to a ground state Dy{sup +} ion and Cl atom. We explain the lack of symmetry in the cross section as due to multiple contributions from one-electron-dominated transitions between the vibrational ground state and several resolved repulsive excited states.« less

Ion Mobility Mass Spectrometry Analysis of Isomeric Disaccharide Precursor, Product and Cluster Ions

PubMed Central

Li, Hongli; Bendiak, Brad; Siems, William F.; Gang, David R.; Hill, Herbert H.

2015-01-01

RATIONALE Carbohydrates are highly variable in structure owing to differences in their anomeric configurations, monomer stereochemistry, inter-residue linkage positions and general branching features. The separation of carbohydrate isomers poses a great challenge for current analytical techniques. METHODS The isomeric heterogeneity of disaccharide ions and monosaccharideglycolaldehyde product ions evaluated using electrospray traveling wave ion mobility mass spectrometry (Synapt G2 high definition mass spectrometer) in both positive and negative ion modes investigation. RESULTS The separation of isomeric disaccharide ions was observed but not fully achieved based on their mobility profiles. The mobilities of isomeric product ions, the monosaccharide-glycolaldehydes, derived from different disaccharide isomers were measured. Multiple mobility peaks were observed for both monosaccharide-glycolaldehyde cations and anions, indicating that there was more than one structural configuration in the gas phase as verified by NMR in solution. More importantly, the mobility patterns for isomeric monosaccharide-glycolaldehyde product ions were different, which enabled partial characterization of their respective disaccharide ions. Abundant disaccharide cluster ions were also observed. The Results showed that a majority of isomeric cluster ions had different drift times and, moreover, more than one mobility peak was detected for a number of specific cluster ions. CONCLUSIONS It is demonstrated that ion mobility mass spectrometry is an advantageous method to assess the isomeric heterogeneity of carbohydrate compounds. It is capable of differentiating different types of carbohydrate ions having identical m/z values as well as multiple structural configurations of single compounds. PMID:24591031

Towards an Autonomic Cluster Management System (ACMS) with Reflex Autonomicity

NASA Technical Reports Server (NTRS)

Truszkowski, Walt; Hinchey, Mike; Sterritt, Roy

2005-01-01

Cluster computing, whereby a large number of simple processors or nodes are combined together to apparently function as a single powerful computer, has emerged as a research area in its own right. The approach offers a relatively inexpensive means of providing a fault-tolerant environment and achieving significant computational capabilities for high-performance computing applications. However, the task of manually managing and configuring a cluster quickly becomes daunting as the cluster grows in size. Autonomic computing, with its vision to provide self-management, can potentially solve many of the problems inherent in cluster management. We describe the development of a prototype Autonomic Cluster Management System (ACMS) that exploits autonomic properties in automating cluster management and its evolution to include reflex reactions via pulse monitoring.

A new EEG measure using the 1D cluster variation method

NASA Astrophysics Data System (ADS)

Maren, Alianna J.; Szu, Harold H.

2015-05-01

A new information measure, drawing on the 1-D Cluster Variation Method (CVM), describes local pattern distributions (nearest-neighbor and next-nearest neighbor) in a binary 1-D vector in terms of a single interaction enthalpy parameter h for the specific case where the fractions of elements in each of two states are the same (x1=x2=0.5). An example application of this method would be for EEG interpretation in Brain-Computer Interfaces (BCIs), especially in the frontier of invariant biometrics based on distinctive and invariant individual responses to stimuli containing an image of a person with whom there is a strong affiliative response (e.g., to a person's grandmother). This measure is obtained by mapping EEG observed configuration variables (z1, z2, z3 for next-nearest neighbor triplets) to h using the analytic function giving h in terms of these variables at equilibrium. This mapping results in a small phase space region of resulting h values, which characterizes local pattern distributions in the source data. The 1-D vector with equal fractions of units in each of the two states can be obtained using the method for transforming natural images into a binarized equi-probability ensemble (Saremi & Sejnowski, 2014; Stephens et al., 2013). An intrinsically 2-D data configuration can be mapped to 1-D using the 1-D Peano-Hilbert space-filling curve, which has demonstrated a 20 dB lower baseline using the method compared with other approaches (cf. SPIE ICA etc. by Hsu & Szu, 2014). This CVM-based method has multiple potential applications; one near-term one is optimizing classification of the EEG signals from a COTS 1-D BCI baseball hat. This can result in a convenient 3-D lab-tethered EEG, configured in a 1-D CVM equiprobable binary vector, and potentially useful for Smartphone wireless display. Longer-range applications include interpreting neural assembly activations via high-density implanted soft, cellular-scale electrodes.

CI+MBPT calculations of Ar I energies, g factors, and transition line strengths

NASA Astrophysics Data System (ADS)

Savukov, I. M.

2018-03-01

Excited states of noble gas atoms present certain challenges to atomic theory for several reasons: first, relativistic effects are important and LS coupling is not optimal; second, energy intervals can be quite small, leading to strong mixing of states; third, many-body perturbation theory for hole states does not converge well. Previously, some attempts were made to solve this problem, using for example the all-order coupled-cluster approach and particle-hole configuration-interaction many-body perturbation theory (CI-MBPT) with modified denominators. However, while these approaches were promising, the accuracy was still limited. In this paper, we calculate Ar I energies, g factors, and transition amplitudes using ab initio CI-MBPT with eight valence electrons to avoid the problem of slow convergence of MBPT due to strong interaction between 3p and 3s states. We also included in CI many dominant states obtained by double excitations of the ground state configuration. Thus perturbation corrections were needed only for 1s, 2s, 2p core electrons non-included in valence-valence CI, which are quite small. We found that energy, g factors, and electric dipole matrix elements are in reasonable agreement with experiments. It is noteworthy that the theory agreed well with accurately measured g factors. Experimental oscillator strengths have large uncertainty, so in some cases we made a comparison with average values.

Complete active space configuration interaction from state-averaged configuration interaction singles natural orbitals: Analytic first derivatives and derivative coupling vectors

NASA Astrophysics Data System (ADS)

Fales, B. Scott; Shu, Yinan; Levine, Benjamin G.; Hohenstein, Edward G.

2017-09-01

A new complete active space configuration interaction (CASCI) method was recently introduced that uses state-averaged natural orbitals from the configuration interaction singles method (configuration interaction singles natural orbital CASCI, CISNO-CASCI). This method has been shown to perform as well or better than state-averaged complete active space self-consistent field for a variety of systems. However, further development and testing of this method have been limited by the lack of available analytic first derivatives of the CISNO-CASCI energy as well as the derivative coupling between electronic states. In the present work, we present a Lagrangian-based formulation of these derivatives as well as a highly efficient implementation of the resulting equations accelerated with graphical processing units. We demonstrate that the CISNO-CASCI method is practical for dynamical simulations of photochemical processes in molecular systems containing hundreds of atoms.

Complete active space configuration interaction from state-averaged configuration interaction singles natural orbitals: Analytic first derivatives and derivative coupling vectors.

PubMed

Fales, B Scott; Shu, Yinan; Levine, Benjamin G; Hohenstein, Edward G

2017-09-07

A new complete active space configuration interaction (CASCI) method was recently introduced that uses state-averaged natural orbitals from the configuration interaction singles method (configuration interaction singles natural orbital CASCI, CISNO-CASCI). This method has been shown to perform as well or better than state-averaged complete active space self-consistent field for a variety of systems. However, further development and testing of this method have been limited by the lack of available analytic first derivatives of the CISNO-CASCI energy as well as the derivative coupling between electronic states. In the present work, we present a Lagrangian-based formulation of these derivatives as well as a highly efficient implementation of the resulting equations accelerated with graphical processing units. We demonstrate that the CISNO-CASCI method is practical for dynamical simulations of photochemical processes in molecular systems containing hundreds of atoms.

Anisotropic orbital occupation and Jahn-Teller distortion of orthorhombic YMnO{sub 3} epitaxial films: A combined experimental and theoretical study on polarization-dependent x-ray absorption spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haw, Shu-Chih; Chen, Shin-Ann; National Synchrotron Radiation Research Center

2014-04-21

The b-axis oriented orthorhombic YMnO{sub 3} (o-YMnO{sub 3}) epitaxial films on a YAlO{sub 3} (010) substrate were fabricated with pulsed-laser deposition. The anisotropic orbital occupation and Jahn-Teller (JT) distortion of an o-YMnO{sub 3} film were investigated with polarization-dependent x-ray absorption spectra and configuration-interaction multiplet-cluster calculations. A significant energy difference, ∼3.8 eV, for the main white line along E//b and E//a in polarization-dependent Mn K-edge spectra of o-YMnO{sub 3} indicates an extraordinary JT distortion and significant anisotropic Mn–O bonding within the ab plane in the o-YMnO{sub 3} film. Most importantly, although the orbital occupation of 3d electrons in o-YMnO{sub 3} filmsmore » is almost the same as that in single crystalline o-DyMnO{sub 3}, the JT distortion of o-YMnO{sub 3} films is larger than that of single crystalline o-DyMnO{sub 3}, deduced from the multiplet calculations. We speculate that this JT distortion predominantly contributes to the origin of the cycloidal spin deformation in bulk o-YMnO{sub 3}, because of a suppressed nearest-neighbor superexchange interaction and an enhanced next-nearest-neighbor superexchange interaction. These complementary results provide insight into the origin of the E-type magnetic configuration of o-YMnO{sub 3}.« less

Energy-consistent small-core pseudopotentials for 3d-transition metals adapted to quantum Monte Carlo calculations.

PubMed

Burkatzki, M; Filippi, Claudia; Dolg, M

2008-10-28

We extend our recently published set of energy-consistent scalar-relativistic Hartree-Fock pseudopotentials by the 3d-transition metal elements, scandium through zinc. The pseudopotentials do not exhibit a singularity at the nucleus and are therefore suitable for quantum Monte Carlo (QMC) calculations. The pseudopotentials and the accompanying basis sets (VnZ with n=T,Q) are given in standard Gaussian representation and their parameter sets are presented. Coupled cluster, configuration interaction, and QMC studies are carried out for the scandium and titanium atoms and their oxides, demonstrating the good performance of the pseudopotentials. Even though the choice of pseudopotential form is motivated by QMC, these pseudopotentials can also be employed in other quantum chemical approaches.

Ab initio potential energy and dipole moment surfaces of the F(-)(H2O) complex.

PubMed

Kamarchik, Eugene; Toffoli, Daniele; Christiansen, Ove; Bowman, Joel M

2014-02-05

We present full-dimensional, ab initio potential energy and dipole moment surfaces for the F(-)(H2O) complex. The potential surface is a permutationally invariant fit to 16,114 coupled-cluster single double (triple)/aVTZ energies, while the dipole surface is a covariant fit to 11,395 CCSD(T)/aVTZ dipole moments. Vibrational self-consistent field/vibrational configuration interaction (VSCF/VCI) calculations of energies and the IR-spectrum are presented both for F(-)(H2O) and for the deuterated analog, F(-)(D2O). A one-dimensional calculation of the splitting of the ground state, due to equivalent double-well global minima, is also reported. Copyright © 2013 Elsevier B.V. All rights reserved.

[Parallel virtual reality visualization of extreme large medical datasets].

PubMed

Tang, Min

2010-04-01

On the basis of a brief description of grid computing, the essence and critical techniques of parallel visualization of extreme large medical datasets are discussed in connection with Intranet and common-configuration computers of hospitals. In this paper are introduced several kernel techniques, including the hardware structure, software framework, load balance and virtual reality visualization. The Maximum Intensity Projection algorithm is realized in parallel using common PC cluster. In virtual reality world, three-dimensional models can be rotated, zoomed, translated and cut interactively and conveniently through the control panel built on virtual reality modeling language (VRML). Experimental results demonstrate that this method provides promising and real-time results for playing the role in of a good assistant in making clinical diagnosis.

Stochastic annealing simulations of defect interactions among subcascades

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heinisch, H.L.; Singh, B.N.

1997-04-01

The effects of the subcascade structure of high energy cascades on the temperature dependencies of annihilation, clustering and free defect production are investigated. The subcascade structure is simulated by closely spaced groups of lower energy MD cascades. The simulation results illustrate the strong influence of the defect configuration existing in the primary damage state on subsequent intracascade evolution. Other significant factors affecting the evolution of the defect distribution are the large differences in mobility and stability of vacancy and interstitial defects and the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. Annealing simulations are also performedmore » on high-energy, subcascade-producing cascades generated with the binary collision approximation and calibrated to MD results.« less

Characterization of the Minimum Energy Paths and Energetics for the Reaction of Vinylidene with Acetylene

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Taylor, Peter R.

1995-01-01

The reaction of vinylidene (CH2C) with acetylene may be an initiating reaction in soot formation. We report minimum energy paths and accurate energetics for a pathway leading to vinyl-acetylene and for a number of isomers of C4H4. The calculations use complete active space self-consistent field (CASSCF) derivative methods to characterize the stationary points and internally contacted configuration interaction (ICCI) and/or coupled cluster singles and doubles with a perturbational estimate of triple excitations (CCSD(T)) to determine the energetics. We find an entrance channel barrier of about 5 kcal/mol for the addition of vinylidene to acetylene, but no barriers above reactants for the reaction pathway leading to vinyl-acetylene.

Characterization of the Minimum Energy Paths and Energetics for the reaction of Vinylidene with Acetylene

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Taylor, Peter R.

1995-01-01

The reaction of vinylidene (CH2C) with acetylene may be an initiating reaction in soot formation. We report minimum energy paths and accurate energetics for a pathway leading to vinylacetylene and for a number of isomers Of C4H4. The calculations use complete active space self-consistent field (CASSCF) derivative methods to characterize the stationary points and internally contacted configuration interaction (ICCI) and/or coupled cluster singles and doubles with a perturbational estimate of triple excitations (CCSD(T)) to determine the energetics. We find an entrance channel barrier of about 5 kcal/mol for the addition of vinylidene to acetylene, but no barriers above reactants for the reaction pathway leading to vinylacetylene.

Experimental Tests of the Algebraic Cluster Model

NASA Astrophysics Data System (ADS)

Gai, Moshe

2018-02-01

The Algebraic Cluster Model (ACM) of Bijker and Iachello that was proposed already in 2000 has been recently applied to 12C and 16O with much success. We review the current status in 12C with the outstanding observation of the ground state rotational band composed of the spin-parity states of: 0+, 2+, 3-, 4± and 5-. The observation of the 4± parity doublet is a characteristic of (tri-atomic) molecular configuration where the three alpha- particles are arranged in an equilateral triangular configuration of a symmetric spinning top. We discuss future measurement with electron scattering, 12C(e,e’) to test the predicted B(Eλ) of the ACM.

Propulsion and airframe aerodynamic interactions of supersonic V/STOL configurations. Volume 4: Summary

NASA Technical Reports Server (NTRS)

Zilz, D. E.; Wallace, H. W.; Hiley, P. E.

1985-01-01

A wind tunnel model of a supersonic V/STOL fighter configuration has been tested to measure the aerodynamic interaction effects which can result from geometrically close-coupled propulsion system/airframe components. The approach was to configure the model to represent two different test techniques. One was a conventional test technique composed of two test modes. In the Flow-Through mode, absolute configuration aerodynamics are measured, including inlet/airframe interactions. In the Jet-Effects mode, incremental nozzle/airframe interactions are measured. The other test technique is a propulsion simulator approach, where a sub-scale, externally powered engine is mounted in the model. This allows proper measurement of inlet/airframe and nozzle/airframe interactions simultaneously. This is Volume 4 of 4: Final Report- Summary.

Heat conduction in diatomic chains with correlated disorder

NASA Astrophysics Data System (ADS)

Savin, Alexander V.; Zolotarevskiy, Vadim; Gendelman, Oleg V.

2017-01-01

The paper considers heat transport in diatomic one-dimensional lattices, containing equal amounts of particles with different masses. Ordering of the particles in the chain is governed by single correlation parameter - the probability for two neighboring particles to have the same mass. As this parameter grows from zero to unity, the structure of the chain varies from regular staggering chain to completely random configuration, and then - to very long clusters of particles with equal masses. Therefore, this correlation parameter allows a control of typical cluster size in the chain. In order to explore different regimes of the heat transport, two interatomic potentials are considered. The first one is an infinite potential wall, corresponding to instantaneous elastic collisions between the neighboring particles. In homogeneous chains such interaction leads to an anomalous heat transport. The other one is classical Lennard-Jones interatomic potential, which leads to a normal heat transport. The simulations demonstrate that the correlated disorder of the particle arrangement does not change the convergence properties of the heat conduction coefficient, but essentially modifies its value. For the collision potential, one observes essential growth of the coefficient for fixed chain length as the limit of large homogeneous clusters is approached. The thermal transport in these models remains superdiffusive. In the Lennard-Jones chain the effect of correlation appears to be not monotonous in the limit of low temperatures. This behavior stems from the competition between formation of long clusters mentioned above, and Anderson localization close to the staggering ordered state.

Targeting excited states in all-trans polyenes with electron-pair states.

PubMed

Boguslawski, Katharina

2016-12-21

Wavefunctions restricted to electron pair states are promising models for strongly correlated systems. Specifically, the pair Coupled Cluster Doubles (pCCD) ansatz allows us to accurately describe bond dissociation processes and heavy-element containing compounds with multiple quasi-degenerate single-particle states. Here, we extend the pCCD method to model excited states using the equation of motion (EOM) formalism. As the cluster operator of pCCD is restricted to electron-pair excitations, EOM-pCCD allows us to target excited electron-pair states only. To model singly excited states within EOM-pCCD, we modify the configuration interaction ansatz of EOM-pCCD to contain also single excitations. Our proposed model represents a simple and cost-effective alternative to conventional EOM-CC methods to study singly excited electronic states. The performance of the excited state models is assessed against the lowest-lying excited states of the uranyl cation and the two lowest-lying excited states of all-trans polyenes. Our numerical results suggest that EOM-pCCD including single excitations is a good starting point to target singly excited states.

Correlated natural transition orbital framework for low-scaling excitation energy calculations (CorNFLEx).

PubMed

Baudin, Pablo; Kristensen, Kasper

2017-06-07

We present a new framework for calculating coupled cluster (CC) excitation energies at a reduced computational cost. It relies on correlated natural transition orbitals (NTOs), denoted CIS(D')-NTOs, which are obtained by diagonalizing generalized hole and particle density matrices determined from configuration interaction singles (CIS) information and additional terms that represent correlation effects. A transition-specific reduced orbital space is determined based on the eigenvalues of the CIS(D')-NTOs, and a standard CC excitation energy calculation is then performed in that reduced orbital space. The new method is denoted CorNFLEx (Correlated Natural transition orbital Framework for Low-scaling Excitation energy calculations). We calculate second-order approximate CC singles and doubles (CC2) excitation energies for a test set of organic molecules and demonstrate that CorNFLEx yields excitation energies of CC2 quality at a significantly reduced computational cost, even for relatively small systems and delocalized electronic transitions. In order to illustrate the potential of the method for large molecules, we also apply CorNFLEx to calculate CC2 excitation energies for a series of solvated formamide clusters (up to 4836 basis functions).

Quadratic canonical transformation theory and higher order density matrices.

PubMed

Neuscamman, Eric; Yanai, Takeshi; Chan, Garnet Kin-Lic

2009-03-28

Canonical transformation (CT) theory provides a rigorously size-extensive description of dynamic correlation in multireference systems, with an accuracy superior to and cost scaling lower than complete active space second order perturbation theory. Here we expand our previous theory by investigating (i) a commutator approximation that is applied at quadratic, as opposed to linear, order in the effective Hamiltonian, and (ii) incorporation of the three-body reduced density matrix in the operator and density matrix decompositions. The quadratic commutator approximation improves CT's accuracy when used with a single-determinant reference, repairing the previous formal disadvantage of the single-reference linear CT theory relative to singles and doubles coupled cluster theory. Calculations on the BH and HF binding curves confirm this improvement. In multireference systems, the three-body reduced density matrix increases the overall accuracy of the CT theory. Tests on the H(2)O and N(2) binding curves yield results highly competitive with expensive state-of-the-art multireference methods, such as the multireference Davidson-corrected configuration interaction (MRCI+Q), averaged coupled pair functional, and averaged quadratic coupled cluster theories.

Optimizing measurements of cluster velocities and temperatures for CCAT-prime and future surveys

NASA Astrophysics Data System (ADS)

Mittal, Avirukt; de Bernardis, Francesco; Niemack, Michael D.

2018-02-01

Galaxy cluster velocity correlations and mass distributions are sensitive probes of cosmology and the growth of structure. Upcoming microwave surveys will enable extraction of velocities and temperatures from many individual clusters for the first time. We forecast constraints on peculiar velocities, electron temperatures, and optical depths of galaxy clusters obtainable with upcoming multi-frequency measurements of the kinematic, thermal, and relativistic Sunyaev-Zeldovich effects. The forecasted constraints are compared for different measurement configurations with frequency bands between 90 GHz and 1 THz, and for different survey strategies for the 6-meter CCAT-prime telescope. We study methods for improving cluster constraints by removing emission from dusty star forming galaxies, and by using X-ray temperature priors from eROSITA. Cluster constraints are forecast for several model cluster masses. A sensitivity optimization for seven frequency bands is presented for a CCAT-prime first light instrument and a next generation instrument that takes advantage of the large optical throughput of CCAT-prime. We find that CCAT-prime observations are expected to enable measurement and separation of the SZ effects to characterize the velocity, temperature, and optical depth of individual massive clusters (~1015 Msolar). Submillimeter measurements are shown to play an important role in separating these components from dusty galaxy contamination. Using a modular instrument configuration with similar optical throughput for each detector array, we develop a rule of thumb for the number of detector arrays desired at each frequency to optimize extraction of these signals. Our results are relevant for a future "Stage IV" cosmic microwave background survey, which could enable galaxy cluster measurements over a larger range of masses and redshifts than will be accessible by other experiments.

The choice of product indicators in latent variable interaction models: post hoc analyses.

PubMed

Foldnes, Njål; Hagtvet, Knut Arne

2014-09-01

The unconstrained product indicator (PI) approach is a simple and popular approach for modeling nonlinear effects among latent variables. This approach leaves the practitioner to choose the PIs to be included in the model, introducing arbitrariness into the modeling. In contrast to previous Monte Carlo studies, we evaluated the PI approach by 3 post hoc analyses applied to a real-world case adopted from a research effort in social psychology. The measurement design applied 3 and 4 indicators for the 2 latent 1st-order variables, leaving the researcher with a choice among more than 4,000 possible PI configurations. Sixty so-called matched-pair configurations that have been recommended in previous literature are of special interest. In the 1st post hoc analysis we estimated the interaction effect for all PI configurations, keeping the real-world sample fixed. The estimated interaction effect was substantially affected by the choice of PIs, also across matched-pair configurations. Subsequently, a post hoc Monte Carlo study was conducted, with varying sample sizes and data distributions. Convergence, bias, Type I error and power of the interaction test were investigated for each matched-pair configuration and the all-pairs configuration. Variation in estimates across matched-pair configurations for a typical sample was substantial. The choice of specific configuration significantly affected convergence and the interaction test's outcome. The all-pairs configuration performed overall better than the matched-pair configurations. A further advantage of the all-pairs over the matched-pairs approach is its unambiguity. The final study evaluates the all-pairs configuration for small sample sizes and compares it to the non-PI approach of latent moderated structural equations. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Interhemispheric differences and solar cycle effects of the high-latitude ionospheric convection patterns deduced from Cluster EDI observations

NASA Astrophysics Data System (ADS)

Förster, Matthias; Haaland, Stein

2015-04-01

Here, we present a study of ionospheric convection at high latitudes that is based on satellite measurements of the Electron Drift Instrument (EDI) on-board the Cluster satellites, which were obtained over a full solar cycle (2001-2013). The mapped drift measurements are covering both hemispheres and a variety of different solar wind and interplanetary magnetic field (IMF) conditions. The large amount of data allows us to perform more detailed statistical studies. We show that flow patterns and polar cap potentials can differ between the two hemispheres on statistical average for a given IMF orientation. In particular, during southward directed IMF conditions, and thus enhanced energy input from the solar wind, we find that the southern polar cap has a higher cross polar cap potential. We also find persistent north-south asymmetries which cannot be explained by external drivers alone. Much of these asymmetries can probably be explained by significant differences in the strength and configuration of the geomagnetic field between the Northern and Southern Hemisphere. Since the ionosphere is magnetically connected to the magnetosphere, this difference will also be reflected in the magnetosphere in the form of different feedback from the two hemispheres. Consequently, local ionospheric conditions and the geomagnetic field configuration are important for north-south asymmetries in large regions of geospace. The average convection is higher during periods with high solar activity. Although local ionospheric conditions may play a role, we mainly attribute this to higher geomagnetic activity due to enhanced solar wind - magnetosphere interactions.

Carbon, oxygen and intrinsic defect interactions in germanium-doped silicon

NASA Astrophysics Data System (ADS)

Londos, C. A.; Sgourou, E. N.; Chroneos, A.; Emtsev, V. V.

2011-10-01

Production and annealing of oxygen-vacancy (VO) and oxygen-carbon (CiOi, CiOiI) defects in germanium-doped Czochralski-grown silicon (Cz-Si) containing carbon are investigated. All the samples were irradiated with 2 MeV fast electrons. Radiation-produced defects are studied using infrared spectroscopy by monitoring the relevant bands in optical spectra. For the VO defects, it is established that the doping with Ge affects the thermal stability of VO (830 cm-1) defects as well as their fraction converted to VO2 (888 cm-1) defects. In Ge-free samples containing carbon, it was found that carbon impurity atoms do not affect the thermal stability of VO defects, although they affect the fraction of VO defects that is converted to VO2 complexes. Considering the oxygen-carbon complexes, it is established that the annealing of the 862 cm-1 band associated with the CiOi defects is accompanied with the emergence of the 1048 cm-1 band, which has earlier been assigned to the CsO2i center. The evolution of the CiOiI bands is also traced. Ge doping does not seem to affect the thermal stability of the CiOi and CiOiI defects. Density functional theory (DFT) calculations provide insights into the stability of the defect clusters (VO, CiOi, CiOiI) at an atomic level. Both experimental and theoretical results are consistent with the viewpoint that Ge affects the stability of the VO but does not influence the stability of the oxygen-carbon clusters. DFT calculations demonstrate that C attracts both Oi and VO pairs predominately forming next nearest neighbor clusters in contrast to Ge where the interactions with Oi and VO are more energetically favorable at nearest neighbor configurations.

Study of clusters and hypernuclei production within PHSD+FRIGA model

NASA Astrophysics Data System (ADS)

Kireyeu, Viktar; Le Fèvre, Arnaud; Bratkovskaya, Elena

2017-03-01

We report on the results on the dynamical modelling of cluster formation with the new combined PHSD+FRIGA model at Nuclotron and NICA energies. The FRIGA clusterization algorithm, which can be applied to the transport models, is based on the simulated annealing technique to obtain the most bound configuration of fragments and nucleons. The PHSD+FRIGA model is able to predict isotope yields as well as hypernucleus production. Based on present predictions of the combined model we study the possibility to detect such clusters and hypernuclei in the BM@N and MPD/NICA detectors.

Propulsion and airframe aerodynamic interactions of supersonic V/STOL configurations. Volume 1: Wind tunnel test pressure data report

NASA Technical Reports Server (NTRS)

Zilz, D. E.; Devereaux, P. A.

1985-01-01

A wind tunnel model of a supersonic V/STOL fighter configuration has been tested to measure the aerodynamic interaction effects which can result from geometrically close-coupled propulsion system/airframe components. The approach was to configure the model to represent two different test techniques. One was a conventional test technique composed of two test modes. In the Flow-Through mode, absolute configuration aerodynamics are measured, including inlet/airframe interactions. In the Jet-Effects mode, incremental nozzle/airframe interactions are measured. The other test technique is a propulsion simulator approach, where a sub-scale, externally powered engine is mounted in the model. This allows proper measurement of inlet/airframe and nozzle/airframe interactions simultaneously. This is Volume 1 of 2: Wind Tunnel Test Pressure Data Report.

Wrapping up BLAST and other applications for use on Unix clusters.

PubMed

Hokamp, Karsten; Shields, Denis C; Wolfe, Kenneth H; Caffrey, Daniel R

2003-02-12

We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the 'MOLLUSC' package. (2) WRAPID, a simple tool for parallelizing large numbers of small instances of programs such as BLAST, FASTA and CLUSTALW. The packages were developed in Perl on a 20-node Linux cluster and are provided together with a configuration script and documentation. They can be freely downloaded from http://wolfe.gen.tcd.ie/wrapper.

Early Program Development

NASA Image and Video Library

1970-01-01

In this 1970 artist's concept, the Nuclear Shuttle is shown in its lunar and geosynchronous orbit configuration and in its planetary mission configuration. As envisioned by Marshall Space Flight Center Program Development plarners, the Nuclear Shuttle would deliver payloads to lunar orbit or other destinations then return to Earth orbit for refueling. A cluster of Nuclear Shuttle units could form the basis for planetary missions.

A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models

PubMed Central

Rolls, David A.; Wang, Peng; McBryde, Emma; Pattison, Philippa; Robins, Garry

2015-01-01

We compare two broad types of empirically grounded random network models in terms of their abilities to capture both network features and simulated Susceptible-Infected-Recovered (SIR) epidemic dynamics. The types of network models are exponential random graph models (ERGMs) and extensions of the configuration model. We use three kinds of empirical contact networks, chosen to provide both variety and realistic patterns of human contact: a highly clustered network, a bipartite network and a snowball sampled network of a “hidden population”. In the case of the snowball sampled network we present a novel method for fitting an edge-triangle model. In our results, ERGMs consistently capture clustering as well or better than configuration-type models, but the latter models better capture the node degree distribution. Despite the additional computational requirements to fit ERGMs to empirical networks, the use of ERGMs provides only a slight improvement in the ability of the models to recreate epidemic features of the empirical network in simulated SIR epidemics. Generally, SIR epidemic results from using configuration-type models fall between those from a random network model (i.e., an Erdős-Rényi model) and an ERGM. The addition of subgraphs of size four to edge-triangle type models does improve agreement with the empirical network for smaller densities in clustered networks. Additional subgraphs do not make a noticeable difference in our example, although we would expect the ability to model cliques to be helpful for contact networks exhibiting household structure. PMID:26555701

Theoretical study of the interaction of N/sub 2/ with water molecules. (H/sub 2/O)/sub n/:N/sub 2/, n = 1--8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curtiss, L.A.; Eisgruber, C.L.

1984-03-01

Ab initio molecular orbital calculations including correlation energy have been carried out on the interaction of a single H/sub 2/O molecule with N/sub 2/. The potential energy surface for H/sub 2/O:N/sub 2/ is found to have a minimum corresponding to a HOH xxx N/sub 2/ structure with a weak (<2 kcal mol/sup -1/) hydrogen bond. A second, less stable, configuration corresponding to a H/sub 2/O xxx N/sub 2/ structure with N/sub 2/ bonded side on to the oxygen of H/sub 2/O was found to be either a minimum or a saddle point in the potential energy surface depending on themore » level of calculation. The minimal STO-3G basis set was used to investigate the interaction of up to eight H/sub 2/O molecules with N/sub 2/. Two types of clusters, one containing only HOH xxx N/sub 2/ interactions and the other containing both HOH xxxN/sub 2/ and H/sub 2/O xxx N/sub 2/ interactions, were investigated for (N/sub 2/:(H/sub 2/O)/sub n/, n = 2--8).« less

Studies of the Virgo cluster. VI - Morphological and kinematical structure of the Virgo cluster

NASA Technical Reports Server (NTRS)

Binggeli, Bruno; Tammann, G. A.; Sandage, Allan

1987-01-01

The structure of the Virgo cluster is analyzed on the basis of the positions, Hubble types, and radial velocities of 1277 Virgo cluster galaxies. The surface distribution of galaxies is considered according to type, and is discussed using maps, isopleths, strip counts, and radial-density distributions. It is found that the Virgo cluster shows pronounced double structure. The main concentration has a large velocity dispersion and is made up predominantly of early-type galaxies, while the secondary concentration has a much smaller velocity dispersion and contains late types. There is a strong spatial segregation of the Hubble types, the early-type galaxies being more concentrated toward the cluster center. There is significant substructure in the cluster core. The irregularity of the Virgo cluster in both configuration and velocity space shows that the core and the envelope are still forming, and hence that the cluster is young.

An exploratory study of alternative configurations of governing boards of substance abuse treatment centers

PubMed Central

Blum, Terry C.; Roman, Paul M.

2011-01-01

Boards of directors are the ultimate governing authorities for most organizations providing substance abuse treatment. A governing board may establish policies, monitor and improve operations, and represent a treatment organization to the public. This paper explores alternative configurations of governing boards in a national sample of 500 substance abuse treatment centers. The study proceeds from the premise that boards may be configured with varying levels of engagement in five aspects of internal management and external connections in treatment center operating environments. Based on interviews with treatment center administrative directors, four clusters emerge, describing boards that are: (1) active and balanced across internal and external domains; (2) active boundary spanners concentrating primarily on external relationships; (3) focused primarily on internal organizational management; and (4) relatively inactive. In post hoc analysis, we found that placement in these clusters is associated with treatment center attributes such as rate of growth and financial results, use of evidence based practices and provision of integrated care. PMID:21489737

An exploratory study of organization design configurations in health care delivery organizations.

PubMed

Sheppeck, Mick; Militello, Jack

2014-01-01

Organizations are configurations of variables that support each other to achieve customer satisfaction. Based on Treacy and Wiersema (1995), we predicted the emergence of two configurations, one supporting a product leadership stance and one predicting the customer intimate approach from a set of 73 for profit health care clinics. In addition, we predicted the emergence of a configuration where the scores on most variables were near the mean for each variable. Using cluster analysis and discriminant function analysis, we identified three configurations: one a "master of two" strategy, one "stuck-in-the-middle," and one showing scores well below the mean on most variables. The implications for organization design and manager actions in the health care industry are discussed.

Fast Multipole Methods for Three-Dimensional N-body Problems

NASA Technical Reports Server (NTRS)

Koumoutsakos, P.

1995-01-01

We are developing computational tools for the simulations of three-dimensional flows past bodies undergoing arbitrary motions. High resolution viscous vortex methods have been developed that allow for extended simulations of two-dimensional configurations such as vortex generators. Our objective is to extend this methodology to three dimensions and develop a robust computational scheme for the simulation of such flows. A fundamental issue in the use of vortex methods is the ability of employing efficiently large numbers of computational elements to resolve the large range of scales that exist in complex flows. The traditional cost of the method scales as Omicron (N(sup 2)) as the N computational elements/particles induce velocities at each other, making the method unacceptable for simulations involving more than a few tens of thousands of particles. In the last decade fast methods have been developed that have operation counts of Omicron (N log N) or Omicron (N) (referred to as BH and GR respectively) depending on the details of the algorithm. These methods are based on the observation that the effect of a cluster of particles at a certain distance may be approximated by a finite series expansion. In order to exploit this observation we need to decompose the element population spatially into clusters of particles and build a hierarchy of clusters (a tree data structure) - smaller neighboring clusters combine to form a cluster of the next size up in the hierarchy and so on. This hierarchy of clusters allows one to determine efficiently when the approximation is valid. This algorithm is an N-body solver that appears in many fields of engineering and science. Some examples of its diverse use are in astrophysics, molecular dynamics, micro-magnetics, boundary element simulations of electromagnetic problems, and computer animation. More recently these N-body solvers have been implemented and applied in simulations involving vortex methods. Koumoutsakos and Leonard (1995) implemented the GR scheme in two dimensions for vector computer architectures allowing for simulations of bluff body flows using millions of particles. Winckelmans presented three-dimensional, viscous simulations of interacting vortex rings, using vortons and an implementation of a BH scheme for parallel computer architectures. Bhatt presented a vortex filament method to perform inviscid vortex ring interactions, with an alternative implementation of a BH scheme for a Connection Machine parallel computer architecture.

Interactive visual exploration and analysis of origin-destination data

NASA Astrophysics Data System (ADS)

Ding, Linfang; Meng, Liqiu; Yang, Jian; Krisp, Jukka M.

2018-05-01

In this paper, we propose a visual analytics approach for the exploration of spatiotemporal interaction patterns of massive origin-destination data. Firstly, we visually query the movement database for data at certain time windows. Secondly, we conduct interactive clustering to allow the users to select input variables/features (e.g., origins, destinations, distance, and duration) and to adjust clustering parameters (e.g. distance threshold). The agglomerative hierarchical clustering method is applied for the multivariate clustering of the origin-destination data. Thirdly, we design a parallel coordinates plot for visualizing the precomputed clusters and for further exploration of interesting clusters. Finally, we propose a gradient line rendering technique to show the spatial and directional distribution of origin-destination clusters on a map view. We implement the visual analytics approach in a web-based interactive environment and apply it to real-world floating car data from Shanghai. The experiment results show the origin/destination hotspots and their spatial interaction patterns. They also demonstrate the effectiveness of our proposed approach.

Concept design and cluster control of advanced space connectable intelligent microsatellite

NASA Astrophysics Data System (ADS)

Wang, Xiaohui; Li, Shuang; She, Yuchen

2017-12-01

In this note, a new type of advanced space connectable intelligent microsatellite is presented to extend the range of potential application of microsatellite and improve the efficiency of cooperation. First, the overall concept of the micro satellite cluster is described, which is characterized by autonomously connecting with each other and being able to realize relative rotation through the external interfaces. Second, the multi-satellite autonomous assembly algorithm and control algorithm of the cluster motion are developed to make the cluster system combine into a variety of configurations in order to achieve different types of functionality. Finally, the design of the satellite cluster system is proposed, and the possible applications are discussed.

Competition between surface chemisorption and cage formation in Fe12O12 clusters

NASA Astrophysics Data System (ADS)

Gutsev, G. L.; Weatherford, C. A.; Jena, P.; Johnson, E.; Ramachandran, B. R.

2013-01-01

The electronic and geometrical structures of the clusters composed of 12 iron and 12 oxygen atoms are obtained using all-electron density functional theory. It is found that the states with geometrical structures corresponding to oxygen chemisorbed on the ground-state Fe12 cluster surface (Fe12O12) are close in total energy to the states whose geometrical configurations are hollow cages (FeO)12. The lowest total energy state is the ferrimagnetic triplet state of Fe12O12. A ferrimagnetic nonet state of (FeO)12 is only marginally higher in total energy. The clusters are rich in nearly degenerate isomers. Oxygen adsorption dramatically quenches the spin of Fe12 clusters.

Combustion of Unconfined Droplet Clusters in Microgravity

NASA Technical Reports Server (NTRS)

Ruff, G. A.; Liu, S.

2001-01-01

Combustion experiments using arrays of droplets seek to provide a link between single droplet combustion phenomena and the behavior of complex spray combustion systems. Both single droplet and droplet array studies have been conducted in microgravity to better isolate the droplet interaction phenomena and eliminate or reduce the confounding effects of buoyancy-induced convection. In most experiments involving droplet arrays, the droplets are supported on fibers to keep them stationary and close together before the combustion event. The presence of the fiber, however, disturbs the combustion process by introducing a source of heat transfer and asymmetry into the configuration. As the number of drops in a droplet array increases, supporting the drops on fibers becomes less practical because of the cumulative effect of the fibers on the combustion process. To eliminate the effect of the fiber, several researchers have conducted microgravity experiments using unsupported droplets. Jackson and Avedisian investigated single, unsupported drops while Nomura et al. studied droplet clouds formed by a condensation technique. The overall objective of this research is to extend the study of unsupported drops by investigating the combustion of well-characterized drop clusters in a microgravity environment. Direct experimental observations and measurements of the combustion of droplet clusters would fill a large gap in our current understanding of droplet and spray combustion and provide unique experimental data for the verification and improvement of spray combustion models. In this work, the formation of drop clusters is precisely controlled using an acoustic levitation system so that dilute, as well as dense clusters can be created and stabilized before combustion in microgravity is begun. This paper describes the design and performance of the 1-g experimental apparatus, some preliminary 1-g results, and plans for testing in microgravity.

Aqueous solvation of Mg(ii) and Ca(ii): A Born-Oppenheimer molecular dynamics study of microhydrated gas phase clusters

NASA Astrophysics Data System (ADS)

León-Pimentel, C. I.; Amaro-Estrada, J. I.; Hernández-Cobos, J.; Saint-Martin, H.; Ramírez-Solís, A.

2018-04-01

The hydration features of [Mg(H2O)n ] 2 + and [Ca(H2O)n ] 2 + clusters with n = 3-6, 8, 18, and 27 were studied by means of Born-Oppenheimer molecular dynamics simulations at the B3LYP/6-31+G** level of theory. For both ions, it is energetically more favorable to have all water molecules in the first hydration shell when n ≤ 6, but stable lower coordination average structures with one water molecule not directly interacting with the ion were found for Mg2+ at room temperature, showing signatures of proton transfer events for the smaller cation but not for the larger one. A more rigid octahedral-type structure for Mg2+ than for Ca2+ was observed in all simulations, with no exchange of water molecules to the second hydration shell. Significant thermal effects on the average structure of clusters were found: while static optimizations lead to compact, spherically symmetric hydration geometries, the effects introduced by finite-temperature dynamics yield more prolate configurations. The calculated vibrational spectra are in agreement with infrared spectroscopy results. Previous studies proposed an increase in the coordination number (CN) from six to eight water molecules for [Ca(H2O)n ] 2 + clusters when n ≥ 12; however, in agreement with recent measurements of binding energies, no transition to a larger CN was found when n > 8. Moreover, the excellent agreement found between the calculated extended X-ray absorption fine structure spectroscopy spectra for the larger cluster and the experimental data of the aqueous solution supports a CN of six for Ca2+.

Development of a picture of the van der Waals interaction energy between clusters of nanometer-range particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arunachalam, V.; Marlow, W.H.; Lu, J.X.

1998-09-01

The importance of the long-range Lifshitz{endash}van der Waals interaction energy between condensed bodies is well known. However, its implementation for interacting bodies that are highly irregular and separated by distances varying from contact to micrometers has received little attention. As part of a study of collisions of irregular aerosol particles, an approach based on the Lifshitz theory of van der Waals interaction has been developed to compute the interaction energy between a sphere and an aggregate of spheres at all separations. In the first part of this study, the iterated sum-over-dipole interactions between pairs of approximately spherical molecular clusters aremore » compared with the Lifshitz and Lifshitz-Hamaker interaction energies for continuum spheres of radii equal to those of the clusters{close_quote} circumscribed spheres and of the same masses as the clusters. The Lifshitz energy is shown to converge to the iterated dipolar energy for quasispherical molecular clusters for sufficiently large separations, while the energy calculated by using the Lifshitz-Hamaker approach does not. Next, the interaction energies between a contacting pair of these molecular clusters and a third cluster in different relative positions are calculated first by coupling all molecules in the three-cluster system and second by ignoring the interactions between the molecules of the adhering clusters. The error calculated by this omission is shown to be very small, and is an indication of the error in computing the long-range interaction energy between a pair of interacting spheres and a third sphere as a simple sum over the Lifshitz energies between individual, condensed-matter spheres. This Lifshitz energy calculation is then combined with the short-separation, nonsingular van der Waals energy calculation of Lu, Marlow, and Arunachalam, to provide an integrated picture of the van der Waals energy from large separations to contact. {copyright} {ital 1998} {ital The American Physical Society}« less

VizieR Online Data Catalog: WOCS. LXXV. Hyades&Praesepe stellar lithium data (Cummings+, 2017)

NASA Astrophysics Data System (ADS)

Cummings, J. D.; Deliyannis, C. P.; Maderak, R. M.; Steinhauer, A.

2018-05-01

The Hyades and Praesepe open star clusters were both observed using the Hydra multi-object spectrograph on the WIYN 3.5-meter telescope using the 316@63.4 echelle grating in order 8 with the X19 filter. The spectra span from 6450 to 6850 Å. All Hyades stars and a majority of Praesepe stars were observed with blue cable, which yielded R~13600. The remaining Praesepe stars were observed with the red cable, which yielded a moderately higher R~17600. The Hyades data were acquired over seven nights from 2009 February 2 to 23. Using two red-cable configurations, we obtained spectra of 34 Praesepe candidate cluster members on 1997 November 16 and 18. Using seven blue cable configurations, we obtained spectra of 66 candidate cluster members during seven nights on 2001 December 2; 2005 May 1 and 2; 2006 January 25 and 26; and 2006 February 2 and 3. (2 data files).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Jia, E-mail: jia-zhu@jxnu.edu.cn, E-mail: zhangyf@fzu.edu.cn; Zhang, Hui; Tong, Yawen

The structures and electronic properties of bimetallic oxide CrW{sub 2}O{sub 9} clusters supported on the perfect and defective MgO(001) surfaces with three different color centers, F{sub S}{sup 0}, F{sub S}{sup +}, and F{sub S}{sup 2+} centers, respectively, have been investigated by density functional theory calculations. Our results show that the configurations, adsorption energies, charge transfers, and bonding modes of dispersed CrW{sub 2}O{sub 9} clusters are sensitive to the charge states of the F{sub S} centers. Compared with the gas-phase configuration, the CrW{sub 2}O{sub 9} clusters supported on the defective surfaces are distorted dramatically, which exhibit different chain structures. On themore » perfect MgO surface, the depositions of clusters do not involve obvious charge transfer, while the situation is quite different on the defective MgO(001) surfaces in which significant electron transfer occurs from the surface to the cluster. Interestingly, this effect becomes more remarkable for electron-rich oxygen vacancies (F{sub S}{sup 0} center) than that for electron-poor oxygen vacancies (F{sub S}{sup +} and F{sub S}{sup 2+} centers). Furthermore, our work reveals a progressive Brønsted acid sites where spin density preferentially localized around the Cr atoms not the W atoms for all kinds of F{sub S}-centers, indicating the better catalytic activities can be expected for CrW{sub 2}O{sub 9} cluster on defective MgO(001) surfaces with respect to the W{sub 3}O{sub 9} cluster.« less

XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data

PubMed Central

2015-01-01

Background Though cluster analysis has become a routine analytic task for bioinformatics research, it is still arduous for researchers to assess the quality of a clustering result. To select the best clustering method and its parameters for a dataset, researchers have to run multiple clustering algorithms and compare them. However, such a comparison task with multiple clustering results is cognitively demanding and laborious. Results In this paper, we present XCluSim, a visual analytics tool that enables users to interactively compare multiple clustering results based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms. The efficacy of XCluSim is shown through case studies with a bioinformatician. Conclusions Compared to other relevant tools, XCluSim enables users to compare multiple clustering results in a more scalable manner. Moreover, XCluSim supports diverse clustering algorithms and dedicated visualizations and interactions for different types of clustering results, allowing more effective exploration of details on demand. Through case studies with a bioinformatics researcher, we received positive feedback on the functionalities of XCluSim, including its ability to help identify stably clustered items across multiple clustering results. PMID:26328893

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ward, Lee H.; Laros, James H., III

This paper describes a methodology for implementing disk-less cluster systems using the Network File System (NFS) that scales to thousands of nodes. This method has been successfully deployed and is currently in use on several production systems at Sandia National Labs. This paper will outline our methodology and implementation, discuss hardware and software considerations in detail and present cluster configurations with performance numbers for various management operations like booting.

Propulsion and airframe aerodynamic interactions of supersonic V/STOL configurations. Volume 2: Wind tunnel test force and moment data report

NASA Technical Reports Server (NTRS)

Zilz, D. E.

1985-01-01

A wind tunnel model of a supersonic V/STOL fighter configuration has been tested to measure the aerodynamic interaction effects which can result from geometrically close-coupled propulsion system/airframe components. The approach was to configure the model to represent two different test techniques. One was a conventional test technique composed of two test modes. In the Flow-Through mode, absolute configuration aerodynamics are measured, including inlet/airframe interactions. In the Jet-Effects mode, incremental nozzle/airframe interactions are measured. The other test technique is a propulsion simulator approach, where a sub-scale, externally powered engine is mounted in the model. This allows proper measurement of inlet/airframe and nozzle/airframe interactions simultaneously. This is Volume 2 of 2: Wind Tunnel Test Force and Moment Data Report.

Tetrahedral 4 α and 12C+α cluster structures in 16O

NASA Astrophysics Data System (ADS)

Kanada-En'yo, Yoshiko

2017-09-01

I have investigated structures of the ground and excited states of 16O with the method of variation after spin-parity projection in the antisymmetrized molecular dynamics model combined with the generator coordinate method of 12C+α cluster. The calculation reasonably reproduces the experimental energy spectra; E 2 , E 3 , E 4 , and I S 1 transitions; and α -decay properties. The formation of 4 α clusters has been confirmed from nucleon degrees of freedom in the AMD model without assuming the existence of any clusters. They form "tetrahedral" 4 α - and 12C+α cluster structures. The 12C+α structure constructs the Kπ=0+ band consisting of the 02+, 21+, and 41+ states and the Kπ=0- band of the 12-, 32-, and 51- states. The 01+, 31-, and 42+ states are assigned to the ground band constructed from the tetrahedral 4 α structure. The 01+ and 31- are approximately interpreted as Td band members with the ideal tetrahedral configuration. The ground-state 4 α correlation plays an important role in the enhancement of the E 3 transition strength to the 31-. The 42+ state is not the ideal Td member but constructed from a distorted tetrahedral 4 α structure. Moreover, significant state mixing of the tetrahedral 4 α and 12C+α cluster structures occurs between 41+ and 42+ states, indicating that the Td configuration of 4 α is rather fragile at Jπ=4+ .

Structural evolution of the [(CO2)n(H2O)]- cluster anions: quantifying the effect of hydration on the excess charge accommodation motif.

PubMed

Muraoka, Azusa; Inokuchi, Yoshiya; Hammer, Nathan I; Shin, Joong-Won; Johnson, Mark A; Nagata, Takashi

2009-08-06

The [(CO2)n(H2O)]- cluster anions are studied using infrared photodissociation (IPD) spectroscopy in the 2800-3800 cm(-1) range. The observed IPD spectra display a drastic change in the vibrational band features at n = 4, indicating a sharp discontinuity in the structural evolution of the monohydrated cluster anions. The n = 2 and 3 spectra are composed of a series of sharp bands around 3600 cm(-1), which are assignable to the stretching vibrations of H2O bound to C2O4- in a double ionic hydrogen-bonding (DIHB) configuration, as was previously discussed (J. Chem. Phys. 2005, 122, 094303). In the n > or = 4 spectrum, a pair of intense bands additionally appears at approximately 3300 cm(-1). With the aid of ab initio calculations at the MP2/6-31+G* level, the 3300 cm(-1) bands are assigned to the bending overtone and the hydrogen-bonded OH vibration of H2O bound to CO2- via a single O-H...O linkage. Thus, the structures of [(CO2)n(H2O)]- evolve with cluster size such that DIHB to C2O4- is favored in the smaller clusters with n = 2 and 3 whereas CO2- is preferentially stabilized via the formation of a single ionic hydrogen-bonding (SIHB) configuration in the larger clusters with n > or = 4.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kira, M., E-mail: mackillo.kira@physik.uni-marburg.de

Atomic Bose–Einstein condensates (BECs) can be viewed as macroscopic objects where atoms form correlated atom clusters to all orders. Therefore, the presence of a BEC makes the direct use of the cluster-expansion approach–lucrative e.g. in semiconductor quantum optics–inefficient when solving the many-body kinetics of a strongly interacting Bose. An excitation picture is introduced with a nonunitary transformation that describes the system in terms of atom clusters within the normal component alone. The nontrivial properties of this transformation are systematically studied, which yields a cluster-expansion friendly formalism for a strongly interacting Bose gas. Its connections and corrections to the standard Hartree–Fock–Bogoliubov approachmore » are discussed and the role of the order parameter and the Bogoliubov excitations are identified. The resulting interaction effects are shown to visibly modify number fluctuations of the BEC. Even when the BEC has a nearly perfect second-order coherence, the BEC number fluctuations can still resolve interaction-generated non-Poissonian fluctuations. - Highlights: • Excitation picture expresses interacting Bose gas with few atom clusters. • Semiconductor and BEC many-body investigations are connected with cluster expansion. • Quantum statistics of BEC is identified in terms of atom clusters. • BEC number fluctuations show extreme sensitivity to many-body correlations. • Cluster-expansion friendly framework is established for an interacting Bose gas.« less

Cluster Size Optimization in Sensor Networks with Decentralized Cluster-Based Protocols

PubMed Central

Amini, Navid; Vahdatpour, Alireza; Xu, Wenyao; Gerla, Mario; Sarrafzadeh, Majid

2011-01-01

Network lifetime and energy-efficiency are viewed as the dominating considerations in designing cluster-based communication protocols for wireless sensor networks. This paper analytically provides the optimal cluster size that minimizes the total energy expenditure in such networks, where all sensors communicate data through their elected cluster heads to the base station in a decentralized fashion. LEACH, LEACH-Coverage, and DBS comprise three cluster-based protocols investigated in this paper that do not require any centralized support from a certain node. The analytical outcomes are given in the form of closed-form expressions for various widely-used network configurations. Extensive simulations on different networks are used to confirm the expectations based on the analytical results. To obtain a thorough understanding of the results, cluster number variability problem is identified and inspected from the energy consumption point of view. PMID:22267882

Self-confinement of finite dust clusters in isotropic plasmas.

PubMed

Miloshevsky, G V; Hassanein, A

2012-05-01

Finite two-dimensional dust clusters are systems of a small number of charged grains. The self-confinement of dust clusters in isotropic plasmas is studied using the particle-in-cell method. The energetically favorable configurations of grains in plasma are found that are due to the kinetic effects of plasma ions and electrons. The self-confinement phenomenon is attributed to the change in the plasma composition within a dust cluster resulting in grain attraction mediated by plasma ions. This is a self-consistent state of a dust cluster in which grain's repulsion is compensated by the reduced charge and floating potential on grains, overlapped ion clouds, and depleted electrons within a cluster. The common potential well is formed trapping dust clusters in the confined state. These results provide both valuable insights and a different perspective to the classical view on the formation of boundary-free dust clusters in isotropic plasmas.

Assigning the Cerium Oxidation State for CH2CeF2 and OCeF2 Based on Multireference Wave Function Analysis.

PubMed

Mooßen, Oliver; Dolg, Michael

2016-06-09

The geometric and electronic structure of the recently experimentally studied molecules ZCeF2 (Z = CH2, O) was investigated by density functional theory (DFT) and wave function-based ab initio methods. Special attention was paid to the Ce-Z metal-ligand bonding, especially to the nature of the interaction between the Ce 4f and the Z 2p orbitals and the possible multiconfigurational character arising from it, as well as to the assignment of an oxidation state of Ce reflecting the electronic structure. Complete active space self-consistent field (CASSCF) calculations were performed, followed by orbital rotations in the active orbital space. The methylene compound CH2CeF2 has an open-shell singlet ground state, which is characterized by a two-configurational wave function in the basis of the strongly mixed natural CASSCF orbitals. The system can also be described in a very compact way by the dominant Ce 4f(1) C 2p(1) configuration, if nearly pure Ce 4f and C 2p orbitals are used. In the basis of these localized orbitals, the molecule is almost monoconfigurational and should be best described as a Ce(III) system. The singlet ground state of the oxygen OCeF2 complex is of closed-shell character when a monoconfigurational wave function with very strongly mixed Ce 4f and O 2p CASSCF natural orbitals is used for the description. The transformation to orbitals localized on the cerium and oxygen atoms leads to a multiconfigurational wave function and reveals characteristics of a mixed valent Ce(IV)/Ce(III) compound. Additionally, the interactions of the localized active orbitals were analyzed by evaluating the expectation values of the charge fluctuation operator and the local spin operator. The Ce 4f and C 2p orbital interaction of the CH2CeF2 compound is weakly covalent and resembles the interaction of the H 1s orbitals in a stretched hydrogen dimer. In contrast, the interaction of the localized active orbitals for OCeF2 shows ionic character. Calculated vibrational Ce-C and Ce-O stretching frequencies at the DFT, CASSCF, second-order Rayleigh-Schrödinger perturbation theory (RS2C), multireference configuration interaction (MRCI), as well as single, doubles, and perturbative triples coupled cluster (CCSD(T)) level are reported and compared to experimental infrared absorption data in a Ne and Ar matrix.

Detection of rhodopsin dimerization in situ by PIE-FCCS, a time-resolved fluorescence spectroscopy.

PubMed

Smith, Adam W

2015-01-01

Rhodopsin self-associates in the plasma membrane. At low concentrations, the interactions are consistent with a monomer-dimer equilibrium (Comar et al., J Am Chem Soc 136(23):8342-8349, 2014). At high concentrations in native tissue, higher-order clusters have been observed (Fotiadis et al., Nature 421:127-128, 2003). The physiological role of rhodopsin dimerization is still being investigated, but it is clear that a quantitative assessment is essential to determining the function of rhodopsin clusters in vision. To quantify rhodopsin interactions, I will outline the theory and methodology of a specialized time-resolved fluorescence spectroscopy for measuring membrane protein-protein interactions called pulsed-interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS). The strength of this technique is its ability to quantify rhodopsin interactions in situ (i.e., a live cell plasma membrane). There are two reasons for restricting the scope to live cell membranes. First, the compositional heterogeneity of the plasma membrane creates a complex milieu with thousands of lipid, protein, and carbohydrate species. This makes it difficult to infer quaternary interactions from detergent solubilized samples or construct a model phospholipid bilayer that recapitulates all of the interactions present in native membranes. Second, organizational structure and dynamics is a key feature of the plasma membrane, and fixation techniques like formaldehyde cross-linking and vitrification will modulate the interactions. PIE-FCCS is based on two-color fluorescence imaging with time-correlated single-photon counting (TCSPC) (Becker et al., Rev Sci Instrum 70:1835-1841, 1999). By time-tagging every detected photon, the data can be analyzed as a fluorescence intensity distribution, fluorescence lifetime histogram, or fluorescence (cross-)correlation spectra (FCS/FCCS) (Becker, Advanced time-correlated single-photon counting techniques, Springer, Berlin, 2005). These analysis tools can then be used to quantify protein concentration, mobility, clustering, and Förster resonance energy transfer (FRET). In this paper I will focus on PIE-FCCS, which interleaves two wavelength excitation events in time so that the effects of spectral cross-talk and FRET can be isolated. In this way it is possible to characterize monomer-dimer-oligomer equilibria with high accuracy (Müller et al., Biophys J 89:3508-3522, 2005). Currently, PIE-FCCS requires a customized equipment configuration that will be described below. There is an excellent protocol that outlines traditional FCCS on a commercially available instrument (Bacia and Schwille, Nat Protoc 2:2842-2856, 2007). The PIE-FCCS approach is a relatively recent advance in FCCS that has been used in live cell assays to quantify lipid-anchored protein clustering (Triffo et al., J Am Chem Soc 134:10833-10842, 2012), epidermal growth factor receptor dimerization (Endres et al., Cell 152:543-556, 2013), and recently the dimerization of opsin (Comar et al., J Am Chem Soc 136(23):8342-8349, 2014). This paper will outline the theory and instrumentation requirements for PIE-FCCS, as well as the data collection and analysis process.

Structure, electronic and magnetic properties of Mn{sub n} (n=2-8) clusters: A DFT investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Vipin; Roy, Debesh R., E-mail: drr@ashd.svnit.ac.in

2016-05-06

A detail studyon the stability, electronic and magnetic properties of Mn{sub n} (n=2-8) cluster series is performed under the utilization ofdensity functional theory (DFT). The binding energy (B.E.), HOMO-LUMO energy gap (HLG), chemical hardness (η), ionization potential (I.P.), electron affinity (E.A)and electronegativity (χ) of these clusters are predicted. We have also studied the magnetic moments associated with the stable cluster isomers. The lowest energy structures for each cluster sizes aredetermined with a systematic search imposing all possible initial magnetic configuration on the cluster. All the calculations are carried out using a popular GGA functional PBE as proposed by Pardew, Burkemore » and Ernzerhof and implemented in the VASP program.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asoudeh, M.; Karimipour, V.

We determine thermal entanglement in mean-field clusters of N spin one-half particles interacting via the anisotropic Heisenberg interaction, with and without external magnetic field. For the xxx cluster in the absence of magnetic field we prove that only the N=2 ferromagnetic cluster shows entanglement. An external magnetic field B can only entangle xxx antiferromagnetic clusters in certain regions of the B-T plane. On the other hand, the xxz clusters of size N>2 are entangled only when the interaction is ferromagnetic. Detailed dependence of the entanglement on various parameters is investigated in each case.

FastSim: A Fast Simulation for the SuperB Detector

NASA Astrophysics Data System (ADS)

Andreassen, R.; Arnaud, N.; Brown, D. N.; Burmistrov, L.; Carlson, J.; Cheng, C.-h.; Di Simone, A.; Gaponenko, I.; Manoni, E.; Perez, A.; Rama, M.; Roberts, D.; Rotondo, M.; Simi, G.; Sokoloff, M.; Suzuki, A.; Walsh, J.

2011-12-01

We have developed a parameterized (fast) simulation for detector optimization and physics reach studies of the proposed SuperB Flavor Factory in Italy. Detector components are modeled as thin sections of planes, cylinders, disks or cones. Particle-material interactions are modeled using simplified cross-sections and formulas. Active detectors are modeled using parameterized response functions. Geometry and response parameters are configured using xml files with a custom-designed schema. Reconstruction algorithms adapted from BaBar are used to build tracks and clusters. Multiple sources of background signals can be merged with primary signals. Pattern recognition errors are modeled statistically by randomly misassigning nearby tracking hits. Standard BaBar analysis tuples are used as an event output. Hadronic B meson pair events can be simulated at roughly 10Hz.

New ab initio adiabatic potential energy surfaces and bound state calculations for the singlet ground X˜ 1A1 and excited C˜ 1B2(21A') states of SO2

NASA Astrophysics Data System (ADS)

Kłos, Jacek; Alexander, Millard H.; Kumar, Praveen; Poirier, Bill; Jiang, Bin; Guo, Hua

2016-05-01

We report new and more accurate adiabatic potential energy surfaces (PESs) for the ground X˜ 1A1 and electronically excited C˜ 1B2(21A') states of the SO2 molecule. Ab initio points are calculated using the explicitly correlated internally contracted multi-reference configuration interaction (icMRCI-F12) method. A second less accurate PES for the ground X ˜ state is also calculated using an explicitly correlated single-reference coupled-cluster method with single, double, and non-iterative triple excitations [CCSD(T)-F12]. With these new three-dimensional PESs, we determine energies of the vibrational bound states and compare these values to existing literature data and experiment.

Molecular dynamics simulations of oxygen vacancy diffusion in SrTiO3.

PubMed

Schie, Marcel; Marchewka, Astrid; Müller, Thomas; De Souza, Roger A; Waser, Rainer

2012-12-05

A classical force-field model with partial ionic charges was applied to study the behaviour of oxygen vacancies in the perovskite oxide strontium titanate (SrTiO(3)). The dynamical behaviour of these point defects was investigated as a function of temperature and defect concentration by means of molecular dynamics (MD) simulations. The interaction between oxygen vacancies and an extended defect, here a Σ3(111) grain boundary, was also examined by means of MD simulations. Analysis of the vacancy distribution revealed considerable accumulation of vacancies in the envelope of the grain boundary. The possible clustering of oxygen vacancies in bulk SrTiO(3) was studied by means of static lattice calculations within the Mott-Littleton approach. All binary vacancy-vacancy configurations were found to be energetically unfavourable.

Interaction of size-selected gold nanoclusters with dopamine

NASA Astrophysics Data System (ADS)

Montone, Georgia R.; Hermann, Eric; Kandalam, Anil K.

2016-12-01

We present density functional theory based results on the interaction of size-selected gold nanoclusters, Au10 and Au20, with dopamine molecule. The gold clusters interact strongly with the nitrogen site of dopamine, thereby forming stable gold-dopamine complexes. Our calculations further show that there is no site specificity on the planar Au10 cluster with all the edge gold atoms equally preferred. On the other hand, in the pyramidal Au20 cluster, the vertex metal atom is the most active site. As the size increased from Au10 to Au20, the interaction strength has shown a declining trend. The effect of aqueous environment on the interaction strengths were also studied by solvation model. It is found that the presence of solvent water stabilizes the interaction between the metal cluster and dopamine molecule, even though for Au10 cluster the energy ordering of the isomers changed from that of the gas-phase.

Assessing the Amazon Cloud Suitability for CLARREO's Computational Needs

NASA Technical Reports Server (NTRS)

Goldin, Daniel; Vakhnin, Andrei A.; Currey, Jon C.

2015-01-01

In this document we compare the performance of the Amazon Web Services (AWS), also known as Amazon Cloud, with the CLARREO (Climate Absolute Radiance and Refractivity Observatory) cluster and assess its suitability for computational needs of the CLARREO mission. A benchmark executable to process one month and one year of PARASOL (Polarization and Anistropy of Reflectances for Atmospheric Sciences coupled with Observations from a Lidar) data was used. With the optimal AWS configuration, adequate data-processing times, comparable to the CLARREO cluster, were found. The assessment of alternatives to the CLARREO cluster continues and several options, such as a NASA-based cluster, are being considered.

Highly correlated configuration interaction calculations on water with large orbital bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almora-Díaz, César X., E-mail: xalmora@fisica.unam.mx

2014-05-14

A priori selected configuration interaction (SCI) with truncation energy error [C. F. Bunge, J. Chem. Phys. 125, 014107 (2006)] and CI by parts [C. F. Bunge and R. Carbó-Dorca, J. Chem. Phys. 125, 014108 (2006)] are used to approximate the total nonrelativistic electronic ground state energy of water at fixed experimental geometry with CI up to sextuple excitations. Correlation-consistent polarized core-valence basis sets (cc-pCVnZ) up to sextuple zeta and augmented correlation-consistent polarized core-valence basis sets (aug-cc-pCVnZ) up to quintuple zeta quality are employed. Truncation energy errors range between less than 1 μhartree, and 100 μhartree for the largest orbital set. Coupledmore » cluster CCSD and CCSD(T) calculations are also obtained for comparison. Our best upper bound, −76.4343 hartree, obtained by SCI with up to sextuple excitations with a cc-pCV6Z basis recovers more than 98.8% of the correlation energy of the system, and it is only about 3 kcal/mol above the “experimental” value. Despite that the present energy upper bounds are far below all previous ones, comparatively large dispersion errors in the determination of the extrapolated energies to the complete basis set do not allow to determine a reliable estimation of the full CI energy with an accuracy better than 0.6 mhartree (0.4 kcal/mol)« less

Nonconventional screening of the Coulomb interaction in FexOy clusters: An ab initio study

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Rossen, S.; Friedrich, C.; Blügel, S.; Katsnelson, M. I.

2017-04-01

From microscopic point-dipole model calculations of the screening of the Coulomb interaction in nonpolar systems by polarizable atoms, it is known that screening strongly depends on dimensionality. For example, in one-dimensional systems, the short-range interaction is screened, while the long-range interaction is antiscreened. This antiscreening is also observed in some zero-dimensional structures, i.e., molecular systems. By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the FLAPW method, we study screening of the Coulomb interaction in FexOy clusters. For completeness, these results are compared with their bulk counterpart magnetite. It appears that the on-site Coulomb interaction is very well screened both in the clusters and bulk. On the other hand, for the intersite Coulomb interaction, the important observation is made that it is almost constant throughout the clusters, while for the bulk it is almost completely screened. More precisely and interestingly, in the clusters antiscreening is observed by means of ab initio calculations.

Structural transition in sputter-deposited amorphous germanium films by aging at ambient temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okugawa, M.; Nakamura, R., E-mail: nakamura@mtr.osakafu-u.ac.jp; Numakura, H.

The structure of amorphous Ge (a-Ge) films prepared by sputter-deposition and the effects of aging at ambient temperature and pressure were studied by pair-distribution-function (PDF) analysis from electron scattering and molecular dynamics simulations. The PDFs of the as-deposited and aged samples for 3–13 months showed that the major peaks for Ge-Ge bonds decrease in intensity and broaden with aging for up to 7 months. In the PDFs of a-Ge of molecular dynamics simulation obtained by quenching liquid at different rates, the major peak intensities of a slowly cooled model are higher than those of a rapidly cooled model. Analyses onmore » short- and medium-range configurations show that the slowly cooled model includes a certain amount of medium-range ordered (MRO) clusters, while the rapidly cooled model includes liquid-like configurations rather than MRO clusters. The similarity between experimental and computational PDFs implies that as-deposited films are similar in structure to the slowly cooled model, whereas the fully aged films are similar to the rapidly cooled model. It is assumed that as they undergo room-temperature aging, the MRO clusters disintegrate and transform into liquid-like regions in the same matrix. This transition in local configurations is discussed in terms of instability and the non-equilibrium of nanoclusters produced by a vapor-deposition process.« less

Incentives, Program Configuration, and Employee Uptake of Workplace Wellness Programs.

PubMed

Huang, Haijing; Mattke, Soeren; Batorsky, Benajmin; Miles, Jeremy; Liu, Hangsheng; Taylor, Erin

2016-01-01

The aim of this study was to determine the effect of wellness program configurations and financial incentives on employee participation rate. We analyze a nationally representative survey on workplace wellness programs from 407 employers using cluster analysis and multivariable regression analysis. Employers who offer incentives and provide a comprehensive set of program offerings have higher participation rates. The effect of incentives differs by program configuration, with the strongest effect found for comprehensive and prevention-focused programs. Among intervention-focused programs, incentives are not associated with higher participation. Wellness programs can be grouped into distinct configurations, which have different workplace health focuses. Although monetary incentives can be effective in improving employee participation, the magnitude and significance of the effect is greater for some program configurations than others.

Construction of CASCI-type wave functions for very large active spaces.

PubMed

Boguslawski, Katharina; Marti, Konrad H; Reiher, Markus

2011-06-14

We present a procedure to construct a configuration-interaction expansion containing arbitrary excitations from an underlying full-configuration-interaction-type wave function defined for a very large active space. Our procedure is based on the density-matrix renormalization group (DMRG) algorithm that provides the necessary information in terms of the eigenstates of the reduced density matrices to calculate the coefficient of any basis state in the many-particle Hilbert space. Since the dimension of the Hilbert space scales binomially with the size of the active space, a sophisticated Monte Carlo sampling routine is employed. This sampling algorithm can also construct such configuration-interaction-type wave functions from any other type of tensor network states. The configuration-interaction information obtained serves several purposes. It yields a qualitatively correct description of the molecule's electronic structure, it allows us to analyze DMRG wave functions converged for the same molecular system but with different parameter sets (e.g., different numbers of active-system (block) states), and it can be considered a balanced reference for the application of a subsequent standard multi-reference configuration-interaction method.

The role of childhood maltreatment in the altered trait and global expression of personality in cocaine addiction

PubMed Central

Brents, Lisa K; Tripathi, Shanti Prakash; Young, Jonathan; James, G Andrew; Kilts, Clinton D

2015-01-01

Background and aims Drug addictions are debilitating disorders that are highly associated with personality abnormalities. Early life stress (ELS) is a common risk factor for addiction and personality disturbances, but the relationships between ELS, addiction, and personality are poorly understood. Methods Ninety-five research participants were assessed for and grouped by ELS history and cocaine dependence. NEO-FFI personality measures were compared between the groups to define ELS− and addiction-related differences in personality traits. ELS and cocaine dependence were then examined as predictors of personality trait scores. Finally, k-means clustering was used to uncover clusters of personality trait configurations within the sample. Odds of cluster membership across subject groups was then determined. Results Trait expression differed significantly across subject groups. Cocaine-dependent subjects with a history of ELS (cocaine+/ELS+) displayed the greatest deviations in normative personality. Cocaine dependence significantly predicted four traits, while ELS predicted neuroticism and agreeableness; there was no interaction effect between ELS and cocaine dependence. The cluster analysis identified four distinct personality profiles: Open, Gregarious, Dysphoric, and Closed. Distribution of these profiles across subject groups differed significantly. Inclusion in cocaine+/ELS+, cocaine−/ELS+, and cocaine−/ELS− groups significantly increased the odds of expressing the Dysphoric, Open and Gregarious profiles, respectively. Conclusions Cocaine dependence and early life stress were significantly and differentially associated with altered expression of individual personality traits and their aggregation as personality profiles, suggesting that individuals who are at-risk for developing addictions due to ELS exposure may benefit from personality centered approaches as an early intervention and prevention. PMID:25805246

Ab initio study of the Coulomb interaction in NbxCo clusters: Strong on-site versus weak nonlocal screening

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Mertig, I.; Katsnelson, M. I.

2018-01-01

By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the full-potential linearized augmented plane wave method, we study the screening of the Coulomb interaction in NbxCo (1 ≤x ≤9 ) clusters. In addition, these results are compared with pure bcc Nb bulk. We find that for all clusters the on-site Coulomb interaction in RPA is strongly screened, whereas the intersite nonlocal Coulomb interaction is weakly screened and for some clusters it is unscreened or even antiscreened. This is in strong contrast with pure Nb bulk, where the intersite Coulomb interaction is almost completely screened. Furthermore, constrained RPA calculations reveal that the contribution of the Co 3 d → 3 d channel to the total screening of the Co 3 d electrons is small. Moreover, we find that both the on-site and intersite Coulomb interaction parameters decrease in a reasonable approximation linearly with the cluster size and for clusters having more than 20 Nb atoms a transition from 0D to 3D screening is expected to take place.

Disentangling giant component and finite cluster contributions in sparse random matrix spectra.

PubMed

Kühn, Reimer

2016-04-01

We describe a method for disentangling giant component and finite cluster contributions to sparse random matrix spectra, using sparse symmetric random matrices defined on Erdős-Rényi graphs as an example and test bed. Our methods apply to sparse matrices defined in terms of arbitrary graphs in the configuration model class, as long as they have finite mean degree.

Quantitative properties of clustering within modern microscopic nuclear models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Volya, A.; Tchuvil’sky, Yu. M., E-mail: tchuvl@nucl-th.sinp.msu.ru

2016-09-15

A method for studying cluster spectroscopic properties of nuclear fragmentation, such as spectroscopic amplitudes, cluster form factors, and spectroscopic factors, is developed on the basis of modern precision nuclear models that take into account the mixing of large-scale shell-model configurations. Alpha-cluster channels are considered as an example. A mathematical proof of the need for taking into account the channel-wave-function renormalization generated by exchange terms of the antisymmetrization operator (Fliessbach effect) is given. Examples where this effect is confirmed by a high quality of the description of experimental data are presented. By and large, the method in question extends substantially themore » possibilities for studying clustering phenomena in nuclei and for improving the quality of their description.« less

Structural, electronic and vibrational properties of GexCy (x+y=2-5) nanoclusters: A B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Goswami, Sohini; Saha, Sushmita; Yadav, R. K.

2015-11-01

An ab-initio study of the stability, structural and electronic properties has been made for 84 germanium carbide nanoclusters, GexCy (x+y=2-5). The configuration possessing the maximum value of final binding energy (FBE), among the various configurations corresponding to a fixed x+y=n value, is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize fully the geometries of the nanoclusters. The binding energies (BE), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps have been obtained for all the clusters and the bond lengths have been reported for the most stable clusters. We have considered the zero point energy (ZPE) corrections. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have also been investigated for the most stable structures. The configurations containing the carbon atoms in majority are seen to be the most stable structures. The strong C-C bond has important role in stabilizing the clusters. For the clusters containing one germanium atom and all the other as carbon atoms, the BE increases monotonically with the number of the carbon atoms. The HOMO-LUMO gap, IPs and EAs fluctuates with increase in the number of atoms. The nanoclusters containing even number of carbon atoms have large HOMO-LUMO gaps and IPs, whereas the nanoclusters containing even number of carbon atoms have small EAs. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA). The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in the experiments.

On the Interpretation of the level structure of the Ground 3d5 Manifold of Mn III, Fe IV, Co V and Ni VI

NASA Astrophysics Data System (ADS)

Leushin, A. M.

2011-10-01

The level structure of the ground 3d5 configuration of Mn2+, Fe3+, Co4+ and Ni5+ ions was theoretically interpreted by means of a least-squares fit of the energy parameters to the observed values within the framework of the single-configuration approximation. In the Hamiltonian in addition to real electrostatic, spin-orbit, and spin-spin interactions, electrostatic and spin-orbit interactions correlated by configuration mixing were included. It was shown that the correct positions of almost all the energy levels are determined when the Hamiltonian includes the terms of the lineal (two-body operators) and nonlinear (three-body operators) theory of the configuration interaction. The most correct theoretical description of the experimental spectra was obtained by taking into account relativistic interactions and correlation effects of spin-orbit interactions. Adjustable parameters of the interactions included into the Hamiltonian were found.

Cluster randomised crossover trials with binary data and unbalanced cluster sizes: application to studies of near-universal interventions in intensive care.

PubMed

Forbes, Andrew B; Akram, Muhammad; Pilcher, David; Cooper, Jamie; Bellomo, Rinaldo

2015-02-01

Cluster randomised crossover trials have been utilised in recent years in the health and social sciences. Methods for analysis have been proposed; however, for binary outcomes, these have received little assessment of their appropriateness. In addition, methods for determination of sample size are currently limited to balanced cluster sizes both between clusters and between periods within clusters. This article aims to extend this work to unbalanced situations and to evaluate the properties of a variety of methods for analysis of binary data, with a particular focus on the setting of potential trials of near-universal interventions in intensive care to reduce in-hospital mortality. We derive a formula for sample size estimation for unbalanced cluster sizes, and apply it to the intensive care setting to demonstrate the utility of the cluster crossover design. We conduct a numerical simulation of the design in the intensive care setting and for more general configurations, and we assess the performance of three cluster summary estimators and an individual-data estimator based on binomial-identity-link regression. For settings similar to the intensive care scenario involving large cluster sizes and small intra-cluster correlations, the sample size formulae developed and analysis methods investigated are found to be appropriate, with the unweighted cluster summary method performing well relative to the more optimal but more complex inverse-variance weighted method. More generally, we find that the unweighted and cluster-size-weighted summary methods perform well, with the relative efficiency of each largely determined systematically from the study design parameters. Performance of individual-data regression is adequate with small cluster sizes but becomes inefficient for large, unbalanced cluster sizes. When outcome prevalences are 6% or less and the within-cluster-within-period correlation is 0.05 or larger, all methods display sub-nominal confidence interval coverage, with the less prevalent the outcome the worse the coverage. As with all simulation studies, conclusions are limited to the configurations studied. We confined attention to detecting intervention effects on an absolute risk scale using marginal models and did not explore properties of binary random effects models. Cluster crossover designs with binary outcomes can be analysed using simple cluster summary methods, and sample size in unbalanced cluster size settings can be determined using relatively straightforward formulae. However, caution needs to be applied in situations with low prevalence outcomes and moderate to high intra-cluster correlations. © The Author(s) 2014.

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity.

PubMed

Nicoludis, John M; Lau, Sze-Yi; Schärfe, Charlotta P I; Marks, Debora S; Weihofen, Wilhelm A; Gaudet, Rachelle

2015-11-03

Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1-EC3, containing the homophilic specificity-determining region, of two mouse clustered Pcdh isoforms (PcdhγA1 and PcdhγC3) to investigate the nature of the homophilic interaction. Within the crystal lattices, we observe antiparallel interfaces consistent with a role in trans cell-cell contact. Antiparallel dimerization is supported by evolutionary correlations. Two interfaces, located primarily on EC2-EC3, involve distinctive clustered Pcdh structure and sequence motifs, lack predicted glycosylation sites, and contain residues highly conserved in orthologs but not paralogs, pointing toward their biological significance as homophilic interaction interfaces. These two interfaces are similar yet distinct, reflecting a possible difference in interaction architecture between clustered Pcdh subfamilies. These structures initiate a molecular understanding of clustered Pcdh assemblies that are required to produce functional neuronal networks. Copyright © 2015 Elsevier Ltd. All rights reserved.

Graph configuration model based evaluation of the education-occupation match

PubMed Central

2018-01-01

To study education—occupation matchings we developed a bipartite network model of education to work transition and a graph configuration model based metric. We studied the career paths of 15 thousand Hungarian students based on the integrated database of the National Tax Administration, the National Health Insurance Fund, and the higher education information system of the Hungarian Government. A brief analysis of gender pay gap and the spatial distribution of over-education is presented to demonstrate the background of the research and the resulted open dataset. We highlighted the hierarchical and clustered structure of the career paths based on the multi-resolution analysis of the graph modularity. The results of the cluster analysis can support policymakers to fine-tune the fragmented program structure of higher education. PMID:29509783

Graph configuration model based evaluation of the education-occupation match.

PubMed

Gadar, Laszlo; Abonyi, Janos

2018-01-01

To study education-occupation matchings we developed a bipartite network model of education to work transition and a graph configuration model based metric. We studied the career paths of 15 thousand Hungarian students based on the integrated database of the National Tax Administration, the National Health Insurance Fund, and the higher education information system of the Hungarian Government. A brief analysis of gender pay gap and the spatial distribution of over-education is presented to demonstrate the background of the research and the resulted open dataset. We highlighted the hierarchical and clustered structure of the career paths based on the multi-resolution analysis of the graph modularity. The results of the cluster analysis can support policymakers to fine-tune the fragmented program structure of higher education.

Re-solution of xenon clusters in plutonium dioxide under the collision cascade impact: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Seitov, D. D.; Nekrasov, K. A.; Kupryazhkin, A. Ya.; Gupta, S. K.; Akilbekov, A. T.

2017-09-01

The interaction of xenon clusters with the collision cascades in the PuO2 crystals is investigated using the molecular dynamics simulation and the approximation of the pair interaction potentials. The potentials of interaction of Xe atoms with the surrounding particles in the crystal lattice are suggested, that are valid in the range of high collision energies. The cascades created by the recoil 235U ions formed as the plutonium α-decay product are considered, and the influence of such cascades on the structure of the xenon clusters is analyzed. It is shown, that the cascade-cluster interaction leads to release of the xenon atoms from the clusters and their subsequent re-solution in the crystal bulk.

Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

PubMed

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

2016-07-07

An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.

General purpose computer program for interacting supersonic configurations: Programmer's manual

NASA Technical Reports Server (NTRS)

Crill, W.; Dale, B.

1977-01-01

The program ISCON (Interacting Supersonic Configuration) is described. The program is in support of the problem to generate a numerical procedure for determining the unsteady dynamic forces on interacting wings and tails in supersonic flow. Subroutines are presented along with the complete FORTRAN source listing.

The energy and stability of helium-related cluster in nickel: A study of molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Gong, Hengfeng; Wang, Chengbin; Zhang, Wei; Xu, Jian; Huai, Ping; Deng, Huiqiu; Hu, Wangyu

2016-02-01

Using molecular dynamics simulation, we investigated the energy and stability of helium-related cluster in nickel. All the binding energies of the He-related clusters are demonstrated to be positive and increase with the cluster sizes. Due to the pre-existed self-interstitial nickel atom, the trapping capability of vacancy to defects becomes weak. Besides, the minimum energy configurations of He-related clusters exhibit the very high symmetry in the local atomistic environment. And for the HeN and HeNV1SIA1 clusters, the average length of He-He bonds shortens, but it elongates for the HeNV1 clusters with helium cluster sizes. The helium-to-vacancy ratio plays a decisive role on the binding energies of HeNVM cluster. These results can provide some excellent clues to insight the initial stage of helium bubbles nucleation and growth in the Ni-based alloys for the Generation-IV Molten Salt Reactor.

Algorithms of maximum likelihood data clustering with applications

NASA Astrophysics Data System (ADS)

Giada, Lorenzo; Marsili, Matteo

2002-12-01

We address the problem of data clustering by introducing an unsupervised, parameter-free approach based on maximum likelihood principle. Starting from the observation that data sets belonging to the same cluster share a common information, we construct an expression for the likelihood of any possible cluster structure. The likelihood in turn depends only on the Pearson's coefficient of the data. We discuss clustering algorithms that provide a fast and reliable approximation to maximum likelihood configurations. Compared to standard clustering methods, our approach has the advantages that (i) it is parameter free, (ii) the number of clusters need not be fixed in advance and (iii) the interpretation of the results is transparent. In order to test our approach and compare it with standard clustering algorithms, we analyze two very different data sets: time series of financial market returns and gene expression data. We find that different maximization algorithms produce similar cluster structures whereas the outcome of standard algorithms has a much wider variability.

Relativistic protons in the Coma galaxy cluster: first gamma-ray constraints ever on turbulent reacceleration

NASA Astrophysics Data System (ADS)

Brunetti, G.; Zimmer, S.; Zandanel, F.

2017-12-01

The Fermi-LAT (Large Area Telescope) collaboration recently published deep upper limits to the gamma-ray emission of the Coma cluster, a cluster hosting the prototype of giant radio haloes. In this paper, we extend previous studies and use a formalism that combines particle reacceleration by turbulence and the generation of secondary particles in the intracluster medium to constrain relativistic protons and their role for the origin of the radio halo. We conclude that a pure hadronic origin of the halo is clearly disfavoured as it would require excessively large magnetic fields. However, secondary particles can still generate the observed radio emission if they are reaccelerated. For the first time the deep gamma-ray limits allow us to derive meaningful constraints if the halo is generated during phases of reacceleration of relativistic protons and their secondaries by cluster-scale turbulence. In this paper, we explore a relevant range of parameter space of reacceleration models of secondaries. Within this parameter space, a fraction of model configurations is already ruled out by current gamma-ray limits, including the cases that assume weak magnetic fields in the cluster core, B ≤ 2-3 μG. Interestingly, we also find that the flux predicted by a large fraction of model configurations assuming magnetic fields consistent with Faraday rotation measures (RMs) is not far from the limits. This suggests that a detection of gamma-rays from the cluster might be possible in the near future, provided that the electrons generating the radio halo are secondaries reaccelerated and the magnetic field in the cluster is consistent with that inferred from RM.

Is HO3 minimum cis or trans? An analytic full-dimensional ab initio isomerization path.

PubMed

Varandas, A J C

2011-05-28

The minimum energy path for isomerization of HO(3) has been explored in detail using accurate high-level ab initio methods and techniques for extrapolation to the complete basis set limit. In agreement with other reports, the best estimates from both valence-only and all-electron single-reference methods here utilized predict the minimum of the cis-HO(3) isomer to be deeper than the trans-HO(3) one. They also show that the energy varies by less than 1 kcal mol(-1) or so over the full isomerization path. A similar result is found from valence-only multireference configuration interaction calculations with the size-extensive Davidson correction and a correlation consistent triple-zeta basis, which predict the energy difference between the two isomers to be of only Δ = -0.1 kcal mol(-1). However, single-point multireference calculations carried out at the optimum triple-zeta geometry with basis sets of the correlation consistent family but cardinal numbers up to X = 6 lead upon a dual-level extrapolation to the complete basis set limit of Δ = (0.12 ± 0.05) kcal mol(-1). In turn, extrapolations with the all-electron single-reference coupled-cluster method including the perturbative triples correction yield values of Δ = -0.19 and -0.03 kcal mol(-1) when done from triple-quadruple and quadruple-quintuple zeta pairs with two basis sets of increasing quality, namely cc-cpVXZ and aug-cc-pVXZ. Yet, if added a value of 0.25 kcal mol(-1) that accounts for the effect of triple and perturbative quadruple excitations with the VTZ basis set, one obtains a coupled cluster estimate of Δ = (0.14 ± 0.08) kcal mol(-1). It is then shown for the first time from systematic ab initio calculations that the trans-HO(3) isomer is more stable than the cis one, in agreement with the available experimental evidence. Inclusion of the best reported zero-point energy difference (0.382 kcal mol(-1)) from multireference configuration interaction calculations enhances further the relative stability to ΔE(ZPE) = (0.51 ± 0.08) kcal mol(-1). A scheme is also suggested to model the full-dimensional isomerization potential-energy surface using a quadratic expansion that is parametrically represented by a Fourier analysis in the torsion angle. The method illustrated at the raw and complete basis-set limit coupled-cluster levels can provide a valuable tool for a future analysis of the available (incomplete thus far) experimental rovibrational data. This journal is © the Owner Societies 2011

Characterization of Glutaredoxin Fe-S Cluster-Binding Interactions Using Circular Dichroism Spectroscopy.

PubMed

Albetel, Angela-Nadia; Outten, Caryn E

2018-01-01

Monothiol glutaredoxins (Grxs) with a conserved Cys-Gly-Phe-Ser (CGFS) active site are iron-sulfur (Fe-S) cluster-binding proteins that interact with a variety of partner proteins and perform crucial roles in iron metabolism including Fe-S cluster transfer, Fe-S cluster repair, and iron signaling. Various analytical and spectroscopic methods are currently being used to monitor and characterize glutaredoxin Fe-S cluster-dependent interactions at the molecular level. The electronic, magnetic, and vibrational properties of the protein-bound Fe-S cluster provide a convenient handle to probe the structure, function, and coordination chemistry of Grx complexes. However, some limitations arise from sample preparation requirements, complexity of individual techniques, or the necessity for combining multiple methods in order to achieve a complete investigation. In this chapter, we focus on the use of UV-visible circular dichroism spectroscopy as a fast and simple initial approach for investigating glutaredoxin Fe-S cluster-dependent interactions. © 2018 Elsevier Inc. All rights reserved.

Mechanism of ubiquinol oxidation by the bc(1) complex: role of the iron sulfur protein and its mobility.

PubMed

Crofts, A R; Guergova-Kuras, M; Huang, L; Kuras, R; Zhang, Z; Berry, E A

1999-11-30

Native structures of ubihydroquinone:cytochrome c oxidoreductase (bc(1) complex) from different sources, and structures with inhibitors in place, show a 16-22 A displacement of the [2Fe-2S] cluster and the position of the C-terminal extrinsic domain of the iron sulfur protein. None of the structures shows a static configuration that would allow catalysis of all partial reactions of quinol oxidation. We have suggested that the different conformations reflect a movement of the subunit necessary for catalysis. The displacement from an interface with cytochrome c(1) in native crystals to an interface with cytochrome b is induced by stigmatellin or 5-n-undecyl-6-hydroxy-4,7-dioxobenzothiazole (UHDBT) and involves ligand formation between His-161 of the [2Fe-2S] binding cluster and the inhibitor. The movement is a rotational displacement, so that the same conserved docking surface on the iron sulfur protein interacts with cytochrome c(1) and with cytochrome b. The mobile extrinsic domain retains essentially the same tertiary structure, and the anchoring N-terminal tail remains in the same position. The movement occurs through an extension of a helical segment in the short linking span. We report details of the protein structure for the two main configurations in the chicken heart mitochondrial complex and discuss insights into mechanism provided by the structures and by mutant strains in which the docking at the cytochrome b interface is impaired. The movement of the iron sulfur protein represents a novel mechanism of electron transfer, in which a tethered mobile head allows electron transfer through a distance without the entropic loss from free diffusion.

Neuronal somata and extrasomal compartments play distinct roles during synapse formation between Lymnaea neurons.

PubMed

Xu, Fenglian; Luk, Collin C; Wiersma-Meems, Ryanne; Baehre, Kelly; Herman, Cameron; Zaidi, Wali; Wong, Noelle; Syed, Naweed I

2014-08-20

Proper synapse formation is pivotal for all nervous system functions. However, the precise mechanisms remain elusive. Moreover, compared with the neuromuscular junction, steps regulating the synaptogenic program at central cholinergic synapses remain poorly defined. In this study, we identified different roles of neuronal compartments (somal vs extrasomal) in chemical and electrical synaptogenesis. Specifically, the electrically synapsed Lymnaea pedal dorsal A cluster neurons were used to study electrical synapses, whereas chemical synaptic partners, visceral dorsal 4 (presynaptic, cholinergic), and left pedal dorsal 1 (LPeD1; postsynaptic) were explored for chemical synapse formation. Neurons were cultured in a soma-soma or soma-axon configuration and synapses explored electrophysiologically. We provide the first direct evidence that electrical synapses develop in a soma-soma, but not soma-axon (removal of soma) configuration, indicating the requirement of gene transcription regulation in the somata of both synaptic partners. In addition, the soma-soma electrical coupling was contingent upon trophic factors present in Lymnaea brain-conditioned medium. Further, we demonstrate that chemical (cholinergic) synapses between soma-soma and soma-axon pairs were indistinguishable, with both exhibiting a high degree of contact site and target cell type specificity. We also provide direct evidence that presynaptic cell contact-mediated, clustering of postsynaptic cholinergic receptors at the synaptic site requires transmitter-receptor interaction, receptor internalization, and a protein kinase C-dependent lateral migration toward the contact site. This study provides novel insights into synaptogenesis between central neurons revealing both distinct and synergistic roles of cell-cell signaling and extrinsic trophic factors in executing the synaptogenic program. Copyright © 2014 the authors 0270-6474/14/3411304-12$15.00/0.

Direct Determination of Wavenumbers of ULF Waves Using the Cluster Multipoint and Multicomponent Measurements

NASA Astrophysics Data System (ADS)

Grison, B.; Escoubet, C.; Santolik, O.; Cornilleau-Wehrlin, N.

2013-12-01

The wavenumber is a key parameter to understand the physics of the interactions between the electromagnetic waves and the ionized particles in space plasmas. Search-coil magnetometers and electric antennas measure time series of both magnetic and electric field fluctuations, respectively. The fleet of four Cluster spacecraft made possible to determine the full wave vector and even to differentiate the waves present at the same frequency in the spacecraft frame through various techniques: k-filtering analysis, wave telescope, phase differentiating method. However the fleet configuration (inter-spacecraft separation, tetrahedron elongation and planarity) limit the possibilities to use these techniques. From single spacecraft measurements, assumptions concerning the wave mode -and thus, concerning the physical processes- are usually required to derive the corresponding wavenumber. Using three orthogonal magnetic components and two electric antennas, it is possible to estimate n/Z where n is the refractive index and Z the transfer function of the interface between the plasma and the electric antennas. For ULF waves we assume Z=1 and we thus obtain the wavenumber. We test this hypothesis on a case where the spacecraft are in a close configuration in the distant cusp region and where we are able to apply the k-filtering analysis, too. The results obtained by multispacecraft and multicomponents analysis are close to each other and permit us to precise the value of Z. We test this procedure on several events (in various regions of the magnetosphere) in order to get more precise wave number measurements from the single spacecraft analysis. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7-SPACE-2010-1) under grant agreement n. 284520 (MAARBLE).

Acid/base equilibria in clusters and their role in proton exchange membranes: Computational insight

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glezakou, Vanda A; Dupuis, Michel; Mundy, Christopher J

2007-10-24

We describe molecular orbital theory and ab initio molecular dynamics studies of acid/base equilibria of clusters AH:(H 2O) n↔A -:H +(H 2O) n in low hydration regime (n = 1-4), where AH is a model of perfluorinated sulfonic acids, RSO 3H (R = CF 3CF 2), encountered in polymeric electrolyte membranes of fuel cells. Free energy calculations on the neutral and ion pair structures for n = 3 indicate that the two configurations are close in energy and are accessible in the fluctuation dynamics of proton transport. For n = 1,2 the only relevant configuration is the neutral form. Thismore » was verified through ab initio metadynamics simulations. These findings suggest that bases are directly involved in the proton transport at low hydration levels. In addition, the gas phase proton affinity of the model sulfonic acid RSO 3H was found to be comparable to the proton affinity of water. Thus, protonated acids can also play a role in proton transport under low hydration conditions and under high concentration of protons. This work was supported by the Division of Chemical Science, Office of Basic Energy Sciences, US Department of Energy (DOE under Contract DE-AC05-76RL)1830. Computations were performed on computers of the Molecular Interactions and Transformations (MI&T) group and MSCF facility of EMSL, sponsored by US DOE and OBER located at PNNL. This work was benefited from resource of the National Energy Research Scientific Computing Centre, supported by the Office of Science of the US DOE, under Contract No. DE-AC03-76SF00098.« less

Cluster Approach to Network Interaction in Pedagogical University

ERIC Educational Resources Information Center

Chekaleva, Nadezhda V.; Makarova, Natalia S.; Drobotenko, Yulia B.

2016-01-01

The study presented in the article is devoted to the analysis of theory and practice of network interaction within the framework of education clusters. Education clusters are considered to be a novel form of network interaction in pedagogical education in Russia. The aim of the article is to show the advantages and disadvantages of the cluster…

Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonate-siliciclastic alternations of the Hainich CZE, central Germany

NASA Astrophysics Data System (ADS)

Kohlhepp, Bernd; Lehmann, Robert; Seeber, Paul; Küsel, Kirsten; Trumbore, Susan E.; Totsche, Kai U.

2017-12-01

The quality of near-surface groundwater reservoirs is controlled, but also threatened, by manifold surface-subsurface interactions. Vulnerability studies typically evaluate the variable interplay of surface factors (land management, infiltration patterns) and subsurface factors (hydrostratigraphy, flow properties) in a thorough way, but disregard the resulting groundwater quality. Conversely, hydrogeochemical case studies that address the chemical evolution of groundwater often lack a comprehensive analysis of the structural buildup. In this study, we aim to reconstruct the actual spatial groundwater quality pattern from a synoptic analysis of the hydrostratigraphy, lithostratigraphy, pedology and land use in the Hainich Critical Zone Exploratory (Hainich CZE). This CZE represents a widely distributed yet scarcely described setting of thin-bedded mixed carbonate-siliciclastic strata in hillslope terrains. At the eastern Hainich low-mountain hillslope, bedrock is mainly formed by alternated marine sedimentary rocks of the Upper Muschelkalk (Middle Triassic) that partly host productive groundwater resources. Spatial patterns of the groundwater quality of a 5.4 km long well transect are derived by principal component analysis and hierarchical cluster analysis. Aquifer stratigraphy and geostructural links were deduced from lithological drill core analysis, mineralogical analysis, geophysical borehole logs and mapping data. Maps of preferential recharge zones and recharge potential were deduced from digital (soil) mapping, soil survey data and field measurements of soil hydraulic conductivities (Ks). By attributing spatially variable surface and subsurface conditions, we were able to reconstruct groundwater quality clusters that reflect the type of land management in their preferential recharge areas, aquifer hydraulic conditions and cross-formational exchange via caprock sinkholes or ascending flow. Generally, the aquifer configuration (spatial arrangement of strata, valley incision/outcrops) and related geostructural links (enhanced recharge areas, karst phenomena) control the role of surface factors (input quality and locations) vs. subsurface factors (water-rock interaction, cross-formational flow) for groundwater quality in the multi-layered aquifer system. Our investigation reveals general properties of alternating sequences in hillslope terrains that are prone to forming multi-layered aquifer systems. This synoptic analysis is fundamental and indispensable for a mechanistic understanding of ecological functioning, sustainable resource management and protection.

Young star clusters in the interacting galaxies of Hickson Compact Group 90

NASA Astrophysics Data System (ADS)

Miah, J. A.; Sharples, R. M.; Cho, J.

2015-03-01

Deep images of Hickson Compact Group 90 (HCG 90) have been obtained using the Advanced Camera for Surveys on the Hubble Space Telescope. We report results for star clusters observed in the interacting pair of galaxies NGC 7174 and NGC 7176. We present magnitude and colour distributions for the observed cluster population and find that the majority of objects show colours similar to intermediate/old age (>1 Gyr) globular clusters. However, a significant population of blue star clusters are also observed which may have formed from the tidal interaction currently occurring between the two galaxies. We find luminosity function turnover magnitudes of m^{TO}g = 25.1 ± 0.1 and m^{TO}z = 24.3 ± 0.1 for the g and z bands, respectively, implying distances of Dg = 28.8 ± 2.6 Mpc and Dz = 34.7 ± 3.1 Mpc to these galaxies, using the globular cluster luminosity function method. Lastly, we determine a total cluster population of approximately NGC ≃ 212 ± 10 over all magnitudes and a low specific frequency of SN ˜ 0.6 ± 0.1 for this pair of interacting elliptical and spiral galaxies. The small globular cluster population is likely due to tidal interactions taking place between the two galaxies which may have stripped many progenitor clusters away and formed the diffuse light observed at the core of HCG 90.

Effects of radiation reaction in the interaction between cluster media and high intensity lasers in the radiation dominant regime

NASA Astrophysics Data System (ADS)

Iwata, Natsumi; Nagatomo, Hideo; Fukuda, Yuji; Matsui, Ryutaro; Kishimoto, Yasuaki

2016-06-01

Interaction between media composed of clusters and high intensity lasers in the radiation dominant regime, i.e., intensity of 10 22 - 23 W / cm 2 , is studied based on the particle-in-cell simulation that includes the radiation reaction. By introducing target materials that have the same total mass but different internal structures, i.e., uniform plasma and cluster media with different cluster radii, we investigate the effect of the internal structure on the interaction dynamics, high energy radiation emission, and its reaction. Intense radiation emission is found in the cluster media where electrons exhibit non-ballistic motions suffering from strong accelerations by both the penetrated laser field and charge separation field of clusters. As a result, the clustered structure increases the energy conversion into high energy radiations significantly at the expense of the conversion into particles, while the total absorption rate into radiation and particles remains unchanged from the absorption rate into particles in the case without radiation reaction. The maximum ion energy achieved in the interaction with cluster media is found to be decreased through the radiation reaction to electrons into the same level with that achieved in the interaction with the uniform plasma. The clustered structure thus enhances high energy radiation emission rather than the ion acceleration in the considered intensity regime.

10B+α states with chain-like structures in 14N

NASA Astrophysics Data System (ADS)

Kanada-En'yo, Yoshiko

2015-12-01

I investigate 10B+α -cluster states of 14N with a 10B+α -cluster model. Near the α -decay threshold energy, I obtain Kπ=3+ and Kπ=1+ rotational bands having 10B(3+) +α and 10B(1+) +α components, respectively. I assign the bandhead state of the Kπ=3+ band to the experimental 3+ at Ex=13.19 MeV of 14N observed in α scattering reactions by 10B and show that the calculated α -decay width is consistent with the experimental data. I discuss an α -cluster motion around the 10B cluster and show that the Kπ=3+ and Kπ=1+ rotational bands contain an enhanced component of a linear-chain 3 α configuration, in which an α cluster is localized in the longitudinal direction around the deformed 10B cluster.

STELLAR ENCOUNTER RATE IN GALACTIC GLOBULAR CLUSTERS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bahramian, Arash; Heinke, Craig O.; Sivakoff, Gregory R.

2013-04-01

The high stellar densities in the cores of globular clusters cause significant stellar interactions. These stellar interactions can produce close binary mass-transferring systems involving compact objects and their progeny, such as X-ray binaries and radio millisecond pulsars. Comparing the numbers of these systems and interaction rates in different clusters drives our understanding of how cluster parameters affect the production of close binaries. In this paper we estimate stellar encounter rates ({Gamma}) for 124 Galactic globular clusters based on observational data as opposed to the methods previously employed, which assumed 'King-model' profiles for all clusters. By deprojecting cluster surface brightness profilesmore » to estimate luminosity density profiles, we treat 'King-model' and 'core-collapsed' clusters in the same way. In addition, we use Monte Carlo simulations to investigate the effects of uncertainties in various observational parameters (distance, reddening, surface brightness) on {Gamma}, producing the first catalog of globular cluster stellar encounter rates with estimated errors. Comparing our results with published observations of likely products of stellar interactions (numbers of X-ray binaries, numbers of radio millisecond pulsars, and {gamma}-ray luminosity) we find both clear correlations and some differences with published results.« less

The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster

NASA Astrophysics Data System (ADS)

Löwe, P.; Klump, J.; Thaler, J.

2012-04-01

Compute clusters can be used as GIS workbenches, their wealth of resources allow us to take on geocomputation tasks which exceed the limitations of smaller systems. To harness these capabilities requires a Geographic Information System (GIS), able to utilize the available cluster configuration/architecture and a sufficient degree of user friendliness to allow for wide application. In this paper we report on the first successful porting of GRASS GIS, the oldest and largest Free Open Source (FOSS) GIS project, onto a compute cluster using Platform Computing's Load Sharing Facility (LSF). In 2008, GRASS6.3 was installed on the GFZ compute cluster, which at that time comprised 32 nodes. The interaction with the GIS was limited to the command line interface, which required further development to encapsulate the GRASS GIS business layer to facilitate its use by users not familiar with GRASS GIS. During the summer of 2011, multiple versions of GRASS GIS (v 6.4, 6.5 and 7.0) were installed on the upgraded GFZ compute cluster, now consisting of 234 nodes with 480 CPUs providing 3084 cores. The GFZ compute cluster currently offers 19 different processing queues with varying hardware capabilities and priorities, allowing for fine-grained scheduling and load balancing. After successful testing of core GIS functionalities, including the graphical user interface, mechanisms were developed to deploy scripted geocomputation tasks onto dedicated processing queues. The mechanisms are based on earlier work by NETELER et al. (2008). A first application of the new GIS functionality was the generation of maps of simulated tsunamis in the Mediterranean Sea for the Tsunami Atlas of the FP-7 TRIDEC Project (www.tridec-online.eu). For this, up to 500 processing nodes were used in parallel. Further trials included the processing of geometrically complex problems, requiring significant amounts of processing time. The GIS cluster successfully completed all these tasks, with processing times lasting up to full 20 CPU days. The deployment of GRASS GIS on a compute cluster allows our users to tackle GIS tasks previously out of reach of single workstations. In addition, this GRASS GIS cluster implementation will be made available to other users at GFZ in the course of 2012. It will thus become a research utility in the sense of "Software as a Service" (SaaS) and can be seen as our first step towards building a GFZ corporate cloud service.

A Fock space coupled cluster study on the electronic structure of the UO(2), UO(2) (+), U(4+), and U(5+) species.

PubMed

Infante, Ivan; Eliav, Ephraim; Vilkas, Marius J; Ishikawa, Yasuyuki; Kaldor, Uzi; Visscher, Lucas

2007-09-28

The ground and excited states of the UO(2) molecule have been studied using a Dirac-Coulomb intermediate Hamiltonian Fock-space coupled cluster approach (DC-IHFSCC). This method is unique in describing dynamic and nondynamic correlation energies at relatively low computational cost. Spin-orbit coupling effects have been fully included by utilizing the four-component Dirac-Coulomb Hamiltonian from the outset. Complementary calculations on the ionized systems UO(2) (+) and UO(2) (2+) as well as on the ions U(4+) and U(5+) were performed to assess the accuracy of this method. The latter calculations improve upon previously published theoretical work. Our calculations confirm the assignment of the ground state of the UO(2) molecule as a (3)Phi(2u) state that arises from the 5f(1)7s(1) configuration. The first state from the 5f(2) configuration is found above 10,000 cm(-1), whereas the first state from the 5f(1)6d(1) configuration is found at 5,047 cm(-1).

Hydration of Atmospheric Molecular Clusters: Systematic Configurational Sampling.

PubMed

Kildgaard, Jens; Mikkelsen, Kurt V; Bilde, Merete; Elm, Jonas

2018-05-09

We present a new systematic configurational sampling algorithm for investigating the potential energy surface of hydrated atmospheric molecular clusters. The algo- rithm is based on creating a Fibonacci sphere around each atom in the cluster and adding water molecules to each point in 9 different orientations. To allow the sam- pling of water molecules to existing hydrogen bonds, the cluster is displaced along the hydrogen bond and a water molecule is placed in between in three different ori- entations. Generated redundant structures are eliminated based on minimizing the root mean square distance (RMSD) of different conformers. Initially, the clusters are sampled using the semiempirical PM6 method and subsequently using density func- tional theory (M06-2X and ωB97X-D) with the 6-31++G(d,p) basis set. Applying the developed algorithm we study the hydration of sulfuric acid with up to 15 water molecules. We find that the additions of the first four water molecules "saturate" the sulfuric acid molecule and are more thermodynamically favourable than the addition of water molecule 5-15. Using the large generated set of conformers, we assess the performance of approximate methods (ωB97X-D, M06-2X, PW91 and PW6B95-D3) in calculating the binding energies and assigning the global minimum conformation compared to high level CCSD(T)-F12a/VDZ-F12 reference calculations. The tested DFT functionals systematically overestimates the binding energies compared to cou- pled cluster calculations, and we find that this deficiency can be corrected by a simple scaling factor.

Adapted managerial mathematical model to study the functions and interactions between enterprises in high-tech cluster

NASA Astrophysics Data System (ADS)

Anguelov, Kiril P.; Kaynakchieva, Vesela G.

2017-12-01

The aim of the current study is to research and analyze Adapted managerial mathematical model to study the functions and interactions between enterprises in high-tech cluster, and his approbation in given high-tech cluster; to create high-tech cluster, taking into account the impact of relationships between individual units in the cluster-Leading Enterprises, network of Enterprises subcontractors, economic infrastructure.

Cluster shell model: I. Structure of 9Be, 9B

NASA Astrophysics Data System (ADS)

Della Rocca, V.; Iachello, F.

2018-05-01

We calculate energy spectra, electromagnetic transition rates, longitudinal and transverse electron scattering form factors and log ft values for beta decay in 9Be, 9B, within the framework of a cluster shell model. By comparing with experimental data, we find strong evidence for the structure of these nuclei to be two α-particles in a dumbbell configuration with Z2 symmetry, plus an additional nucleon.

A density functional theory study on the structural and electronic properties of PbxSbySez (x + y + z = 2, 3) clusters

NASA Astrophysics Data System (ADS)

Peköz, Rengi˙n; Erkoç, Şaki˙r

2018-01-01

The structural and electronic properties of neutral ternary PbxSbySez clusters (x + y + z = 2, 3) in their ground states have been explored by means of density functional theory calculations. The geometric structures and binding energies are systematically explored and for the most stable configurations of each cluster type vibrational frequencies, charges on atoms, energy difference between highest occupied and lowest unoccupied molecular orbitals, and the possible dissociations channels have been analyzed. Depending on being binary or ternary cluster and composition, the most energetic structures have singlet, doublet or triplet ground states, and trimers prefer to form isosceles, equilateral or scalene triangle structure.

Interaction between ionic liquid cation and water: Infrared predissociation study of [bmim] +·(H 2O) n clusters

DOE PAGES

Voss, Jonathan M.; Marsh, Brett M.; Zhou, Jia; ...

2016-06-29

The infrared predissociation spectra of [bmim] +·(H 2O) n, n = 1–8, in the 2800–3800 cm –1 region are presented and analyzed with the help of electronic structure calculations. The results show that the water molecules solvate [bmim]+ by predominately interacting with the imidazolium C2–H moiety for the small n = 1 and 2 clusters. This is characterized by a redshifted and relatively intense C2–H stretch. For n ≥ 4 clusters, hydrogen-bond interactions between the water molecules drive the formation of ring isomers which interact on top of the imidazolium ring without any direct interaction with the C2–H. The watermore » arrangement in [bmim]+·(H 2O) n is similar to the low energy isomers of neutral water clusters up to the n = 6 cluster. This is not the case for the n = 8 cluster, which has the imidazolium ring disrupting the otherwise preferred cubic water structure. Here, the evolution of the solvation network around [bmim]+ illustrates the competing [bmim]+–water and water–water interactions.« less

W and X Photoluminescence Centers in Crystalline Si: Chasing Candidates at Atomic Level Through Multiscale Simulations

NASA Astrophysics Data System (ADS)

Aboy, María; Santos, Iván; López, Pedro; Marqués, Luis A.; Pelaz, Lourdes

2018-04-01

Several atomistic techniques have been combined to identify the structure of defects responsible for X and W photoluminescence lines in crystalline Si. We used kinetic Monte Carlo simulations to reproduce irradiation and annealing conditions used in photoluminescence experiments. We found that W and X radiative centers are related to small Si self-interstitial clusters but coexist with larger Si self-interstitials clusters that can act as nonradiative centers. We used molecular dynamics simulations to explore the many different configurations of small Si self-interstitial clusters, and selected those having symmetry compatible with W and X photoluminescence centers. Using ab initio simulations, we calculated their formation energy, donor levels, and energy of local vibrational modes. On the basis of photoluminescence experiments and our multiscale theoretical calculations, we discuss the possible atomic configurations responsible for W and X photoluminescence centers in Si. Our simulations also reveal that the intensity of photoluminescence lines is the result of competition between radiative centers and nonradiative competitors, which can explain the experimental quenching of W and X lines even in the presence of the photoluminescence centers.

Analysis of candidates for interacting galaxy clusters. I. A1204 and A2029/A2033

NASA Astrophysics Data System (ADS)

Gonzalez, Elizabeth Johana; de los Rios, Martín; Oio, Gabriel A.; Lang, Daniel Hernández; Tagliaferro, Tania Aguirre; Domínguez R., Mariano J.; Castellón, José Luis Nilo; Cuevas L., Héctor; Valotto, Carlos A.

2018-04-01

Context. Merging galaxy clusters allow for the study of different mass components, dark and baryonic, separately. Also, their occurrence enables to test the ΛCDM scenario, which can be used to put constraints on the self-interacting cross-section of the dark-matter particle. Aim. It is necessary to perform a homogeneous analysis of these systems. Hence, based on a recently presented sample of candidates for interacting galaxy clusters, we present the analysis of two of these cataloged systems. Methods: In this work, the first of a series devoted to characterizing galaxy clusters in merger processes, we perform a weak lensing analysis of clusters A1204 and A2029/A2033 to derive the total masses of each identified interacting structure together with a dynamical study based on a two-body model. We also describe the gas and the mass distributions in the field through a lensing and an X-ray analysis. This is the first of a series of works which will analyze these type of system in order to characterize them. Results: Neither merging cluster candidate shows evidence of having had a recent merger event. Nevertheless, there is dynamical evidence that these systems could be interacting or could interact in the future. Conclusions: It is necessary to include more constraints in order to improve the methodology of classifying merging galaxy clusters. Characterization of these clusters is important in order to properly understand the nature of these systems and their connection with dynamical studies.

Looking for Interacting Binaries in Old Open Clusters

NASA Technical Reports Server (NTRS)

Grindley, Jonathan

2005-01-01

We requested a 12 ks observation of the old open cluster NGC7142 with the aim to investigate the population of interacting binaries, and compare the properties with those of interacting binaries in other old open clusters. Unfortunately, the observation suffered from long periods of background flaring, and as a result the effective exposure time was shortened to only approximately 25% of the planned exposure. The sensitivity to detect sources in the cluster was therefore much reduced, hampering a useful comparison with other clusters observed with Chandra and XMM. We detect 5 sources (all less than 300 counts) in the full field of view of the detectors; based on the large separations from the cluster center, we expect that at least 3-4 are not associated with the cluster. A brief paper that reports the results is in preparation.

Quasi-planar elemental clusters in pair interactions approximation

NASA Astrophysics Data System (ADS)

Chkhartishvili, Levan

2016-01-01

The pair-interactions approximation, when applied to describe elemental clusters, only takes into account bonding between neighboring atoms. According to this approach, isomers of wrapped forms of 2D clusters - nanotubular and fullerene-like structures - and truly 3D clusters, are generally expected to be more stable than their quasi-planar counterparts. This is because quasi-planar clusters contain more peripheral atoms with dangling bonds and, correspondingly, fewer atoms with saturated bonds. However, the differences in coordination numbers between central and peripheral atoms lead to the polarization of bonds. The related corrections to the molar binding energy can make small, quasi-planar clusters more stable than their 2D wrapped allotropes and 3D isomers. The present work provides a general theoretical frame for studying the relative stability of small elemental clusters within the pair interactions approximation.

Electric dipole moment of diatomic molecules by configuration interaction. V - Two states of /2/Sigma/+/ symmetry in CN.

NASA Technical Reports Server (NTRS)

Green, S.

1972-01-01

Previous accurate dipole moment calculation techniques are modified to be applicable to higher excited states of symmetry. The self-consistent fields and configuration interactions are calculated for the X(2)Sigma(+) and B(2)Sigma(+) states of CN. Spin hyperfine constants and spin density at the nucleus are considered in the context of one-electron operator properties. The values of the self-consistent field and configuration interaction for the spin density are compared with experimental values for several diatomic molecules.

Initial Stage of Aerosol Formation from Oversaturated Vapors

NASA Astrophysics Data System (ADS)

Lushnikov, A. A.; Zagainov, V. A.; Lyubovtseva, Yu. S.

2018-03-01

The formation of aerosol particles from oversaturated vapor was considered assuming that the stable nuclei of the new phase contain two (dimers) or three (trimers) condensing vapor molecules. Exact expressions were derived and analyzed for the partition functions of the dimer and trimer suspended in a carrier gas for the rectangular well and repulsive core intermolecular potentials. The equilibrium properties of these clusters and the nucleation rate of aerosol particles were discussed. The bound states of clusters were introduced using a limitation on their total energy: molecular clusters with a negative total energy were considered to exclude configurations with noninteracting fragments.

Study of Clusters and Hypernuclei production within PHSD+FRIGA model

NASA Astrophysics Data System (ADS)

Kireyeu, V.; Le Fèvre, A.; Bratkovskaya, E.

2017-01-01

We report on the results on the dynamical modelling of cluster formation with the new combined PHSD+FRIGA model at Nuclotron and NICA energies. The FRIGA clusterisation algorithm, which can be applied to the transport models, is based on the simulated annealing technique to obtain the most bound configuration of fragments and nucleons. The PHSD+FRIGA model is able to predict isotope yields as well as hyper-nucleus production. Based on present predictions of the combined model we study the possibility to detect such clusters and hypernuclei in the BM@N and MPD/NICA detectors.

IR spectroscopy of protonation in benzene-water nanoclusters: hydronium, zundel, and eigen at a hydrophobic interface.

PubMed

Cheng, Timothy C; Bandyopadhyay, Biswajit; Mosley, Jonathan D; Duncan, Michael A

2012-08-08

The structure of ions in water at a hydrophobic interface influences important processes throughout chemistry and biology. However, experiments to measure these structures are limited by the distribution of configurations present and the inability to selectively probe the interfacial region. Here, protonated nanoclusters containing benzene and water are produced in the gas phase, size-selected, and investigated with infrared laser spectroscopy. Proton stretch, free OH, and hydrogen-bonding vibrations uniquely define protonation sites and hydrogen-bonding networks. The structures consist of protonated water clusters binding to the hydrophobic interface of neutral benzene via one or more π-hydrogen bonds. Comparison to the spectra of isolated hydronium, zundel, or eigen ions reveals the inductive effects and local ordering induced by the interface. The structures and interactions revealed here represent key features expected for aqueous hydrophobic interfaces.

In-Medium Similarity Renormalization Group Approach to the Nuclear Many-Body Problem

NASA Astrophysics Data System (ADS)

Hergert, Heiko; Bogner, Scott K.; Lietz, Justin G.; Morris, Titus D.; Novario, Samuel J.; Parzuchowski, Nathan M.; Yuan, Fei

We present a pedagogical discussion of Similarity Renormalization Group (SRG) methods, in particular the In-Medium SRG (IMSRG) approach for solving the nuclear many-body problem. These methods use continuous unitary transformations to evolve the nuclear Hamiltonian to a desired shape. The IMSRG, in particular, is used to decouple the ground state from all excitations and solve the many-body Schrödinger equation. We discuss the IMSRG formalism as well as its numerical implementation, and use the method to study the pairing model and infinite neutron matter. We compare our results with those of Coupled cluster theory (Chap. 8), Configuration-Interaction Monte Carlo (Chap. 9), and the Self-Consistent Green's Function approach discussed in Chap. 11 The chapter concludes with an expanded overview of current research directions, and a look ahead at upcoming developments.

Velocity Space Evolution of Dayside Reconnection Outflow

NASA Astrophysics Data System (ADS)

Broll, J. M.; Fuselier, S. A.; Trattner, K. J.

2015-12-01

Magnetic reconnection is a universal phenomenon occurring when energy stored in a complicated magnetic field topology is released into the surrounding plasma as the field simplifies its configuration. At Earth's dayside magnetopause, reconnection is responsible for mass and energy input from the solar wind into the magnetosphere. We describe the evolution of the velocity-space evolution of plasma outflow from a dayside magnetic reconnection region. We analyze Cluster magnetopause crossings between 1 and 10 Earth radii from the reconnection X-line predicted by the maximum magnetic shear model. The effects of nonadiabatic processes, such as deformation of the profile due to finite-gyroradius-induced pitch-angle scattering and wave-particle interactions, are described. We compare observations and simulation results to describe the outflow evolution and infer the field-aligned distance between an observation and the reconnection site producing it.

Excitation energies of particle-hole states in {sup 208}Pb and the surface delta interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heusler, A., E-mail: A.Heusler@mpi-hd.mpg.de; Jolos, R. V., E-mail: Jolos@theor.jinr.ru; Brentano, P. von, E-mail: Brentano@ikp.uni-koeln.de

2013-07-15

The schematic shell model without residual interaction (SSM) assumes the same excitation energy for all spins in each particle-hole configuration multiplet. In {sup 208}Pb, more than forty states are known to contain almost the full strength of a single particle-hole configuration. The experimental excitation energy for a state with a certain spin differs from the energy predicted by the SSM by -0.2 to +0.6 MeV. The multiplet splitting is calculated with the surface delta interaction; it corresponds to the diagonal matrix element of the residual interaction in the SSM. For states containing more than 90% strength of a certain configurationmore » and for the centroid of several completely observed configurations, the calculated multiplet splitting often approximates the experimental excitation energy within 30 keV. The strong mixing within some pairs of states containing the full strengths of two configurations is explained.« less

Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

PubMed Central

Ringer, Ashley L.; Senenko, Anastasia; Sherrill, C. David

2007-01-01

S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S–benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems. PMID:17766371

cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud.

PubMed

Hodor, Paul; Chawla, Amandeep; Clark, Andrew; Neal, Lauren

2016-01-15

: One of the solutions proposed for addressing the challenge of the overwhelming abundance of genomic sequence and other biological data is the use of the Hadoop computing framework. Appropriate tools are needed to set up computational environments that facilitate research of novel bioinformatics methodology using Hadoop. Here, we present cl-dash, a complete starter kit for setting up such an environment. Configuring and deploying new Hadoop clusters can be done in minutes. Use of Amazon Web Services ensures no initial investment and minimal operation costs. Two sample bioinformatics applications help the researcher understand and learn the principles of implementing an algorithm using the MapReduce programming pattern. Source code is available at https://bitbucket.org/booz-allen-sci-comp-team/cl-dash.git. hodor_paul@bah.com. © The Author 2015. Published by Oxford University Press.

cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud

PubMed Central

Hodor, Paul; Chawla, Amandeep; Clark, Andrew; Neal, Lauren

2016-01-01

Summary: One of the solutions proposed for addressing the challenge of the overwhelming abundance of genomic sequence and other biological data is the use of the Hadoop computing framework. Appropriate tools are needed to set up computational environments that facilitate research of novel bioinformatics methodology using Hadoop. Here, we present cl-dash, a complete starter kit for setting up such an environment. Configuring and deploying new Hadoop clusters can be done in minutes. Use of Amazon Web Services ensures no initial investment and minimal operation costs. Two sample bioinformatics applications help the researcher understand and learn the principles of implementing an algorithm using the MapReduce programming pattern. Availability and implementation: Source code is available at https://bitbucket.org/booz-allen-sci-comp-team/cl-dash.git. Contact: hodor_paul@bah.com PMID:26428290

Large Eddy Simulation of Vertical Axis Wind Turbines

NASA Astrophysics Data System (ADS)

Hezaveh, Seyed Hossein

Due to several design advantages and operational characteristics, particularly in offshore farms, vertical axis wind turbines (VAWTs) are being reconsidered as a complementary technology to horizontal axial turbines (HAWTs). However, considerable gaps remain in our understanding of VAWT performance since they have been significantly less studied than HAWTs. This thesis examines the performance of isolated VAWTs based on different design parameters and evaluates their characteristics in large wind farms. An actuator line model (ALM) is implemented in an atmospheric boundary layer large eddy simulation (LES) code, with offline coupling to a high-resolution blade-scale unsteady Reynolds-averaged Navier-Stokes (URANS) model. The LES captures the turbine-to-farm scale dynamics, while the URANS captures the blade-to-turbine scale flow. The simulation results are found to be in good agreement with existing experimental datasets. Subsequently, a parametric study of the flow over an isolated VAWT is carried out by varying solidities, height-to-diameter aspect ratios, and tip speed ratios. The analyses of the wake area and power deficits yield an improved understanding of the evolution of VAWT wakes, which in turn enables a more informed selection of turbine designs for wind farms. One of the most important advantages of VAWTs compared to HAWTs is their potential synergistic interactions that increase their performance when placed in close proximity. Field experiments have confirmed that unlike HAWTs, VAWTs can enhance and increase the total power production when placed near each other. Based on these experiments and using ALM-LES, we also present and test new approaches for VAWT farm configuration. We first design clusters with three turbines then configure farms consisting of clusters of VAWTs rather than individual turbines. The results confirm that by using a cluster design, the average power density of wind farms can be increased by as much as 60% relative to regular arrays. Finally, the thesis conducts an investigation of the influence of farm length (parallel to the wind) to assess the fetch needed for equilibrium to be reached, as well as the origin of the kinetic energy extracted by the turbines.

Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

2014-01-14

The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei (CCN), and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems.more » The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics (PIMD) method at the density functional theory (DFT) level of theory. We observe a small zero-point effect on the the equilibrium structures of certain clusters. One configuration is found to display a bimodal behaviour at 300 K in contrast to the stable ionised state suggested from a zero temperature classical geometry optimisation. The general effect of zero-point motion is to promote the extent of proton transfer with respect to classical behaviour. We thank Prof. Angelos Michaelides and his group in University College London (UCL) for practical advice and helpful discussions. This work benefited from interactions with the Thomas Young Centre through seminar and discussions involving the PIMD method. SMK was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. JLS and IJF were supported by the IMPACT scheme at UCL and by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. We are grateful for use of the UCL Legion High Performance Computing Facility and the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy, Office of Science of the under Contract No. DE-AC02-05CH11231.« less

Orbitally invariant internally contracted multireference unitary coupled cluster theory and its perturbative approximation: theory and test calculations of second order approximation.

PubMed

Chen, Zhenhua; Hoffmann, Mark R

2012-07-07

A unitary wave operator, exp (G), G(+) = -G, is considered to transform a multiconfigurational reference wave function Φ to the potentially exact, within basis set limit, wave function Ψ = exp (G)Φ. To obtain a useful approximation, the Hausdorff expansion of the similarity transformed effective Hamiltonian, exp (-G)Hexp (G), is truncated at second order and the excitation manifold is limited; an additional separate perturbation approximation can also be made. In the perturbation approximation, which we refer to as multireference unitary second-order perturbation theory (MRUPT2), the Hamiltonian operator in the highest order commutator is approximated by a Mo̸ller-Plesset-type one-body zero-order Hamiltonian. If a complete active space self-consistent field wave function is used as reference, then the energy is invariant under orbital rotations within the inactive, active, and virtual orbital subspaces for both the second-order unitary coupled cluster method and its perturbative approximation. Furthermore, the redundancies of the excitation operators are addressed in a novel way, which is potentially more efficient compared to the usual full diagonalization of the metric of the excited configurations. Despite the loss of rigorous size-extensivity possibly due to the use of a variational approach rather than a projective one in the solution of the amplitudes, test calculations show that the size-extensivity errors are very small. Compared to other internally contracted multireference perturbation theories, MRUPT2 only needs reduced density matrices up to three-body even with a non-complete active space reference wave function when two-body excitations within the active orbital subspace are involved in the wave operator, exp (G). Both the coupled cluster and perturbation theory variants are amenable to large, incomplete model spaces. Applications to some widely studied model systems that can be problematic because of geometry dependent quasidegeneracy, H4, P4, and BeH(2), are performed in order to test the new methods on problems where full configuration interaction results are available.

An Archival Search For Young Globular Clusters in Galaxies

NASA Astrophysics Data System (ADS)

Whitmore, Brad

1995-07-01

One of the most intriguing results from HST has been the discovery of ultraluminous star clusters in interacting and merging galaxies. These clusters have the luminosities, colors, and sizes that would be expected of young globular clusters produced by the interaction. We propose to use the data in the HST Archive to determine how prevalent this phenomena is, and to determine whether similar clusters are produced in other environments. Three samples will be extracted and studied in a systematic and consistent manner: 1} interacting and merging galaxies, 2} starburst galaxies, 3} a control sample of ``normal'' galaxies. A preliminary search of the archives shows that there are at least 20 galaxies in each of these samples, and the number will grow by about 50 observations become available. The data will be used to determine the luminosity function, color histogram , spatial distribution, and structural properties of the clusters using the same techniques employed in our study of NGC 7252 {``Atoms -for-Peace'' galaxy} and NGC 4038/4039 {``The Antennae''}. Our ultimate goals are: 1} to understand how globular clusters form, and 2} to use the clusters as evolutionary tracers to unravel the histories of interacting galaxies.

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Formation of fivefold axes in the FCC-metal nanoclusters

NASA Astrophysics Data System (ADS)

Myasnichenko, Vladimir S.; Starostenkov, Mikhail D.

2012-11-01

Formation of atomistic structures of metallic Cu, Au, Ag clusters and bimetallic Cu-Au clusters was studied with the help of molecular dynamics using the many-body tight-binding interatomic potential. The simulation of the crystallization process of clusters with the number of atoms ranging from 300 to 1092 was carried out. The most stable configurations of atoms in the system, corresponding to the minimum of potential energy, was found during super-fast cooling from 1000 K. Atoms corresponding to fcc, hcp, and Ih phases were identified by the method of common neighbor analysis. Incomplete icosahedral core can be discovered at the intersection of one of the Ih axes with the surface of monometallic cluster. The decahedron-shaped structure of bimetallic Cu-Au cluster with seven completed icosahedral cores was obtained. The principles of the construction of small bimetallic clusters with icosahedral symmetry and increased fractal dimensionality were offered.

Transcription factor clusters regulate genes in eukaryotic cells

PubMed Central

Hedlund, Erik G; Friemann, Rosmarie; Hohmann, Stefan

2017-01-01

Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in vivo stoichiometry and spatiotemporal dynamics of a GFP tagged repressor, Mig1, from a paradigm signaling pathway of Saccharomyces cerevisiae. We find the repressor operates in clusters, which upon extracellular signal detection, translocate from the cytoplasm, bind to nuclear targets and turnover. Simulations of Mig1 configuration within a 3D yeast genome model combined with a promoter-specific, fluorescent translation reporter confirmed clusters are the functional unit of gene regulation. In vitro and structural analysis on reconstituted Mig1 suggests that clusters are stabilized by depletion forces between intrinsically disordered sequences. We observed similar clusters of a co-regulatory activator from a different pathway, supporting a generalized cluster model for transcription factors that reduces promoter search times through intersegment transfer while stabilizing gene expression. PMID:28841133

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

Probing the non-thermal emission in Abell 2146 and the Perseus cluster with the JVLA

NASA Astrophysics Data System (ADS)

Gendron-Marsolais, Marie-Lou; Hlavacek-Larrondo, Julie; van Weeren, Reinout; Clarke, Tracy; Intema, Huib; Russell, Helen; Edge, Alastair; Fabian, Andy; Olamaie, Malak; Rumsey, Clare; King, Lindsay; McNamara, Brian; Fecteau-Beaucage, David; Hogan, Michael; Mezcua, Mar; Taylor, Gregory; Blundell, Katherine; Sanders, Jeremy

2018-01-01

Jets created from accretion onto supermassive black holes release relativistic particles on large distances. These strongly affect the intracluster medium when located in the center of a brightest cluster galaxy. The hierarchical merging of subclusters and groups, from which cluster originate, also generates perturbations into the intracluster medium through shocks and turbulence, constituting a potential source of reacceleration for these particles. I will present deep multi-configuration low radio frequency observations from the Karl G. Jansky Very Large Array of two unique clusters, probing the non-thermal emission from the old particle population of the AGN outflows.Recently awarded of 550 hours of Chandra observations, Abell 2146 is one of the rare clusters undergoing a spectacular merger in the plane of the sky. Our recent deep multi-configuration JVLA 1.4 GHz observations have revealed the presence of a structure extending to 850 kpc in size, consisting of one component associated with the upstream shock and classified as a radio relic, and one associated with the subcluster core, consistent with a radio halo bounded by the bow shock. Theses structures have some of the lowest radio powers detected thus far in any cluster. The flux measurements of the halo, its morphology and measurements of the dynamical state of the cluster suggest that the halo was recently created (~ 0.3 Gyr after core passage). This makes A2146 extremely interesting to study, allowing us to probe the complete evolutionary stages of halos.I will also present results on 230-470 MHz JVLA observations of the Perseus cluster. Our observations of this nearby relaxed cool core cluster have revealed a multitude of new structures associated with the mini-halo, extending to hundreds of kpc in size. Its irregular morphology seems to be have been influenced both by the AGN activity and by the sloshing motion of the cluster’ gas. In addition, it has a filamentary structure similar to that seen in radio relics found in merging clusters.These results both illustrate the high-quality images that can be obtained with the new JVLA at low radio-frequencies.

Quantum-Mechanical Combinatorial Design of Solids having Target Properties

NASA Astrophysics Data System (ADS)

Zunger, Alex

2007-03-01

(1) One of the most striking aspects of solid state physics is the diversity of structural forms in which crystals appear in Nature. Not only are there many distinct crystal-types, but combinations of two or more crystalline materials (alloys) give rise to various local geometric atomic patters. The already rich repertoire of such forms has recently been significantly enhanced by the advent of artificial crystal growth techniques (MBE, STM- atom positioning, etc.) that can create desired structural forms, such as superlattices and impurity clusters even in defiance of the rules of equilibrium thermodynamics. (2) At the same time, the fields of chemistry of nanostructures and physics of structural phase-transitions have long revealed that different atomic configurations generally lead to different physical properties even without altering the chemical makeup. While the most widely - known illustration of such ``form controls function'' rule is the dramatically different color, conductivity and hardness of the allotropical forms of pure carbon (diamond,graphite, C60), the physics of semiconductor superstructures and nanostructures is full of striking examples of how optical, magnetic and transport properties depend sensitively on atomic configuration. (3) Yet, the history of material research has generally occurred via accidental discoveries of material structures having interesting physical property (semiconductivity, ferromagnetism; superconductivity etc.). This begs the question: can this discovery process be inverted, i.e. can we first articulate a desired target physical property, then search (within a class) for the configuration that has this property? (4) The number of potentially interesting atomic configurations exhibits a combinatorial explosion, so even fast synthesis or fast computations can not survey all. (5) This talk describes the recent steps made by solid state theory + computational physics to address this ``Inverse Design'' (Franceschetti & Zunger, Nature, 402, 60 (1999) problem. I will show how Genetic Algorithms, in combination with efficient (``Order N'') solutions to the Pseudopotential Schrodinger equation allow us to investigate astronomical spaces of atomic configurations in search of the structure with a target physical property. Only a small fraction of all (˜ 10**14 in our case) configurations need to be examined. Physical properties are either calculated on-the-fly (if it's easy), or first ``Cluster-Expanded'' (if the theory is difficult). I will illustrate this Inverse Band Structure approach for (a) Design of required band-gaps in semiconductor superlattices; (b) architecture of impurity --clusters with desired optical properties (PRL 97, 046401, 2006) (c) search for configuration of magnetic ions in semiconductors that maximize the ferromagnetic Curie temperature (PRL, 97, 047202, 2006).

Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy

2018-05-01

This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters. Copyright © 2018 Elsevier Inc. All rights reserved.

Dynamics of Magnetopause Reconnection in Response to Variable Solar Wind Conditions

NASA Astrophysics Data System (ADS)

Berchem, J.; Richard, R. L.; Escoubet, C. P.; Pitout, F.

2017-12-01

Quantifying the dynamics of magnetopause reconnection in response to variable solar wind driving is essential to advancing our predictive understanding of the interaction of the solar wind/IMF with the magnetosphere. To this end we have carried out numerical studies that combine global magnetohydrodynamic (MHD) and Large-Scale Kinetic (LSK) simulations to identify and understand the effects of solar wind/IMF variations. The use of the low dissipation, high resolution UCLA MHD code incorporating a non-linear local resistivity allows the representation of the global configuration of the dayside magnetosphere while the use of LSK ion test particle codes with distributed particle detectors allows us to compare the simulation results with spacecraft observations such as ion dispersion signatures observed by the Cluster spacecraft. We present the results of simulations that focus on the impacts of relatively simple solar wind discontinuities on the magnetopause and examine how the recent history of the interaction of the magnetospheric boundary with solar wind discontinuities can modify the dynamics of magnetopause reconnection in response to the solar wind input.

The Role of the Upper Atmosphere for Dawn-Dusk and Interhemispheric Differences in the Coupled Magnetosphere-Ionosphere-Thermosphere System

NASA Astrophysics Data System (ADS)

Foerster, M.; Doornbos, E.; Haaland, S.

2016-12-01

Solar wind and IMF interaction with the geomagnetic field sets up a large-scale plasma circulation in the Earth's magnetosphere and the magnetically tightly connected ionosphere. The ionospheric ExB ion drift at polar latitudes accelerates the neutral gas as a nondivergent momentum source primarily in force balance with pressure gradients, while the neutral upper thermosphere circulation is essentially modified by apparent forces due to Earth's rotation (Coriolis and centrifugal forces) as well as advection and viscous forces. The apparent forces affect the dawn and dusk side asymmetrically, favouring a large dusk-side neutral wind vortex, while the non-dipolar portions of the Earth's magnetic field constitute significant hemispheric differences in magnetic flux and field configurations that lead to essential interhemispheric differences of the ion-neutral interaction. We present statistical studies of both the high-latitude ionospheric convection and the upper thermospheric circulation patterns based on measurements of the electron drift instrument (EDI) on board the Cluster satellites and by the accelerometer on board the CHAMP, GOCE, and Swarm spacecraft, respectively.

Modeling Physical Processes at the Nanoscale—Insight into Self-Organization of Small Systems (abstract)

NASA Astrophysics Data System (ADS)

Proykova, Ana

2009-04-01

Essential contributions have been made in the field of finite-size systems of ingredients interacting with potentials of various ranges. Theoretical simulations have revealed peculiar size effects on stability, ground state structure, phases, and phase transformation of systems confined in space and time. Models developed in the field of pure physics (atomic and molecular clusters) have been extended and successfully transferred to finite-size systems that seem very different—small-scale financial markets, autoimmune reactions, and social group reactions to advertisements. The models show that small-scale markets diverge unexpectedly fast as a result of small fluctuations; autoimmune reactions are sequences of two discontinuous phase transitions; and social groups possess critical behavior (social percolation) under the influence of an external field (advertisement). Some predicted size-dependent properties have been experimentally observed. These findings lead to the hypothesis that restrictions on an object's size determine the object's total internal (configuration) and external (environmental) interactions. Since phases are emergent phenomena produced by self-organization of a large number of particles, the occurrence of a phase in a system containing a small number of ingredients is remarkable.

Role of the oxyallyl substructure in the near infrared (NIR) absorption in symmetrical dye derivatives: A computational study.

PubMed

Prabhakar, Ch; Chaitanya, G Krishna; Sitha, Sanyasi; Bhanuprakash, K; Rao, V Jayathirtha

2005-03-24

It is well-known from experimental studies that the oxyallyl-substructure-based squarylium and croconium dyes absorb in the NIR region of the spectrum. Recently, another dye has been reported (J. Am. Chem. Soc. 2003, 125, 348) which contains the same basic chromophore, but the absorption is red-shifted by at least 300 nm compared to the former dyes and is observed near 1100 nm. To analyze the reasons behind the large red shift, in this work we have carried out symmetry-adapted cluster-configuration interaction (SAC-CI) studies on some of these NIR dyes which contain the oxyallyl substructure. From this study, contrary to the earlier reports, it is seen that the donor groups do not seem to play a major role in the red-shift of the absorption. On the other hand, on the basis of the results of the high-level calculations carried out here and using qualitative molecular orbital theory, it is observed that the orbital interactions play a key role in the red shift. Finally, design principles for the oxyallyl-substructure-based NIR dyes are suggested.

Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales.

PubMed

Huang, Shiping

2017-11-13

The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids. To this end, Green's function molecular dynamics (GFMD) is used to study both how the contact cluster evolves from the atomic scale to the macroscopic scale and the interaction between clusters. It is found that the interaction between clusters has a strong effect on their formation. The formation and distribution of the contact clusters is far more complicated than that predicted by the asperity model. Ignorance of the interaction between them leads to overestimating the contacting force. In real contact, contacting clusters are smaller and more discrete due to the interaction between the asperities. Understanding the exact nature of the contact area with the normal load is essential to the following research on friction.

Detection of protein complex from protein-protein interaction network using Markov clustering

NASA Astrophysics Data System (ADS)

Ochieng, P. J.; Kusuma, W. A.; Haryanto, T.

2017-05-01

Detection of complexes, or groups of functionally related proteins, is an important challenge while analysing biological networks. However, existing algorithms to identify protein complexes are insufficient when applied to dense networks of experimentally derived interaction data. Therefore, we introduced a graph clustering method based on Markov clustering algorithm to identify protein complex within highly interconnected protein-protein interaction networks. Protein-protein interaction network was first constructed to develop geometrical network, the network was then partitioned using Markov clustering to detect protein complexes. The interest of the proposed method was illustrated by its application to Human Proteins associated to type II diabetes mellitus. Flow simulation of MCL algorithm was initially performed and topological properties of the resultant network were analysed for detection of the protein complex. The results indicated the proposed method successfully detect an overall of 34 complexes with 11 complexes consisting of overlapping modules and 20 non-overlapping modules. The major complex consisted of 102 proteins and 521 interactions with cluster modularity and density of 0.745 and 0.101 respectively. The comparison analysis revealed MCL out perform AP, MCODE and SCPS algorithms with high clustering coefficient (0.751) network density and modularity index (0.630). This demonstrated MCL was the most reliable and efficient graph clustering algorithm for detection of protein complexes from PPI networks.

Evolution of the Contact Area with Normal Load for Rough Surfaces: from Atomic to Macroscopic Scales

NASA Astrophysics Data System (ADS)

Huang, Shiping

2017-11-01

The evolution of the contact area with normal load for rough surfaces has great fundamental and practical importance, ranging from earthquake dynamics to machine wear. This work bridges the gap between the atomic scale and the macroscopic scale for normal contact behavior. The real contact area, which is formed by a large ensemble of discrete contacts (clusters), is proven to be much smaller than the apparent surface area. The distribution of the discrete contact clusters and the interaction between them are key to revealing the mechanism of the contacting solids. To this end, Green's function molecular dynamics (GFMD) is used to study both how the contact cluster evolves from the atomic scale to the macroscopic scale and the interaction between clusters. It is found that the interaction between clusters has a strong effect on their formation. The formation and distribution of the contact clusters is far more complicated than that predicted by the asperity model. Ignorance of the interaction between them leads to overestimating the contacting force. In real contact, contacting clusters are smaller and more discrete due to the interaction between the asperities. Understanding the exact nature of the contact area with the normal load is essential to the following research on friction.

ICAP: An Interactive Cluster Analysis Procedure for analyzing remotely sensed data. [to classify the radiance data to produce a thematic map

NASA Technical Reports Server (NTRS)

Wharton, S. W.

1980-01-01

An Interactive Cluster Analysis Procedure (ICAP) was developed to derive classifier training statistics from remotely sensed data. The algorithm interfaces the rapid numerical processing capacity of a computer with the human ability to integrate qualitative information. Control of the clustering process alternates between the algorithm, which creates new centroids and forms clusters and the analyst, who evaluate and elect to modify the cluster structure. Clusters can be deleted or lumped pairwise, or new centroids can be added. A summary of the cluster statistics can be requested to facilitate cluster manipulation. The ICAP was implemented in APL (A Programming Language), an interactive computer language. The flexibility of the algorithm was evaluated using data from different LANDSAT scenes to simulate two situations: one in which the analyst is assumed to have no prior knowledge about the data and wishes to have the clusters formed more or less automatically; and the other in which the analyst is assumed to have some knowledge about the data structure and wishes to use that information to closely supervise the clustering process. For comparison, an existing clustering method was also applied to the two data sets.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Ling-Jian

A gamma ray detector apparatus comprises a solid state detector that includes a plurality of anode pixels and at least one cathode. The solid state detector is configured for receiving gamma rays during an interaction and inducing a signal in an anode pixel and in a cathode. An anode pixel readout circuit is coupled to the plurality of anode pixels and is configured to read out and process the induced signal in the anode pixel and provide triggering and addressing information. A waveform sampling circuit is coupled to the at least one cathode and configured to read out and processmore » the induced signal in the cathode and determine energy of the interaction, timing of the interaction, and depth of interaction.« less

Predicting the points of interaction of small molecules in the NF-κB pathway

PubMed Central

2011-01-01

Background The similarity property principle has been used extensively in drug discovery to identify small compounds that interact with specific drug targets. Here we show it can be applied to identify the interactions of small molecules within the NF-κB signalling pathway. Results Clusters that contain compounds with a predominant interaction within the pathway were created, which were then used to predict the interaction of compounds not included in the clustering analysis. Conclusions The technique successfully predicted the points of interactions of compounds that are known to interact with the NF-κB pathway. The method was also shown to be successful when compounds for which the interaction points were unknown were included in the clustering analysis. PMID:21342508

Beyond the Young-Laplace model for cluster growth during dewetting of thin films: effective coarsening exponents and the role of long range dewetting interactions.

PubMed

Constantinescu, Adi; Golubović, Leonardo; Levandovsky, Artem

2013-09-01

Long range dewetting forces acting across thin films, such as the fundamental van der Waals interactions, may drive the formation of large clusters (tall multilayer islands) and pits, observed in thin films of diverse materials such as polymers, liquid crystals, and metals. In this study we further develop the methodology of the nonequilibrium statistical mechanics of thin films coarsening within continuum interface dynamics model incorporating long range dewetting interactions. The theoretical test bench model considered here is a generalization of the classical Mullins model for the dynamics of solid film surfaces. By analytic arguments and simulations of the model, we study the coarsening growth laws of clusters formed in thin films due to the dewetting interactions. The ultimate cluster growth scaling laws at long times are strongly universal: Short and long range dewetting interactions yield the same coarsening exponents. However, long range dewetting interactions, such as the van der Waals forces, introduce a distinct long lasting early time scaling behavior characterized by a slow growth of the cluster height/lateral size aspect ratio (i.e., a time-dependent Young angle) and by effective coarsening exponents that depend on cluster size. In this study, we develop a theory capable of analytically calculating these effective size-dependent coarsening exponents characterizing the cluster growth in the early time regime. Such a pronounced early time scaling behavior has been indeed seen in experiments; however, its physical origin has remained elusive to this date. Our theory attributes these observed phenomena to ubiquitous long range dewetting interactions acting across thin solid and liquid films. Our results are also applicable to cluster growth in initially very thin fluid films, formed by depositing a few monolayers or by a submonolayer deposition. Under this condition, the dominant coarsening mechanism is diffusive intercluster mass transport while the cluster coalescence plays a minor role, both in solid and in fluid films.

Atomic-scale dynamics of a model glass-forming metallic liquid: Dynamical crossover, dynamical decoupling, and dynamical clustering

DOE PAGES

Jaiswal, Abhishek; Egami, Takeshi; Zhang, Yang

2015-04-01

The phase behavior of multi-component metallic liquids is exceedingly complex because of the convoluted many-body and many-elemental interactions. Herein, we present systematic studies of the dynamic aspects of such a model ternary metallic liquid Cu 40Zr 51Al 9 using molecular dynamics simulation with embedded atom method. We observed a dynamical crossover from Arrhenius to super-Arrhenius behavior in the transport properties (diffusion coefficient, relaxation times, and shear viscosity) bordered at T x ~1300K. Unlike in many molecular and macromolecular liquids, this crossover phenomenon occurs in the equilibrium liquid state well above the melting temperature of the system (T m ~ 900K),more » and the crossover temperature is roughly twice of the glass-transition temperature (T g). Below T x, we found the elemental dynamics decoupled and the Stokes-Einstein relation broke down, indicating the onset of heterogeneous spatially correlated dynamics in the system mediated by dynamic communications among local configurational excitations. To directly characterize and visualize the correlated dynamics, we employed a non-parametric, unsupervised machine learning technique and identified dynamical clusters of atoms with similar atomic mobility. The revealed average dynamical cluster size shows an accelerated increase below T x and mimics the trend observed in other ensemble averaged quantities that are commonly used to quantify the spatially heterogeneous dynamics such as the non-Gaussian parameter and the four-point correlation function.« less

Lattice strain in irradiated materials unveils a prevalent defect evolution mechanism

NASA Astrophysics Data System (ADS)

Debelle, Aurélien; Crocombette, Jean-Paul; Boulle, Alexandre; Chartier, Alain; Jourdan, Thomas; Pellegrino, Stéphanie; Bachiller-Perea, Diana; Carpentier, Denise; Channagiri, Jayanth; Nguyen, Tien-Hien; Garrido, Frédérico; Thomé, Lionel

2018-01-01

Modification of materials using ion beams has become a widespread route to improve or design materials for advanced applications, from ion doping for microelectronic devices to emulation of nuclear reactor environments. Yet, despite decades of studies, major issues regarding ion/solid interactions are not solved, one of them being the lattice-strain development process in irradiated crystals. In this work, we address this question using a consistent approach that combines x-ray diffraction (XRD) measurements with both molecular dynamics (MD) and rate equation cluster dynamics (RECD) simulations. We investigate four distinct materials that differ notably in terms of crystalline structure and nature of the atomic bonding. We demonstrate that these materials exhibit a common behavior with respect to the strain development process. In fact, a strain build-up followed by a strain relaxation is observed in the four investigated cases. The strain variation is unambiguously ascribed to a change in the defect configuration, as revealed by MD simulations. Strain development is due to the clustering of interstitial defects into dislocation loops, while the strain release is associated with the disappearance of these loops through their integration into a network of dislocation lines. RECD calculations of strain depth profiles, which are in agreement with experimental data, indicate that the driving force for the change in the defect nature is the defect clustering process. This study paves the way for quantitative predictions of the microstructure changes in irradiated materials.

Measurements of ion energies from the explosion of large hydrogen iodide clusters irradiated by intense femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Tisch, J. W. G.; Hay, N.; Springate, E.; Gumbrell, E. T.; Hutchinson, M. H. R.; Marangos, J. P.

1999-10-01

We present measurements of ion energies from the interaction of intense, femtosecond laser pulses with large mixed-species clusters. Multi-keV protons and ~100-keV iodine ions are observed from the explosion of HI clusters produced in a gas jet operated at room temperature. Clusters formed from molecular gases such as HI are thus seen to extend the advantages of the laser-cluster interaction to elements that do not readily form single-species clusters. In the light of recently reported nuclear fusion in laser-heated clusters, we also examine the possibility of boosting the explosion energies of low-Z ions through the use of mixed species clusters.

Cluster Analysis of Downscaled and Explicitly Simulated North Atlantic Tropical Cyclone Tracks

DOE PAGES

Daloz, Anne S.; Camargo, S. J.; Kossin, J. P.; ...

2015-02-11

A realistic representation of the North Atlantic tropical cyclone tracks is crucial as it allows, for example, explaining potential changes in U.S. landfalling systems. Here, the authors present a tentative study that examines the ability of recent climate models to represent North Atlantic tropical cyclone tracks. Tracks from two types of climate models are evaluated: explicit tracks are obtained from tropical cyclones simulated in regional or global climate models with moderate to high horizontal resolution (1°–0.25°), and downscaled tracks are obtained using a downscaling technique with large-scale environmental fields from a subset of these models. Here, for both configurations, tracksmore » are objectively separated into four groups using a cluster technique, leading to a zonal and a meridional separation of the tracks. The meridional separation largely captures the separation between deep tropical and subtropical, hybrid or baroclinic cyclones, while the zonal separation segregates Gulf of Mexico and Cape Verde storms. The properties of the tracks’ seasonality, intensity, and power dissipation index in each cluster are documented for both configurations. The authors’ results show that, except for the seasonality, the downscaled tracks better capture the observed characteristics of the clusters. The authors also use three different idealized scenarios to examine the possible future changes of tropical cyclone tracks under 1) warming sea surface temperature, 2) increasing carbon dioxide, and 3) a combination of the two. The response to each scenario is highly variable depending on the simulation considered. Lastly, the authors examine the role of each cluster in these future changes and find no preponderant contribution of any single cluster over the others.« less

Simulating the Galaxy Cluster “El Gordo”: Gas Motion, Kinetic Sunyaev–Zel’dovich Signal, and X-Ray Line Features

NASA Astrophysics Data System (ADS)

Zhang, Congyao; Yu, Qingjuan; Lu, Youjun

2018-03-01

The massive galaxy cluster “El Gordo” (ACT-CL J0102–4915) is a rare merging system with a high collision speed suggested by multi-wavelength observations and theoretical modeling. Zhang et al. propose two types of mergers, a nearly head-on merger and an off-axis merger with a large impact parameter, to reproduce most of the observational features of the cluster using numerical simulations. The different merger configurations of the two models result in different gas motion in the simulated clusters. In this paper, we predict the kinetic Sunyaev–Zel’dovich (kSZ) effect, the relativistic correction of the thermal Sunyaev–Zel’dovich (tSZ) effect, and the X-ray spectrum of this cluster, based on the two proposed models. We find that (1) the amplitudes of the kSZ effect resulting from the two models are both on the order of ΔT/T ∼ 10‑5 but their morphologies are different, which trace the different line-of-sight velocity distributions of the systems; (2) the relativistic correction of the tSZ effect around 240 GHz can be possibly used to constrain the temperature of the hot electrons heated by the shocks; and (3) the shift between the X-ray spectral lines emitted from different regions of the cluster can be significantly different in the two models. The shift and the line broadening can be up to ∼25 eV and 50 eV, respectively. We expect that future observations of the kSZ effect and the X-ray spectral lines (e.g., by ALMA, XARM) will provide a strong constraint on the gas motion and the merger configuration of ACT-CL J0102–4915.

Robust and Efficient Spin Purification for Determinantal Configuration Interaction.

PubMed

Fales, B Scott; Hohenstein, Edward G; Levine, Benjamin G

2017-09-12

The limited precision of floating point arithmetic can lead to the qualitative and even catastrophic failure of quantum chemical algorithms, especially when high accuracy solutions are sought. For example, numerical errors accumulated while solving for determinantal configuration interaction wave functions via Davidson diagonalization may lead to spin contamination in the trial subspace. This spin contamination may cause the procedure to converge to roots with undesired ⟨Ŝ 2 ⟩, wasting computer time in the best case and leading to incorrect conclusions in the worst. In hopes of finding a suitable remedy, we investigate five purification schemes for ensuring that the eigenvectors have the desired ⟨Ŝ 2 ⟩. These schemes are based on projection, penalty, and iterative approaches. All of these schemes rely on a direct, graphics processing unit-accelerated algorithm for calculating the S 2 c matrix-vector product. We assess the computational cost and convergence behavior of these methods by application to several benchmark systems and find that the first-order spin penalty method is the optimal choice, though first-order and Löwdin projection approaches also provide fast convergence to the desired spin state. Finally, to demonstrate the utility of these approaches, we computed the lowest several excited states of an open-shell silver cluster (Ag 19 ) using the state-averaged complete active space self-consistent field method, where spin purification was required to ensure spin stability of the CI vector coefficients. Several low-lying states with significant multiply excited character are predicted, suggesting the value of a multireference approach for modeling plasmonic nanomaterials.

The Global Optimization of Pt13 Cluster Using the First-Principle Molecular Dynamics with the Quenching Technique

NASA Astrophysics Data System (ADS)

Chen, Xiangping; Duan, Haiming; Cao, Biaobing; Long, Mengqiu

2018-03-01

The high-temperature first-principle molecular dynamics method used to obtain the low energy configurations of clusters [L. L. Wang and D. D. Johnson, PRB 75, 235405 (2007)] is extended to a considerably large temperature range by combination with the quenching technique. Our results show that there are strong correlations between the possibilities for obtaining the ground-state structure and the temperatures. Larger possibilities can be obtained at relatively low temperatures (as corresponds to the pre-melting temperature range). Details of the structural correlation with the temperature are investigated by taking the Pt13 cluster as an example, which suggests a quite efficient method to obtain the lowest-energy geometries of metal clusters.

Motivational and emotional profiles in university undergraduates: a self-determination theory perspective.

PubMed

González, Antonio; Paoloni, Verónica; Donolo, Danilo; Rinaudo, Cristina

2012-11-01

Previous research has focused on specific forms of self-determined motivation or discrete class-related emotions, but few studies have simultaneously examined both constructs. The aim of this study on 472 undergraduates was twofold: to perform cluster analysis to identify homogeneous groups of motivation in the sample; and to determine the profile of each cluster for emotions and academic achievement. Cluster analysis configured four groups in terms of motivation: controlled, autonomous, both high, and both low. Each cluster revealed a distinct emotional profile, autonomous motivation being the most adaptable with high scores for academic achievement and pleasant emotions and low values for unpleasant emotions. The results are discussed in the light of their implications for academic adjustment.

Ab initio calculation of diffusion barriers for Cu adatom hopping on Cu(1 0 0) surface and evolution of atomic configurations

NASA Astrophysics Data System (ADS)

Zhang, Wei; Gan, Jie; Li, Qian; Gao, Kun; Sun, Jian; Xu, Ning; Ying, Zhifeng; Wu, Jiada

2011-06-01

The self-diffusion dynamics of Cu adatoms on Cu(1 0 0) surface has been studied based on the calculation of the energy barriers for various hopping events using lattice-gas based approach and a modified model. To simplify the description of the interactions and the calculation of the energy barrier, a three-tier hierarchy of description of atomic configurations was conceived in which the active adatom and its nearest atoms were chosen to constitute basic configuration and taken as a whole to study many-body interactions of the atoms in various atomic configurations, whereas the impacts of the next nearest atoms on the diffusion of the active adatom were considered as multi-site interactions. Besides the simple hopping of single adatoms, the movements of dimers and trimers as the results of multiple hopping events have also been examined. Taking into account the hopping events of all adatoms, the stability of atomic configurations has been examined and the evolution of atomic configurations has also been analyzed.

The ss(bar sign) component of the proton and the strangeness magnetic moment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riska, D. O.; Zou, B. S.

2006-07-11

The implications of the empirical indications for a positive strangeness magnetic moment on the possible configurations of the uudss(bar sign) component of the proton are analysed. A positive value for {mu}s is obtained in the ss(bar sign) configuration where the uuds subsystem is in an orbitally excited state with [4]FS[22]F[22]S flavor-spin symmetry, which is likely to have the lowest energy. The configurations in which the s-bar is orbitally excited, which include the conventional K+{lambda}0 configuration, with exception of that in which the uuds component has spin 2, yield negative values for {mu}s. The hidden strangeness analogues of recently proposed quarkmore » cluster models for the {theta}+ pentaquark give differing signs for {mu}s.« less

Measurement-based quantum computation on two-body interacting qubits with adiabatic evolution.

PubMed

Kyaw, Thi Ha; Li, Ying; Kwek, Leong-Chuan

2014-10-31

A cluster state cannot be a unique ground state of a two-body interacting Hamiltonian. Here, we propose the creation of a cluster state of logical qubits encoded in spin-1/2 particles by adiabatically weakening two-body interactions. The proposal is valid for any spatial dimensional cluster states. Errors induced by thermal fluctuations and adiabatic evolution within finite time can be eliminated ensuring fault-tolerant quantum computing schemes.

Micromagnetics of antiskyrmions in ultrathin films

NASA Astrophysics Data System (ADS)

Camosi, Lorenzo; Rougemaille, Nicolas; Fruchart, Olivier; Vogel, Jan; Rohart, Stanislas

2018-04-01

We present a combined analytical and numerical micromagnetic study of the equilibrium energy, size, and shape of antiskyrmionic magnetic configurations. Antiskyrmions can be stabilized when the Dzyaloshinskii-Moriya interaction has opposite signs along two orthogonal in-plane directions, breaking the magnetic circular symmetry. We compare the equilibrium energy, size, and shape of antiskyrmions and skyrmions that are stabilized in environments with anisotropic and isotropic Dzyaloshinskii-Moriya interactions, respectively, but with the same strength of the magnetic interactions. When the dipolar interactions are neglected, the skyrmion and the antiskyrmion have the same energy, shape, and size in their respective environments. However, when dipolar interactions are considered, the energy of the antiskyrmion is strongly reduced, and its equilibrium size increases with respect to that of the skyrmion. While the skyrmion configuration shows homochiral Néel magnetization rotations, antiskyrmions show partly Néel and partly Bloch rotations. The latter do not produce magnetic charges and thus cost less dipolar energy. Both magnetic configurations are stable when the magnetic energies almost cancel each other, which means that a small variation of one parameter can drastically change their configurations, sizes, and energies.

The stress intensity factors for a periodic array of interacting coplanar penny-shaped cracks

PubMed Central

Lekesiz, Huseyin; Katsube, Noriko; Rokhlin, Stanislav I.; Seghi, Robert R.

2013-01-01

The effect of crack interactions on stress intensity factors is examined for a periodic array of coplanar penny-shaped cracks. Kachanov’s approximate method for crack interactions (Int. J. Solid. Struct. 1987; 23(1):23–43) is employed to analyze both hexagonal and square crack configurations. In approximating crack interactions, the solution converges when the total truncation number of the cracks is 109. As expected, due to high density packing crack interaction in the hexagonal configuration is stronger than that in the square configuration. Based on the numerical results, convenient fitting equations for quick evaluation of the mode I stress intensity factors are obtained as a function of crack density and angle around the crack edge for both crack configurations. Numerical results for the mode II and III stress intensity factors are presented in the form of contour lines for the case of Poisson’s ratio ν =0.3. Possible errors for these problems due to Kachanov’s approximate method are estimated. Good agreement is observed with the limited number of results available in the literature and obtained by different methods. PMID:27175035

Pyglidein - A Simple HTCondor Glidein Service

NASA Astrophysics Data System (ADS)

Schultz, D.; Riedel, B.; Merino, G.

2017-10-01

A major challenge for data processing and analysis at the IceCube Neutrino Observatory presents itself in connecting a large set of individual clusters together to form a computing grid. Most of these clusters do not provide a “standard” grid interface. Using a local account on each submit machine, HTCondor glideins can be submitted to virtually any type of scheduler. The glideins then connect back to a main HTCondor pool, where jobs can run normally with no special syntax. To respond to dynamic load, a simple server advertises the number of idle jobs in the queue and the resources they request. The submit script can query this server to optimize glideins to what is needed, or not submit if there is no demand. Configuring HTCondor dynamic slots in the glideins allows us to efficiently handle varying memory requirements as well as whole-node jobs. One step of the IceCube simulation chain, photon propagation in the ice, heavily relies on GPUs for faster execution. Therefore, one important requirement for any workload management system in IceCube is to handle GPU resources properly. Within the pyglidein system, we have successfully configured HTCondor glideins to use any GPU allocated to it, with jobs using the standard HTCondor GPU syntax to request and use a GPU. This mechanism allows us to seamlessly integrate our local GPU cluster with remote non-Grid GPU clusters, including specially allocated resources at XSEDE supercomputers.

Search for ternary fission of chromium-48

NASA Astrophysics Data System (ADS)

Dummer, Andrew K.

1999-07-01

Both alpha cluster model calculations and macroscopic energy calculations that allow for a double-neck shape of the compound nucleus suggest the possibility of a novel three 16O, chain-like configuration in 48 Cr. Such a configuration might lead to an enhanced cross section for three-16O breakup. To explore this possibility, the three-body exit channels for the 36Ar + 12C reaction at a beam energy of 210 MeV have been studied. The cross section for 16O + 16O + 16O breakup has been deduced and has been found to be in excess of what would be expected to result from a sequential binary fission process. However, the observation of a similarly enhanced 12C + 16O + 20Ne breakup cross section suggests that the observed 16O + 16O + 16O yields might still be associated with a statistical fission process. The results are discussed in the context of the fission of light nuclear systems and a simple cluster model calculation. This latter, ``Harvey model'' calculation suggests a possible inhibition of the formation of a three- 16O chain configuration from the 36Ar + 12C entrance channel. A further measurement using the 20Ne + 28Si-entrance channel is suggested.

Atomically precise cluster catalysis towards quantum controlled catalysts

PubMed Central

Watanabe, Yoshihide

2014-01-01

Catalysis of atomically precise clusters supported on a substrate is reviewed in relation to the type of reactions. The catalytic activity of supported clusters has generally been discussed in terms of electronic structure. Several lines of evidence have indicated that the electronic structure of clusters and the geometry of clusters on a support, including the accompanying cluster-support interaction, are strongly correlated with catalytic activity. The electronic states of small clusters would be easily affected by cluster–support interactions. Several studies have suggested that it is possible to tune the electronic structure through atomic control of the cluster size. It is promising to tune not only the number of cluster atoms, but also the hybridization between the electronic states of the adsorbed reactant molecules and clusters in order to realize a quantum-controlled catalyst. PMID:27877723

Light controllable catalytic activity of Au clusters decorated with photochromic molecules.

PubMed

Guo, Na; Yam, Kah Meng; Zhang, Chun

2018-06-15

By ab initio calculations, we show that when decorated with a photochromic molecule, the catalytic activity of an Au nanocluster can be reversibly controlled by light. The combination of a photochromic thiol-pentacarbonyl azobenzene (TPA) molecule and an Au 8 cluster is chosen as a model catalyst. The TPA molecule has two configurations (trans and cis) that can be reversibly converted to each other upon photo-excitation. Our calculations show that when the TPA takes the trans configuration, the combined system (trans-Au 8 ) is an excellent catalyst for CO oxidation. The reaction barrier of the catalyzed CO oxidation is less than 0.4 eV. While, the reaction barrier of CO oxidation catalyzed by cis-Au 8 is very high (>2.7 eV), indicating that the catalyst is inactive. These results pave the way for a new class of light controllable nanoscale catalysts.

A study of QM/Langevin-MD simulation for oxygen-evolving center of photosystem II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uchida, Waka; Kimura, Yoshiro; Wakabayashi, Masamitsu

2013-12-10

We have performed three QM/Langevin-MD simulations for oxygen-evolving complex (OEC) and surrounding residues, which are different configurations of the oxidation numbers on Mn atoms in the Mn{sub 4}O{sub 5}Ca cluster. By analyzing these trajectories, we have observed sensitivity of the change to the configuration of Mn oxidation state on O atoms of carboxyl on three amino acids, Glu354, Ala344, and Glu333. The distances from Mn to O atoms in residues contacting with the Mn{sub 4}O{sub 5}Ca cluster were analyzed for the three trajectories. We found the good correlation of the distances among the simulations. However, the distances with Glu354, Ala344,more » and Glu333 have not shown the correlation. These residues can be sensitive index of the changes of Mn oxidation numbers.« less

Light controllable catalytic activity of Au clusters decorated with photochromic molecules

NASA Astrophysics Data System (ADS)

Guo, Na; Meng Yam, Kah; Zhang, Chun

2018-06-01

By ab initio calculations, we show that when decorated with a photochromic molecule, the catalytic activity of an Au nanocluster can be reversibly controlled by light. The combination of a photochromic thiol-pentacarbonyl azobenzene (TPA) molecule and an Au8 cluster is chosen as a model catalyst. The TPA molecule has two configurations (trans and cis) that can be reversibly converted to each other upon photo-excitation. Our calculations show that when the TPA takes the trans configuration, the combined system (trans-Au8) is an excellent catalyst for CO oxidation. The reaction barrier of the catalyzed CO oxidation is less than 0.4 eV. While, the reaction barrier of CO oxidation catalyzed by cis-Au8 is very high (>2.7 eV), indicating that the catalyst is inactive. These results pave the way for a new class of light controllable nanoscale catalysts.

VizieR Online Data Catalog: Photometric analysis of contact binaries (Lapasset+ 1996)

NASA Astrophysics Data System (ADS)

Lapasset, E.; Gomez, M.; Farinas, R.

1996-09-01

We present BV light-curve synthetic analyses of three short-period contact (W UMa) binaries: HY Pavonis (P=~0.35days), AW Virginis (P=~0.35days), and BP Velorum (P=~0.26days). Different possible configurations for wide range of the mass ratio were explored in each case making use of the Wilson-Devinney code. The photometric parameters of the systems were determined from the synthetic light-curve solutions that best fit the observations. AW Vir has two components of very similar temperatures and therefore the subtype (A or W) remains undetermined. HY Pav and BP Vel are best modeled by W-type configurations and the asymmetries in the light curves are reproduced by introducing cool spots on the more massive secondary components. Although BP Vel lies in the region of the open cluster Cr 173, its distance modulus, in principle, rules it out as a cluster member. (6 data files).

The variety of primary healthcare organisations in Australia: a taxonomy.

PubMed

Rodwell, John; Gulyas, Andre

2013-04-08

Healthcare policy appears to treat healthcare organisations as being homogenous, despite evidence that they vary considerably. This study develops a taxonomy of primary health care practices using characteristics associated with the job satisfaction of general medical practitioners (GPs) and the practices. The study used data from 3,662 survey respondents who were GPs in the 2009 wave of the MABEL survey. Cluster analyses were used to determine natural groups of medical practices based on multidimensional characteristics. Seven configurations of primary health care practices emerged from multivariate cluster analyses: optimised team, independent craft, reactive, winding down, classic, practitioner flexible, and scale efficiency. This taxonomy of configurations moves beyond simplistic categorisations such as geographic location and highlights the complexity of primary health care organisations in Australia. Health policy, workforce and procedure interventions informed by taxonomies can engage the diversity of primary health care practices.

Predicted performance of an integrated modular engine system

NASA Technical Reports Server (NTRS)

Binder, Michael; Felder, James L.

1993-01-01

Space vehicle propulsion systems are traditionally comprised of a cluster of discrete engines, each with its own set of turbopumps, valves, and a thrust chamber. The Integrated Modular Engine (IME) concept proposes a vehicle propulsion system comprised of multiple turbopumps, valves, and thrust chambers which are all interconnected. The IME concept has potential advantages in fault-tolerance, weight, and operational efficiency compared with the traditional clustered engine configuration. The purpose of this study is to examine the steady-state performance of an IME system with various components removed to simulate fault conditions. An IME configuration for a hydrogen/oxygen expander cycle propulsion system with four sets of turbopumps and eight thrust chambers has been modeled using the Rocket Engine Transient Simulator (ROCETS) program. The nominal steady-state performance is simulated, as well as turbopump thrust chamber and duct failures. The impact of component failures on system performance is discussed in the context of the system's fault tolerant capabilities.

Evolution of Late-type Galaxies in a Cluster Environment: Effects of High-speed Multiple Encounters with Early-type Galaxies

NASA Astrophysics Data System (ADS)

Hwang, Jeong-Sun; Park, Changbom; Banerjee, Arunima; Hwang, Ho Seong

2018-04-01

Late-type galaxies falling into a cluster would evolve being influenced by the interactions with both the cluster and the nearby cluster member galaxies. Most numerical studies, however, tend to focus on the effects of the former with little work done on those of the latter. We thus perform a numerical study on the evolution of a late-type galaxy interacting with neighboring early-type galaxies at high speed using hydrodynamic simulations. Based on the information obtained from the Coma cluster, we set up the simulations for the case where a Milky Way–like late-type galaxy experiences six consecutive collisions with twice as massive early-type galaxies having hot gas in their halos at the closest approach distances of 15–65 h ‑1 kpc at the relative velocities of 1500–1600 km s‑1. Our simulations show that the evolution of the late-type galaxy can be significantly affected by the accumulated effects of the high-speed multiple collisions with the early-type galaxies, such as on cold gas content and star formation activity of the late-type galaxy, particularly through the hydrodynamic interactions between cold disk and hot gas halos. We find that the late-type galaxy can lose most of its cold gas after the six collisions and have more star formation activity during the collisions. By comparing our simulation results with those of galaxy–cluster interactions, we claim that the role of the galaxy–galaxy interactions on the evolution of late-type galaxies in clusters could be comparable with that of the galaxy–cluster interactions, depending on the dynamical history.

Relaxation dynamics of maximally clustered networks

NASA Astrophysics Data System (ADS)

Klaise, Janis; Johnson, Samuel

2018-01-01

We study the relaxation dynamics of fully clustered networks (maximal number of triangles) to an unclustered state under two different edge dynamics—the double-edge swap, corresponding to degree-preserving randomization of the configuration model, and single edge replacement, corresponding to full randomization of the Erdős-Rényi random graph. We derive expressions for the time evolution of the degree distribution, edge multiplicity distribution and clustering coefficient. We show that under both dynamics networks undergo a continuous phase transition in which a giant connected component is formed. We calculate the position of the phase transition analytically using the Erdős-Rényi phenomenology.

Calculating the Motion and Direction of Flux Transfer Events with Cluster

NASA Technical Reports Server (NTRS)

Collado-Vega, Yaireska M.; Sibeck, David Gary

2011-01-01

We use multi-point timing analysis to determine the orientation and motion of flux transfer events (FTEs) detected by the four Cluster spacecraft on the high-latitude dayside and flank magnetopause during 2002 and 2003. During these years, the distances between the Cluster spacecraft were greater than 1000 km, providing the tetrahedral configuration needed to select events and determine velocities. Each velocity and location will be examined in detail and compared to the velocities and locations determined by the predictions of the component and antiparallel reconnection models for event formation, orientation, motion, and acceleration for a wide range of spacecraft locations and solar wind conditions.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mannix, A. J.; Zhou, X. -F.; Kiraly, B.

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

HRLSim: a high performance spiking neural network simulator for GPGPU clusters.

PubMed

Minkovich, Kirill; Thibeault, Corey M; O'Brien, Michael John; Nogin, Aleksey; Cho, Youngkwan; Srinivasa, Narayan

2014-02-01

Modeling of large-scale spiking neural models is an important tool in the quest to understand brain function and subsequently create real-world applications. This paper describes a spiking neural network simulator environment called HRL Spiking Simulator (HRLSim). This simulator is suitable for implementation on a cluster of general purpose graphical processing units (GPGPUs). Novel aspects of HRLSim are described and an analysis of its performance is provided for various configurations of the cluster. With the advent of inexpensive GPGPU cards and compute power, HRLSim offers an affordable and scalable tool for design, real-time simulation, and analysis of large-scale spiking neural networks.

Microgravity

NASA Image and Video Library

2000-11-15

Watching molecules of the iron-storing protein apoferritin come together to form a nucleus reveals some interesting behavior. In this series of images, researchers observed clusters of four molecules at the corners of a diamond shape (top). As more molecules attach to the cluster, they arrange themselves into rods (second from top), and a raft-like configuration of molecules forms the critical nucleus (third from top), suggesting that crystal growth is much slower than it could be were the molecules arranged in a more compact formation. In the final image, a crystallite consisting of three layers containing approximately 60 to 70 molecules each is formed. Atomic force microscopy made visualizing the process of nucleation possible for the first time. The principal investigator is Peter Vekilov, of the University of Alabama in Huntsville. Vekilov's team at UAH studies protein solutions as they change phases from liquids to crystalline solids. They want to know if the molecules in the solution interact with one another, and if so, how, from the perspectives of thermodynamics and kinetics. They want to understand which forces -- electrical, electrostatic, hydrodynamic, or other kinds of forces -- are responsible for the interactions. They also study nucleation, the begirning stage of crystallization. This process is important to understand because it sets the stage for crystal growth in all kinds of solutions and liquid melts that are important in such diverse fields as agriculture, medicine, and the fabrication of metal components. Nucleation can determine the rate of crystal growth, the number of crystals that will be formed, and the quality and size of the crystals.

TripAdvisor^{N-D}: A Tourism-Inspired High-Dimensional Space Exploration Framework with Overview and Detail.

PubMed

Nam, Julia EunJu; Mueller, Klaus

2013-02-01

Gaining a true appreciation of high-dimensional space remains difficult since all of the existing high-dimensional space exploration techniques serialize the space travel in some way. This is not so foreign to us since we, when traveling, also experience the world in a serial fashion. But we typically have access to a map to help with positioning, orientation, navigation, and trip planning. Here, we propose a multivariate data exploration tool that compares high-dimensional space navigation with a sightseeing trip. It decomposes this activity into five major tasks: 1) Identify the sights: use a map to identify the sights of interest and their location; 2) Plan the trip: connect the sights of interest along a specifyable path; 3) Go on the trip: travel along the route; 4) Hop off the bus: experience the location, look around, zoom into detail; and 5) Orient and localize: regain bearings in the map. We describe intuitive and interactive tools for all of these tasks, both global navigation within the map and local exploration of the data distributions. For the latter, we describe a polygonal touchpad interface which enables users to smoothly tilt the projection plane in high-dimensional space to produce multivariate scatterplots that best convey the data relationships under investigation. Motion parallax and illustrative motion trails aid in the perception of these transient patterns. We describe the use of our system within two applications: 1) the exploratory discovery of data configurations that best fit a personal preference in the presence of tradeoffs and 2) interactive cluster analysis via cluster sculpting in N-D.

Rapid transitions between defect configurations in a block copolymer melt.

PubMed

Tsarkova, Larisa; Knoll, Armin; Magerle, Robert

2006-07-01

With in situ scanning force microscopy, we image the ordering of cylindrical microdomains in a thin film of a diblock copolymer melt. Tracking the evolution of individual defects reveals elementary steps of defect motion via interfacial undulations and repetitive transitions between distinct defect configurations on a time scale of tens of seconds. The velocity of these transitions suggests a cooperative movement of clusters of chains. The activation energy for the opening/closing of a connection between two cylinders is estimated.

Regulation of human Nfu activity in Fe-S cluster delivery-characterization of the interaction between Nfu and the HSPA9/Hsc20 chaperone complex.

PubMed

Wachnowsky, Christine; Liu, Yushi; Yoon, Taejin; Cowan, J A

2018-01-01

Iron-sulfur cluster biogenesis is a complex, but highly regulated process that involves de novo cluster formation from iron and sulfide ions on a scaffold protein, and subsequent delivery to final targets via a series of Fe-S cluster-binding carrier proteins. The process of cluster release from the scaffold/carrier for transfer to the target proteins may be mediated by a dedicated Fe-S cluster chaperone system. In human cells, the chaperones include heat shock protein HSPA9 and the J-type chaperone Hsc20. While the role of chaperones has been somewhat clarified in yeast and bacterial systems, many questions remain over their functional roles in cluster delivery and interactions with a variety of human Fe-S cluster proteins. One such protein, Nfu, has recently been recognized as a potential interaction partner of the chaperone complex. Herein, we examined the ability of human Nfu to function as a carrier by interacting with the human chaperone complex. Human Nfu is shown to bind to both chaperone proteins with binding affinities similar to those observed for IscU binding to the homologous HSPA9 and Hsc20, while Nfu can also stimulate the ATPase activity of HSPA9. Additionally, the chaperone complex was able to promote Nfu function by enhancing the second-order rate constants for Fe-S cluster transfer to target proteins and providing directionality in cluster transfer from Nfu by eliminating promiscuous transfer reactions. Together, these data support a hypothesis in which Nfu can serve as an alternative carrier protein for chaperone-mediated cluster release and delivery in Fe-S cluster biogenesis and trafficking. © 2017 Federation of European Biochemical Societies.

Simulations of stellar winds and planetary bodies: Magnetized obstacles in a super-Alfvénic flow with southward IMF

NASA Astrophysics Data System (ADS)

Vernisse, Y.; Riousset, J. A.; Motschmann, U.; Glassmeier, K.-H.

2018-03-01

This study addresses the issue of the electromagnetic interactions between a stellar wind and planetary magnetospheres with various dipole field strengths by means of hybrid simulations. Focus is placed on the configuration where the upstream plasma magnetic field is parallel to the planetary magnetic moment (also called "Southward-IMF" configuration), leading to anti-parallel magnetic fields in the dayside interaction region. Each type of plasma interaction is characterized by means of currents flowing in the interaction region. Reconnection triggered in the tail in such configuration is shown to affect significantly the structure of the magnetotail at early stages. On the dayside, only the magnetopause current is observable for moderate planetary dipole field amplitude, while both bow-shock and magnetotail currents are identifiable downtail from the terminator. Strong differences in term of temperature for ions are particularly noticeable in the magnetosheath and in the magnetotail, when the present results are compared with our previous study, which focused on "Northward-IMF" configuration.

Older but still fluent? Insights from the intrinsically active baseline configuration of the aging brain using a data driven graph-theoretical approach.

PubMed

Muller, Angela M; Mérillat, Susan; Jäncke, Lutz

2016-02-15

A major part of our knowledge about the functioning of the aging brain comes from task-induced activation paradigms. However, the aging brain's intrinsic functional organization may be already a limiting factor for the outcome of an actual behavior. In order to get a better understanding of how this functional baseline configuration of the aging brain may affect cognitive performance, we analyzed task-free fMRI data of older 186 participants (mean age=70.4, 97 female) and their performance data in verbal fluency: First, we conducted an intrinsic connectivity contrast analysis (ICC) for the purpose of evaluating the brain regions whose degree of connectedness was significantly correlated with fluency performance. Secondly, using connectivity analyses we investigated how the clusters from the ICC functionally related to the other major resting-state networks. Apart from the importance of intact fronto-parietal long-range connections, the preserved capacity of the DMN for a finely attuned interaction with the executive-control network and the language network seems to be crucial for successful verbal fluency performance in older people. We provide further evidence that the right frontal regions might be more prominently affected by age-related decline. Copyright © 2015 Elsevier Inc. All rights reserved.

Perturbational treatment of spin-orbit coupling for generally applicable high-level multi-reference methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mai, Sebastian; Marquetand, Philipp; González, Leticia

2014-08-21

An efficient perturbational treatment of spin-orbit coupling within the framework of high-level multi-reference techniques has been implemented in the most recent version of the COLUMBUS quantum chemistry package, extending the existing fully variational two-component (2c) multi-reference configuration interaction singles and doubles (MRCISD) method. The proposed scheme follows related implementations of quasi-degenerate perturbation theory (QDPT) model space techniques. Our model space is built either from uncontracted, large-scale scalar relativistic MRCISD wavefunctions or based on the scalar-relativistic solutions of the linear-response-theory-based multi-configurational averaged quadratic coupled cluster method (LRT-MRAQCC). The latter approach allows for a consistent, approximatively size-consistent and size-extensive treatment of spin-orbitmore » coupling. The approach is described in detail and compared to a number of related techniques. The inherent accuracy of the QDPT approach is validated by comparing cuts of the potential energy surfaces of acrolein and its S, Se, and Te analoga with the corresponding data obtained from matching fully variational spin-orbit MRCISD calculations. The conceptual availability of approximate analytic gradients with respect to geometrical displacements is an attractive feature of the 2c-QDPT-MRCISD and 2c-QDPT-LRT-MRAQCC methods for structure optimization and ab inito molecular dynamics simulations.« less

Combined Experimental and Theoretical Investigations on Optical Activities of Möbius Aromatic and Möbius Antiaromatic Hexaphyrin Phosphorus Complexes.

PubMed

Mori, Tadashi; Tanaka, Takayuki; Higashino, Tomohiro; Yoshida, Kota; Osuka, Atsuhiro

2016-06-23

Intrinsically chiral Möbius aromatic [28]hexaphyrin monophosphorus(V) and Möbius antiaromatic [30]hexaphyrin bisphosphorus(V) complexes have been optically resolved and their absolute configurations (ACs) were determined by combined experimental and theoretical investigations on their circular dichroisms (CDs). First elutes in chiral HPLC exhibited strong positive Cotton effects (CEs) at the B-band, characteristic for the ML configurations in their Möbius strips. Weak CEs at the Q-band, if attainable, complemented their AC assignment. The whole CD pattern and intensity were well reproduced by time-dependent approximate coupled cluster theory using model systems that omit five outward meso-aryl substituents (inward-meso-retained model), providing a solid basis for AC assignment. The cost efficient TD-DFT method with appropriate functionals for fully substituted (nontruncated) complexes well reproduced CEs around the B-band (but less satisfactory at the Q-band), also allows the rapid AC estimation for their Möbius strips. Observed difference in CDs between aromatic and antiaromatic hexaphyrins were better interpreted by their shifts in energy levels and altered interactions of relevant molecular orbitals, rather than small differences in Möbius geometries nor aromatic/antiaromatic character, despite the correlations recently claimed in planar π-systems.

Upper Atmosphere Research Satellite (UARS) trade analysis

NASA Technical Reports Server (NTRS)

Fox, M. M.; Nebb, J.

1983-01-01

The Upper Atmosphere Research Satellite (UARS) which will collect data pertinent to the Earth's upper atmosphere is described. The collected data will be sent to the central data handling facility (CDHF) via the UARS ground system and the data will be processed and distributed to the remote analysis computer systems (RACS). An overview of the UARS ground system is presented. Three configurations were developed for the CDHF-RACS system. The CDHF configurations are discussed. The IBM CDHF configuration, the UNIVAC CDHF configuration and the vax cluster CDHF configuration are presented. The RACS configurations, the IBM RACS configurations, UNIVAC RACS and VAX RACS are detailed. Due to the large on-line data estimate to approximately 100 GB, a mass storage system is considered essential to the UARS CDHF. Mass storage systems were analyzed and the Braegan ATL, the RCA optical disk, the IBM 3850 and the MASSTOR M860 are discussed. It is determined that the type of mass storage system most suitable to UARS is the automated tape/cartridge device. Two devices of this type, the IBM 3850 and the MASSTOR MSS are analyzed and the applicable tape/cartridge device is incorporated into the three CDHF-RACS configurations.

Comparative analysis of ArnCl2 (2 ? n ? 30) clusters taking into account molecular relaxation effects

NASA Astrophysics Data System (ADS)

Ferreira, G. G.; Borges, E.; Braga, J. P.; Belchior, J. C.

Cluster structures are discussed in a nonrigid analysis, using a modified minima search method based on stochastic processes and classical dynamics simulations. The relaxation process is taken into account considering the internal motion of the Cl2 molecule. Cluster structures are compared with previous works in which the Cl2 molecule is assumed to be rigid. The interactions are modeled using pair potentials: the Aziz and Lennard-Jones potentials for the Ar==Ar interaction, a Morse potential for the Cl==Cl interaction, and a fully spherical/anisotropic Morse-Spline-van der Waals (MSV) potential for the Ar==Cl interaction. As expected, all calculated energies are lower than those obtained in a rigid approximation; one reason may be attributed to the nonrigid contributions of the internal motion of the Cl2 molecule. Finally, the growing processes in molecular clusters are discussed, and it is pointed out that the growing mechanism can be affected due to the nonrigid initial conditions of smaller clusters such as ArnCl2 (n ? 4 or 5), which are seeds for higher-order clusters.

Oxidation of Sn doped Cu cluster: A first principle study

NASA Astrophysics Data System (ADS)

Parida, Ganesh; Majumder, Chiranjib

2017-05-01

Bimetallic clusters have immense potential to exhibit tunable properties in the emerging field of nano catalysis. Using plane wave based pseudopotential approach we have investigated the oxidation behavior of pure and Sn doped Cu13 clusters. The results showed significant modification of the cluster geometry upon interaction with oxygen molecule. The interaction of oxygen with Cu13, Cu12Sn1 and Cu11Sn2 clusters show dissociative chemisorption is more favorable than molecular adsorption. In addition, the adsorption energy is found to decrease with the increase in Sn concentration.

Electron attachment to molecules in a cluster environment: suppression and enhancement effects

NASA Astrophysics Data System (ADS)

Fabrikant, Ilya I.

2018-05-01

Cluster environments can strongly influence dissociative electron attachment (DEA) processes. These effects are important in many applications, particularly for surface chemistry, radiation damage, and atmospheric physics. We review several mechanisms for DEA suppression and enhancement due to cluster environments, particularly due to microhydration. Long-range electron-molecule and electron-cluster interactions play often a significant role in these effects and can be analysed by using theoretical models. Nevertheless many observations remain unexplained due to complexity of the physics and chemistry of interaction of DEA fragments with the cluster environment.

Assessing the performance of dispersionless and dispersion-accounting methods: helium interaction with cluster models of the TiO2(110) surface.

PubMed

de Lara-Castells, María Pilar; Stoll, Hermann; Mitrushchenkov, Alexander O

2014-08-21

As a prototypical dispersion-dominated physisorption problem, we analyze here the performance of dispersionless and dispersion-accounting methodologies on the helium interaction with cluster models of the TiO2(110) surface. A special focus has been given to the dispersionless density functional dlDF and the dlDF+Das construction for the total interaction energy (K. Pernal, R. Podeswa, K. Patkowski, and K. Szalewicz, Phys. Rev. Lett. 2009, 109, 263201), where Das is an effective interatomic pairwise functional form for the dispersion. Likewise, the performance of symmetry-adapted perturbation theory (SAPT) method is evaluated, where the interacting monomers are described by density functional theory (DFT) with the dlDF, PBE, and PBE0 functionals. Our benchmarks include CCSD(T)-F12b calculations and comparative analysis on the nuclear bound states supported by the He-cluster potentials. Moreover, intra- and intermonomer correlation contributions to the physisorption interaction are analyzed through the method of increments (H. Stoll, J. Chem. Phys. 1992, 97, 8449) at the CCSD(T) level of theory. This method is further applied in conjunction with a partitioning of the Hartree-Fock interaction energy to estimate individual interaction energy components, comparing them with those obtained using the different SAPT(DFT) approaches. The cluster size evolution of dispersionless and dispersion-accounting energy components is then discussed, revealing the reduced role of the dispersionless interaction and intramonomer correlation when the extended nature of the surface is better accounted for. On the contrary, both post-Hartree-Fock and SAPT(DFT) results clearly demonstrate the high-transferability character of the effective pairwise dispersion interaction whatever the cluster model is. Our contribution also illustrates how the method of increments can be used as a valuable tool not only to achieve the accuracy of CCSD(T) calculations using large cluster models but also to evaluate the performance of SAPT(DFT) methods for the physically well-defined contributions to the total interaction energy. Overall, our work indicates the excellent performance of a dlDF+Das approach in which the parameters are optimized using the smallest cluster model of the target surface to treat van der Waals adsorbate-surface interactions.

Cluster adsorption on amorphous and crystalline surfaces - A molecular dynamics study of model Pt on Cu and model Pd on Pt

NASA Technical Reports Server (NTRS)

Garofalini, S. H.; Halicioglu, T.; Pound, G. M.

1981-01-01

Molecular dynamics was used to study the structure, dispersion and short-time behavior of ten-atom clusters adsorbed onto amorphous and crystalline substrates, in which the cluster atoms differed from the substrate atoms. Two adatom-substrate model systems were chosen; one, in which the interaction energy between adatom pairs was greater than that between substrate pairs, and the other, in which the reverse was true. At relatively low temperature ranges, increased dispersion of cluster atoms occurred: (a) on the amorphous substrate as compared to the FCC(100) surface, (b) with increasing reduced temperature, and (c) with adatom-substrate interaction energy stronger than adatom-adatom interaction. Two-dimensional clusters (rafts) on the FCC(100) surface displayed migration of edge atoms only, indicating a mechanism for the cluster rotation and shape changes found in experimental studies.

Magnetic cluster expansion model for random and ordered magnetic face-centered cubic Fe-Ni-Cr alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lavrentiev, M. Yu., E-mail: Mikhail.Lavrentiev@ukaea.uk; Nguyen-Manh, D.; Dudarev, S. L.

A Magnetic Cluster Expansion model for ternary face-centered cubic Fe-Ni-Cr alloys has been developed, using DFT data spanning binary and ternary alloy configurations. Using this Magnetic Cluster Expansion model Hamiltonian, we perform Monte Carlo simulations and explore magnetic structures of alloys over the entire range of compositions, considering both random and ordered alloy structures. In random alloys, the removal of magnetic collinearity constraint reduces the total magnetic moment but does not affect the predicted range of compositions where the alloys adopt low-temperature ferromagnetic configurations. During alloying of ordered fcc Fe-Ni compounds with Cr, chromium atoms tend to replace nickel rathermore » than iron atoms. Replacement of Ni by Cr in ordered alloys with high iron content increases the Curie temperature of the alloys. This can be explained by strong antiferromagnetic Fe-Cr coupling, similar to that found in bcc Fe-Cr solutions, where the Curie temperature increase, predicted by simulations as a function of Cr concentration, is confirmed by experimental observations. In random alloys, both magnetization and the Curie temperature decrease abruptly with increasing chromium content, in agreement with experiment.« less

A cluster expansion model for predicting activation barrier of atomic processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rehman, Tafizur; Jaipal, M.; Chatterjee, Abhijit, E-mail: achatter@iitk.ac.in

2013-06-15

We introduce a procedure based on cluster expansion models for predicting the activation barrier of atomic processes encountered while studying the dynamics of a material system using the kinetic Monte Carlo (KMC) method. Starting with an interatomic potential description, a mathematical derivation is presented to show that the local environment dependence of the activation barrier can be captured using cluster interaction models. Next, we develop a systematic procedure for training the cluster interaction model on-the-fly, which involves: (i) obtaining activation barriers for handful local environments using nudged elastic band (NEB) calculations, (ii) identifying the local environment by analyzing the NEBmore » results, and (iii) estimating the cluster interaction model parameters from the activation barrier data. Once a cluster expansion model has been trained, it is used to predict activation barriers without requiring any additional NEB calculations. Numerical studies are performed to validate the cluster expansion model by studying hop processes in Ag/Ag(100). We show that the use of cluster expansion model with KMC enables efficient generation of an accurate process rate catalog.« less

Time‐resolved detection of stimulus/task‐related networks, via clustering of transient intersubject synchronization

PubMed Central

Macaluso, Emiliano

2015-01-01

Abstract Several methods are available for the identification of functional networks of brain areas using functional magnetic resonance imaging (fMRI) time‐series. These typically assume a fixed relationship between the signal of the areas belonging to the same network during the entire time‐series (e.g., positive correlation between the areas belonging to the same network), or require a priori information about when this relationship may change (task‐dependent changes of connectivity). We present a fully data‐driven method that identifies transient network configurations that are triggered by the external input and that, therefore, include only regions involved in stimulus/task processing. Intersubject synchronization with short sliding time‐windows was used to identify if/when any area showed stimulus/task‐related responses. Next, a first clustering step grouped together areas that became engaged concurrently and repetitively during the time‐series (stimulus/task‐related networks). Finally, for each network, a second clustering step grouped together all the time‐windows with the same BOLD signal. The final output consists of a set of network configurations that show stimulus/task‐related activity at specific time‐points during the fMRI time‐series. We label these configurations: “brain modes” (bModes). The method was validated using simulated datasets and a real fMRI experiment with multiple tasks and conditions. Future applications include the investigation of brain functions using complex and naturalistic stimuli. Hum Brain Mapp 36:3404–3425, 2015. © 2015 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:26095530

Does the spatial arrangement of vegetation and anthropogenic land cover features matter? Case studies of urban warming and cooling in Phoenix and Las Vegas

NASA Astrophysics Data System (ADS)

Myint, S. W.; Zheng, B.; Fan, C.; Kaplan, S.; Brazel, A.; Middel, A.; Smith, M.

2014-12-01

While the relationship between fractional cover of anthropogenic and vegetation features and the urban heat island has been well studied, the effect of spatial arrangements (e.g., clustered, dispersed) of these features on urban warming or cooling are not well understood. The goal of this study is to examine if and how spatial configuration of land cover features influence land surface temperatures (LST) in urban areas. This study focuses on Phoenix, AZ and Las Vegas, NV that have undergone dramatic urban expansion. The data used to classify detailed urban land cover types include Geoeye-1 (Las Vegas) and QuickBird (Phoenix). The Geoeye-1 image (3 m resolution) was acquired on October 12, 2011 and the QuickBird image (2.4 m resolution) was taken on May 29, 2007. Classification was performed using object based image analysis (OBIA). We employed a spatial autocorrelation approach (i.e., Moran's I) that measures the spatial dependence of a point to its neighboring points and describes how clustered or dispersed points are arranged in space. We used Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) data acquired over Phoenix (daytime on June 10, 2011 and nighttime on October 17, 2011) and Las Vegas (daytime on July 6, 2005 and nighttime on August 27, 2005) to examine daytime and nighttime LST with regards to the spatial arrangement of anthropogenic and vegetation features. We spatially correlate Moran's I values of each land cover per surface temperature, and develop regression models. The spatial configuration of grass and trees shows strong negative correlations with LST, implying that clustered vegetation lowers surface temperatures more effectively. In contrast, a clustered spatial arrangement of anthropogenic land-cover features, especially impervious surfaces, significantly elevates surface temperatures. Results from this study suggest that the spatial configuration of anthropogenic and vegetation features influence urban warming and cooling.

Key-lock colloids in a nematic liquid crystal.

PubMed

Silvestre, Nuno M; Tasinkevych, M

2017-01-01

The Landau-de Gennes free energy is used to study theoretically the effective interaction of spherical "key" and anisotropic "lock" colloidal particles. We assume identical anchoring properties of the surfaces of the key and of the lock particles, and we consider planar degenerate and perpendicular anchoring conditions separately. The lock particle is modeled as a spherical particle with a spherical dimple. When such a particle is introduced into a nematic liquid crystal, it orients its dimple at an oblique angle θ_{eq} with respect to the far field director n_{∞}. This angle depends on the depth of the dimple. Minimization results show that the free energy of a pair of key and lock particles exhibits a global minimum for the configuration when the key particle is facing the dimple of the lock colloidal particle. The preferred orientation ϕ_{eq} of the key-lock composite doublet relative to n_{∞} is robust against thermal fluctuations. The preferred orientation θ_{eq}^{(2)} of the dimple particle in the doublet is different from the isolated situation. This is related to the "direct" interaction of defects accompanying the key particle with the edge of the dimple. We propose that this nematic-amplified key-lock interaction can play an important role in self-organization and clustering of mixtures of colloidal particles with dimple colloids present.

Fluid design studies of integrated modular engine system

NASA Technical Reports Server (NTRS)

Frankenfield, Bruce; Carek, Jerry

1993-01-01

A study was performed to develop a fluid system design and show the feasibility of constructing an integrated modular engine (IME) configuration, using an expander cycle engine. The primary design goal of the IME configuration was to improve the propulsion system reliability. The IME fluid system was designed as a single fault tolerant system, while minimizing the required fluid components. This study addresses the design of the high pressure manifolds, turbopumps and thrust chambers for the IME configuration. A physical layout drawing was made, which located each of the fluid system components, manifolds and thrust chambers. Finally, a comparison was made between the fluid system designs of an IME system and a non-network (clustered) engine system.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

NASA Astrophysics Data System (ADS)

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

Security management based on trust determination in cognitive radio networks

NASA Astrophysics Data System (ADS)

Li, Jianwu; Feng, Zebing; Wei, Zhiqing; Feng, Zhiyong; Zhang, Ping

2014-12-01

Security has played a major role in cognitive radio networks. Numerous researches have mainly focused on attacking detection based on source localization and detection probability. However, few of them took the penalty of attackers into consideration and neglected how to implement effective punitive measures against attackers. To address this issue, this article proposes a novel penalty mechanism based on cognitive trust value. The main feature of this mechanism has been realized by six functions: authentication, interactive, configuration, trust value collection, storage and update, and punishment. Data fusion center (FC) and cluster heads (CHs) have been put forward as a hierarchical architecture to manage trust value of cognitive users. Misbehaving users would be punished by FC by declining their trust value; thus, guaranteeing network security via distinguishing attack users is of great necessity. Simulation results verify the rationality and effectiveness of our proposed mechanism.

Enhanced hydrogen storage on Li-doped defective graphene with B substitution: A DFT study

NASA Astrophysics Data System (ADS)

Zhou, Yanan; Chu, Wei; Jing, Fangli; Zheng, Jian; Sun, Wenjing; Xue, Ying

2017-07-01

The characteristics of hydrogen adsorption on Li-doped defective graphene systems were investigated using density functional theory (DFT) calculations. Four types of defective structures were selected. Li atoms were well dispersed on the defective graphene without clustering, evidenced by the binding energy value between Li and defective graphene than that of Li-Lix. Additionally, as the amount of adsorbed H2 molecules increase, the H2 molecules show tilting configuration toward the Li adatom. This is beneficial for more hydrogen adsorption under the electrostatic interaction. On these four stable structures, there were up to three polarized H2 molecules adsorbed on per Li adatom, with the average hydrogen adsorption energy in the range of approximately 0.2-0.4 eV. These results provide new focus on the nature of Li-doped defective graphene with sometimes B substitution medium, which could be considered as a promising candidate for hydrogen storage.

Vibrational Frequencies and Spectroscopic Constants for 1(sup 3)A' HNC and 1(sup 3)A' HOC+ from High-Accuracy Quartic Force Fields

NASA Technical Reports Server (NTRS)

Fortenberry, Ryan C.; Crawford, T. Daniel; Lee, Timothy J.

2014-01-01

The spectroscopic constants and vibrational frequencies for the 1(sup 3)A' states of HNC, DNC, HOC+, and DOC+ are computed and discussed in this work. The reliable CcCR quartic force field based on high-level coupled cluster ab initio quantum chemical computations is exclusively utilized to provide the anharmonic potential. Then, second order vibrational perturbation theory and vibrational configuration interaction methods are employed to treat the nuclear Schroedinger equation. Second-order perturbation theory is also employed to provide spectroscopic data for all molecules examined. The relationship between these molecules and the corresponding 1(sup 3)A' HCN and HCO+ isomers is further developed here. These data are applicable to laboratory studies involving formation of HNC and HOC+ as well as astronomical observations of chemically active astrophysical environments.

Aerodynamics of Engine-Airframe Interaction

NASA Technical Reports Server (NTRS)

Caughey, D. A.

1986-01-01

The report describes progress in research directed towards the efficient solution of the inviscid Euler and Reynolds-averaged Navier-Stokes equations for transonic flows through engine inlets, and past complete aircraft configurations, with emphasis on the flowfields in the vicinity of engine inlets. The research focusses upon the development of solution-adaptive grid procedures for these problems, and the development of multi-grid algorithms in conjunction with both, implicit and explicit time-stepping schemes for the solution of three-dimensional problems. The work includes further development of mesh systems suitable for inlet and wing-fuselage-inlet geometries using a variational approach. Work during this reporting period concentrated upon two-dimensional problems, and has been in two general areas: (1) the development of solution-adaptive procedures to cluster the grid cells in regions of high (truncation) error;and (2) the development of a multigrid scheme for solution of the two-dimensional Euler equations using a diagonalized alternating direction implicit (ADI) smoothing algorithm.

Contributions to the NUCLEI SciDAC-3 Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bogner, Scott; Nazarewicz, Witek

This is the Final Report for Michigan State University for the NUCLEI SciDAC-3 project. The NUCLEI project, as defined by the scope of work, has developed, implemented and run codes for large-scale computations of many topics in low-energy nuclear physics. Physics studied included the properties of nuclei and nuclear decays, nuclear structure and reactions, and the properties of nuclear matter. The computational techniques used included Configuration Interaction, Coupled Cluster, and Density Functional methods. The research program emphasized areas of high interest to current and possible future DOE nuclear physics facilities, including ATLAS at ANL and FRIB at MSU (nuclear structuremore » and reactions, and nuclear astrophysics), TJNAF (neutron distributions in nuclei, few body systems, and electroweak processes), NIF (thermonuclear reactions), MAJORANA and FNPB (neutrinoless double-beta decay and physics beyond the Standard Model), and LANSCE (fission studies).« less

Nuclear Computational Low Energy Initiative (NUCLEI)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, Sanjay K.

This is the final report for University of Washington for the NUCLEI SciDAC-3. The NUCLEI -project, as defined by the scope of work, will develop, implement and run codes for large-scale computations of many topics in low-energy nuclear physics. Physics to be studied include the properties of nuclei and nuclear decays, nuclear structure and reactions, and the properties of nuclear matter. The computational techniques to be used include Quantum Monte Carlo, Configuration Interaction, Coupled Cluster, and Density Functional methods. The research program will emphasize areas of high interest to current and possible future DOE nuclear physics facilities, including ATLAS andmore » FRIB (nuclear structure and reactions, and nuclear astrophysics), TJNAF (neutron distributions in nuclei, few body systems, and electroweak processes), NIF (thermonuclear reactions), MAJORANA and FNPB (neutrino-less double-beta decay and physics beyond the Standard Model), and LANSCE (fission studies).« less

The energy separation between the classical and nonclassical isomers of protonated acetylene - An extensive study in one- and n-particle space saturation

NASA Technical Reports Server (NTRS)

Lindh, Roland; Rice, Julia E.; Lee, Timothy J.

1991-01-01

The energy separation between the classical and nonclassical forms of protonated acetylene has been reinvestigated in light of the recent experimentally deduced lower bound to this value of 6.0 kcal/mol. The objective of the present study is to use state-of-the-art ab initio quantum mechanical methods to establish this energy difference to within chemical accuracy (i.e., about 1 kcal/mol). The one-particle basis sets include up to g-type functions and the electron correlation methods include single and double excitation coupled-cluster (CCSD), the CCSD(T) extension, multireference configuration interaction, and the averaged coupled-pair functional methods. A correction for zero-point vibrational energies has also been included, yielding a best estimate for the energy difference between the classical and nonclassical forms of 3.7 + or - 1.3 kcal/mol.

Supra-Nanoparticle Functional Assemblies through Programmable Stacking

DOE PAGES

Tian, Cheng; Cordeiro, Marco Aurelio L.; Lhermitte, Julien; ...

2017-05-25

The quest for the by-design assembly of material and devices from nanoscale inorganic components is well recognized. Conventional self-assembly is often limited in its ability to control material morphology and structure simultaneously. We report a general method of assembling nanoparticles in a linear “pillar” morphology with regulated internal configurations. Our approach is inspired by supramolecular systems, where intermolecular stacking guides the assembly process to form diverse linear morphologies. Programmable stacking interactions were realized through incorporation of DNA coded recognition between the designed planar nanoparticle clusters. This resulted in the formation of multilayered pillar architectures with a well-defined internal nanoparticle organization.more » Furthermore, by controlling the number, position, size, and composition of the nanoparticles in each layer, a broad range of nanoparticle pillars were assembled and characterized in detail. In addition, we demonstrated the utility of this stacking assembly strategy for investigating plasmonic and electrical transport properties.« less

Supra-Nanoparticle Functional Assemblies through Programmable Stacking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Cheng; Cordeiro, Marco Aurelio L.; Lhermitte, Julien

The quest for the by-design assembly of material and devices from nanoscale inorganic components is well recognized. Conventional self-assembly is often limited in its ability to control material morphology and structure simultaneously. We report a general method of assembling nanoparticles in a linear “pillar” morphology with regulated internal configurations. Our approach is inspired by supramolecular systems, where intermolecular stacking guides the assembly process to form diverse linear morphologies. Programmable stacking interactions were realized through incorporation of DNA coded recognition between the designed planar nanoparticle clusters. This resulted in the formation of multilayered pillar architectures with a well-defined internal nanoparticle organization.more » Furthermore, by controlling the number, position, size, and composition of the nanoparticles in each layer, a broad range of nanoparticle pillars were assembled and characterized in detail. In addition, we demonstrated the utility of this stacking assembly strategy for investigating plasmonic and electrical transport properties.« less

Supra-Nanoparticle Functional Assemblies through Programmable Stacking.

PubMed

Tian, Cheng; Cordeiro, Marco Aurelio L; Lhermitte, Julien; Xin, Huolin L; Shani, Lior; Liu, Mingzhao; Ma, Chunli; Yeshurun, Yosef; DiMarzio, Donald; Gang, Oleg

2017-07-25

The quest for the by-design assembly of material and devices from nanoscale inorganic components is well recognized. Conventional self-assembly is often limited in its ability to control material morphology and structure simultaneously. Here, we report a general method of assembling nanoparticles in a linear "pillar" morphology with regulated internal configurations. Our approach is inspired by supramolecular systems, where intermolecular stacking guides the assembly process to form diverse linear morphologies. Programmable stacking interactions were realized through incorporation of DNA coded recognition between the designed planar nanoparticle clusters. This resulted in the formation of multilayered pillar architectures with a well-defined internal nanoparticle organization. By controlling the number, position, size, and composition of the nanoparticles in each layer, a broad range of nanoparticle pillars were assembled and characterized in detail. In addition, we demonstrated the utility of this stacking assembly strategy for investigating plasmonic and electrical transport properties.

Exciton characteristics in graphene epoxide.

PubMed

Zhu, Xi; Su, Haibin

2014-02-25

Exciton characteristics in graphene epoxide (GE) are investigated by density functional theory with quasi-particle corrections and many-body interactions. The nature of the exciton is influenced by epoxide content and detailed geometric configurations. Two kinds of excitons are identified in GE: Frenkel-like exciton originated from the sp(2) carbon cluster and charge-transfer exciton formed by localized states involving both oxygen and carbon atoms. The unusual blue shift associated with the Frenkel-like exciton leaking is highlighted. One scaling relationship is proposed to address the power-law dependence of Frenkel-like exciton binding strength on its size. The charge-transfer exciton appears in GE samples with the high oxygen coverage. Particularly, the exciton in GE structures exhibits long lifetime by analyzing both radiative and nonradiative decay processes. This study sheds light on the potential applications of GE-based structures with attractive high quantum yield in light emission and optoelectronic technology.

Astrophysics. Multiple images of a highly magnified supernova formed by an early-type cluster galaxy lens.

PubMed

Kelly, Patrick L; Rodney, Steven A; Treu, Tommaso; Foley, Ryan J; Brammer, Gabriel; Schmidt, Kasper B; Zitrin, Adi; Sonnenfeld, Alessandro; Strolger, Louis-Gregory; Graur, Or; Filippenko, Alexei V; Jha, Saurabh W; Riess, Adam G; Bradac, Marusa; Weiner, Benjamin J; Scolnic, Daniel; Malkan, Matthew A; von der Linden, Anja; Trenti, Michele; Hjorth, Jens; Gavazzi, Raphael; Fontana, Adriano; Merten, Julian C; McCully, Curtis; Jones, Tucker; Postman, Marc; Dressler, Alan; Patel, Brandon; Cenko, S Bradley; Graham, Melissa L; Tucker, Bradley E

2015-03-06

In 1964, Refsdal hypothesized that a supernova whose light traversed multiple paths around a strong gravitational lens could be used to measure the rate of cosmic expansion. We report the discovery of such a system. In Hubble Space Telescope imaging, we have found four images of a single supernova forming an Einstein cross configuration around a redshift z = 0.54 elliptical galaxy in the MACS J1149.6+2223 cluster. The cluster's gravitational potential also creates multiple images of the z = 1.49 spiral supernova host galaxy, and a future appearance of the supernova elsewhere in the cluster field is expected. The magnifications and staggered arrivals of the supernova images probe the cosmic expansion rate, as well as the distribution of matter in the galaxy and cluster lenses. Copyright © 2015, American Association for the Advancement of Science.

Rotationally induced magnetic chirality in clusters of single-domain permalloy islands and gapped nanorings

NASA Astrophysics Data System (ADS)

Zhang, Sheng; Li, Jie; Bartell, Jason; Lammert, Paul; Crespi, Vincent; Schiffer, Peter

2011-03-01

We have studied magnetic moment configurations of clusters of single-domain ferromagnetic islands in different geometries. The magnetic moments of these clusters are imaged by MFM after rotational demagnetization, following our previous protocols. We observed that two types of the clusters showed a significant imbalance of their two-fold degenerate ground states after demagnetization, and this inequality is correlated to the rotational direction of the demagnetization. A similar imbalance was also found in nano-scale rings with a small gap: the chirality of their magnetic state can be precisely controlled by the rotational direction during demagnetization. We acknowledge the financial support from DOE and Army Research Office. We are grateful to Prof. Chris Leighton and Mike Erickson for assistance with sample preparation.

Collective Yu-Shiba-Rusinov states in magnetic clusters at superconducting surfaces

NASA Astrophysics Data System (ADS)

Körber, Simon; Trauzettel, Björn; Kashuba, Oleksiy

2018-05-01

We study the properties of collective Yu-Shiba-Rusinov (YSR) states generated by multiple magnetic adatoms (clusters) placed on the surface of a superconductor. For magnetic clusters with equal distances between their constituents, we demonstrate the formation of effectively spin-unpolarized YSR states with subgap energies independent of the spin configuration of the magnetic impurities. We solve the problem analytically for arbitrary spin structure and analyze both spin-polarized (dispersive energy levels) and spin-unpolarized (pinned energy levels) solutions. While the energies of the spin-polarized solutions can be characterized solely by the net magnetic moment of the cluster, the wave functions of the spin-unpolarized solutions effectively decouple from it. This decoupling makes them stable against thermal fluctuation and detectable in scanning tunneling microscopy experiments.

Low-symmetry structures of Au32Z (Z = +1, 0, -1) clusters.

PubMed

Jalbout, Abraham F; Contreras-Torres, Flavio F; Pérez, Luis A; Garzón, Ignacio L

2008-01-24

In this work, we have explored new stable structures of the Au32Z (Z = +1, 0, -1) clusters. Theoretical calculations using density functional theory within the generalized-gradient approximation were performed. Our results show that, in the anion state (Au32-), low-symmetry (disordered) structures are preferred over the caged fullerene-like isomer. In addition, the cationic cluster (Au32+) also exhibits a disordered low-symmetry structure as its lowest energy configuration, but it is much closer in energy to the fullerene-like isomer. These results, obtained at T = 0 K, indicate that disordered structures for the Au32- and Au32+ clusters may be detected not only at room temperature, as was experimentally verified for the Au32- one, but also at much lower temperatures.

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly

PubMed Central

Cook, Jeremy D.; Kondapalli, Kalyan C.; Rawat, Swati; Childs, William C.; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L.

2010-01-01

Frataxin, a conserved nuclear encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich’s ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two: Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone n the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to better understand the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry (ITC). Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into a Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly. PMID:20815377

Molecular Details of the Yeast Frataxin-Isu1 Interaction during Mitochondrial Fe-S Cluster Assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, J.; Kondapalli, K; Rawat, S

2010-01-01

Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural modulemore » to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.« less

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly.

PubMed

Cook, Jeremy D; Kondapalli, Kalyan C; Rawat, Swati; Childs, William C; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L

2010-10-12

Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.

Jammed systems of oriented needles always percolate on square lattices

NASA Astrophysics Data System (ADS)

Kondrat, Grzegorz; Koza, Zbigniew; Brzeski, Piotr

2017-08-01

Random sequential adsorption (RSA) is a standard method of modeling adsorption of large molecules at the liquid-solid interface. Several studies have recently conjectured that in the RSA of rectangular needles, or k -mers, on a square lattice, percolation is impossible if the needles are sufficiently long (k of order of several thousand). We refute these claims and present rigorous proof that in any jammed configuration of nonoverlapping, fixed-length, horizontal, or vertical needles on a square lattice, all clusters are percolating clusters.

A Hybrid Approach to Composite Damage and Failure Analysis Combining Synergistic Damage Mechanics and Peridynamics

DTIC Science & Technology

2016-09-30

far from uniform . The final nonuniform distribution of fibers consists of clustered regions and resin pockets. The clustered fiber regions promote...period. Approach and Results A novel procedure has been devised to create nonuniform fiber distributions from the initial fiber bundle (with...used in simulations to produce nonuniform configurations. 2 . , •• ... . .. ·~ · . .. 000 8oa~.f𔄂oo o0~&mt~ go ... ·~· %(1 "’ ,~o ooif-l /j

Coupled multipolar interactions in small-particle metallic clusters.

PubMed

Pustovit, Vitaly N; Sotelo, Juan A; Niklasson, Gunnar A

2002-03-01

We propose a new formalism for computing the optical properties of small clusters of particles. It is a generalization of the coupled dipole-dipole particle-interaction model and allows one in principle to take into account all multipolar interactions in the long-wavelength limit. The method is illustrated by computations of the optical properties of N = 6 particle clusters for different multipolar approximations. We examine the effect of separation between particles and compare the optical spectra with the discrete-dipole approximation and the generalized Mie theory.

An ensemble framework for clustering protein-protein interaction networks.

PubMed

Asur, Sitaram; Ucar, Duygu; Parthasarathy, Srinivasan

2007-07-01

Protein-Protein Interaction (PPI) networks are believed to be important sources of information related to biological processes and complex metabolic functions of the cell. The presence of biologically relevant functional modules in these networks has been theorized by many researchers. However, the application of traditional clustering algorithms for extracting these modules has not been successful, largely due to the presence of noisy false positive interactions as well as specific topological challenges in the network. In this article, we propose an ensemble clustering framework to address this problem. For base clustering, we introduce two topology-based distance metrics to counteract the effects of noise. We develop a PCA-based consensus clustering technique, designed to reduce the dimensionality of the consensus problem and yield informative clusters. We also develop a soft consensus clustering variant to assign multifaceted proteins to multiple functional groups. We conduct an empirical evaluation of different consensus techniques using topology-based, information theoretic and domain-specific validation metrics and show that our approaches can provide significant benefits over other state-of-the-art approaches. Our analysis of the consensus clusters obtained demonstrates that ensemble clustering can (a) produce improved biologically significant functional groupings; and (b) facilitate soft clustering by discovering multiple functional associations for proteins. Supplementary data are available at Bioinformatics online.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

Oxygen Vacancy Linear Clustering in a Perovskite Oxide

DOE PAGES

Eom, Kitae; Choi, Euiyoung; Choi, Minsu; ...

2017-07-14

Oxygen vacancies have been implicitly assumed isolated ones, and understanding oxide materials possibly containing oxygen vacancies remains elusive within the scheme of the isolated vacancies, although the oxygen vacancies have been playing a decisive role in oxide materials. We report the presence of oxygen vacancy linear clusters and their orientation along a specific crystallographic direction in SrTiO 3, a representative of a perovskite oxide. The presence of the linear clusters and associated electron localization was revealed by an electronic structure represented in the increase in the Ti 2+ valence state or corresponding Ti 3d 2 electronic configuration along with divacancymore » cluster model analysis and transport measurement. The orientation of the linear clusters along the [001] direction in perovskite SrTiO 3 was verified by further X-ray diffuse scattering analysis. And because SrTiO 3 is an archetypical perovskite oxide, the vacancy linear clustering with the specific aligned direction and electron localization can be extended to a wide variety of the perovskite oxides.« less

Oxygen Vacancy Linear Clustering in a Perovskite Oxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eom, Kitae; Choi, Euiyoung; Choi, Minsu

Oxygen vacancies have been implicitly assumed isolated ones, and understanding oxide materials possibly containing oxygen vacancies remains elusive within the scheme of the isolated vacancies, although the oxygen vacancies have been playing a decisive role in oxide materials. We report the presence of oxygen vacancy linear clusters and their orientation along a specific crystallographic direction in SrTiO 3, a representative of a perovskite oxide. The presence of the linear clusters and associated electron localization was revealed by an electronic structure represented in the increase in the Ti 2+ valence state or corresponding Ti 3d 2 electronic configuration along with divacancymore » cluster model analysis and transport measurement. The orientation of the linear clusters along the [001] direction in perovskite SrTiO 3 was verified by further X-ray diffuse scattering analysis. And because SrTiO 3 is an archetypical perovskite oxide, the vacancy linear clustering with the specific aligned direction and electron localization can be extended to a wide variety of the perovskite oxides.« less

Effect of channel coupling on the elastic scattering of lithium isotopes

NASA Astrophysics Data System (ADS)

Furumoto, T.; Suhara, T.; Itagaki, N.

2018-04-01

Herein, we investigated the channel coupling (CC) effect on the elastic scatterings of lithium (Li) isotopes (A =6 -9) for 12C and 28Si targets at E /A =50 -60 MeV. The wave functions of the Li isotopes were obtained using the stochastic multi-configuration mixing method based on the microscopic-cluster model. The proton radii of the 7Li, 8Li, and 9Li nuclei became smaller as the number of valence neutrons increased. The valence neutrons in the 8Li and 9Li nuclei exhibited a glue-like behavior, thereby attracting the α and t clusters. Based on the transition densities derived from these microscopic wave functions, the elastic-scattering cross section was calculated using a microscopic coupled-channel method with a complex G -matrix interaction. The existing experimental data for the elastic scatterings of the Li isotopes and 10Be nuclei were well reproduced. The Li isotope elastic cross sections were demonstrated for the 12C and 28Si targets at E /A =53 MeV. The glue-like effect of the valence neutrons on the Li isotope was clearly demonstrated by the CC effect on elastic scattering. Finally, we realize that the valence neutrons stabilized the bindings of the core parts and the CC effect related to core excitation was indeed reduced.

Internal proton transfer and H2 rotations in the H5(+) cluster: a marked influence on its thermal equilibrium state.

PubMed

de Tudela, Ricardo Pérez; Barragán, Patricia; Prosmiti, Rita; Villarreal, Pablo; Delgado-Barrio, Gerardo

2011-03-31

Classical and path integral Monte Carlo (CMC, PIMC) "on the fly" calculations are carried out to investigate anharmonic quantum effects on the thermal equilibrium structure of the H5(+) cluster. The idea to follow in our computations is based on using a combination of the above-mentioned nuclear classical and quantum statistical methods, and first-principles density functional (DFT) electronic structure calculations. The interaction energies are computed within the DFT framework using the B3(H) hybrid functional, specially designed for hydrogen-only systems. The global minimum of the potential is predicted to be a nonplanar configuration of C(2v) symmetry, while the next three low-lying stationary points on the surface correspond to extremely low-energy barriers for the internal proton transfer and to the rotation of the H2 molecules, around the C2 axis of H5(+), connecting the symmetric C(2v) minima in the planar and nonplanar orientations. On the basis of full-dimensional converged PIMC calculations, results on the quantum vibrational zero-point energy (ZPE) and state of H5(+) are reported at a low temperature of 10 K, and the influence of the above-mentioned topological features of the surface on its probability distributions is clearly demonstrated.

Elucidation of sevadicin, a novel non-ribosomal peptide secondary metabolite produced by the honey bee pathogenic bacterium Paenibacillus larvae.

PubMed

Garcia-Gonzalez, Eva; Müller, Sebastian; Ensle, Paul; Süssmuth, Roderich D; Genersch, Elke

2014-05-01

American foulbrood (AFB) caused by the bee pathogenic bacterium Paenibacillus larvae is the most devastating bacterial disease of honey bees worldwide. From AFB-dead larvae, pure cultures of P. larvae can normally be cultivated indicating that P. larvae is able to defend its niche against all other bacteria present. Recently, comparative genome analysis within the species P. larvae suggested the presence of gene clusters coding for multi-enzyme complexes, such as non-ribosomal peptide synthetases (NRPSs). The products of these enzyme complexes are known to have a wide range of biological activities including antibacterial activities. We here present our results on antibacterial activity exhibited by vegetative P. larvae and the identification and analysis of a novel antibacterially active P. larvae tripeptide (called sevadicin; Sev) produced by a NRPS encoded by a gene cluster found in the genome of P. larvae. Identification of Sev was ultimately achieved by comparing the secretome of wild-type P. larvae with knockout mutants of P. larvae lacking production of Sev. Subsequent mass spectrometric studies, enantiomer analytics and chemical synthesis revealed the sequence and configuration of the tripeptide, D-Phe-D-ALa-Trp, which was shown to have antibacterial activity. The relevance of our findings is discussed in respect to host-pathogen interactions.

Quantum mechanical characterization of the He4ICl weakly bound complex.

PubMed

Valdés, Álvaro; Prosmiti, Rita

2013-08-15

Vibrational calculations are performed for the 12-dimensional He4ICl van der Waals complex using the multiconfiguration time-dependent Hartree (MCTDH) method. The potential energy surface of the cluster is represented as a sum of the triatomic He-ICl ab initio parametrized terms plus the He-He interactions. The topology of the potential presents higher anisotropy compared to the one with a homonuclear dopant, and this is clearly reflected in the structure and energetics of the low-lying conformers of the system. In order to take advantage of the MCTDH method, natural potential fits are employed for the potential energy operator, and also, a mode combination scheme is introduced in order to speed up the computations. Zero-point energy, binding energies, and vibrationally averaged structures of different isomers of the He4ICl cluster are obtained. The present results predict that the (3,1,0) structure, involving three He atoms in the near T-shaped and one He atom in the linear configurations, to be the most stable one in accord with recent experimental findings. Comparisons with previous theoretical and experimental data are presented, and the stability of the high-order conformers is discussed in connection with the multiple minima (global and local) of the underlying potential surface.

Dislocation loops in ultra-high purity Fe(Cr) alloys after 7.2 MeV proton irradiation

NASA Astrophysics Data System (ADS)

Chen, J.; Duval, F.; Jung, P.; Schäublin, R.; Gao, N.; Barthe, M. F.

2018-05-01

Ultra-high purity Fe(Cr) alloys (from 0 wt% Cr to 14 wt% Cr) were 3D homogeneously irradiated by 0-7.2 MeV protons to 0.3 dpa at nominal temperatures from 270 °C to 500 °C. Microstructural changes were observed by transmission electron microscopy (TEM). The results showed that evolution of dislocation loops depends on the Cr content. Below 300 °C, large ½ a0 <111> loops are dominating. Above 300 °C, a0 <100> loops with a habit plane {100} appear. Loop sizes of both types are more or less the same. At temperatures from 310 °C to 400 °C, a0 <100> loops form clusters with the same {100} habit plane as the one of the loops forming them. This indicates that <100> loops of the same variant start gliding under mutual elastic interaction. At 500 °C, dislocation loops form disc shaped clusters about 1000 nm in diameter and sitting on {111} and/or {100} planes in the pure Fe samples. Based on these observations a quantitative analysis of the dislocation loops configurations and their temperature dependence is made, leading to an understanding of the basic mechanisms of formation of these loops.

Infrared Spectra of M^+(2-AMINO-1-PHENYL ETHANOL)(H_2O)_{n=0-2}Ar (M=Na, K)

NASA Astrophysics Data System (ADS)

Nicely, Amy L.; Lisy, James M.

2009-06-01

A balance of competing electrostatic and hydrogen bonding interactions directs the structure of hydrated gas-phase cluster ions. Because of this, a biologically relevant model of cluster structures should include the effects of surrounding water molecules and metal ions such as sodium and potassium, which are found in high concentrations in the bloodstream. The molecule 2-amino-1-phenyl ethanol (APE) serves as a model for the neurotransmitters ephedrine and adrenaline. The neutral APE molecule contains an internal hydrogen bond between the amino and hydroxyl groups. In the M^+(APE) complex, the cation can either interrupt the internal hydrogen bond or position itself above the phenyl group, leaving the internal hydrogen bond intact. The former is preferred based on DFT calculations (B3LYP/6-31+G*) for both K^+ and Na^+ across the entire range from 0-400K, but infrared photodissociation (IRPD) spectra indicate a preference for the latter configuration at low temperatures. The IRPD spectra of M^+(H_2O)_{n=1-2} and M^+(H_2O)_{n=0-2}Ar (M=Na, K) will be presented along with parallel DFT and thermodynamics calculations to assist with the identification of the isomers present in each experiment.

Cluster dynamics and cluster size distributions in systems of self-propelled particles

NASA Astrophysics Data System (ADS)

Peruani, F.; Schimansky-Geier, L.; Bär, M.

2010-12-01

Systems of self-propelled particles (SPP) interacting by a velocity alignment mechanism in the presence of noise exhibit rich clustering dynamics. Often, clusters are responsible for the distribution of (local) information in these systems. Here, we investigate the properties of individual clusters in SPP systems, in particular the asymmetric spreading behavior of clusters with respect to their direction of motion. In addition, we formulate a Smoluchowski-type kinetic model to describe the evolution of the cluster size distribution (CSD). This model predicts the emergence of steady-state CSDs in SPP systems. We test our theoretical predictions in simulations of SPP with nematic interactions and find that our simple kinetic model reproduces qualitatively the transition to aggregation observed in simulations.

Clustering effects in ionic polymers: Molecular dynamics simulations.

PubMed

Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S

2015-08-01

Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. These ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Decrease in electrostatic interaction significantly enhances the mobility of the polymer.

Studies of cluster-assembled materials: From gas phase to condensed phase

NASA Astrophysics Data System (ADS)

Gao, Lin

Clusters, defined as "a number of similar things that occur together" in Webster's dictionary, has different meanings depending on the given subject. To physicists and chemists, the word cluster means "a group of atoms or molecules formed by interactions ranging from very weak van der Waals interactions to strong ionic bonds." Unlike molecules, which are made by nature and are stable under ambient conditions, clusters discovered in a laboratory are often metastable. Molecules have specific stoichiometry, whereas the cluster's composition can usually be altered atom by atom. Thus, clusters can be taken as intrinsically "artificial molecules" with considerably more tunabilities in their properties. Research into the relative stability and instability of clusters has in recent years become a very active research area, especially following the study by Khanna and Castleman that first suggested that by varying size and composition, clusters can expand the periodic table to the 3 rd-dimension; that is, clusters can mimic the chemistry of atoms and may, therefore, be used as the building blocks of new materials. The discovery of Met-Cars has drawn worldwide interests and has been actively investigated by researchers from a variety of fields, including physics, chemistry and material science. However, the unsuccessful search for a solvent capable of isolating Met-Cars has impeded progress in characterizing the material in the condensed state and, hence, limited its potential applications as a novel nanoscale material. An alternative method involving the deposition of mass-gated species and the subsequent structural investigation via Transmission Electron Microscopy (TEM) has been employed. With particularly interesting results, soft-landed deposits of zirconium Met-Cars were found to form a face-centered-cubic (FCC) structure with a lattice parameter ˜ 15A. The production of Met-Cars is conducted with the direct laser vaporization (DLV) of metal/graphite composite pellets. After being mass gated in a reflectron equipped time-of-flight mass spectrometer (TOF-MS) and deposited onto TEM grids, the resultant specimens can be loaded onto high-resolution TEM investigation via electron diffraction. In conclusion, soft-landing of mass selected clusters has been shown to be a successful approach to obtain structural information on Zr-Met-Car cluster-assembled materials collected from the gas phase. TEM images indicate the richness of the morphologies associated with these cluster crystals. However, passivation methods are expected to be examined further to overcome the limited stabilities of these novel clusters. From this initial study, it's shown the promising opportunity to study other Met-Cars species and more cluster-based materials. Experimental results of reactions run with a solvothermal synthesis method obtained while searching for new Zr-C cluster assembled materials, are reported. One unexpected product in single crystal form was isolated and tentatively identified by X-ray diffraction to be [Zr6i O(OH)O12·2(Bu)4], with space group P2 1/n and lattice parameters of a = 12.44 A, b = 22.06 A, c = 18.40 A, alpha = 90°, beta = 105°, gamma = 90°, V = 4875 A3 and R 1 = 3.15% for the total observed data (I ≥ 2 sigma I) and oR2 = 2.82%. This novel hexanuclear Zr(IV)-oxo-hydroxide cluster anion may be the first member in polyoxometalates class with metal atoms from the IVB group and having Oh symmetry. Alternatively, it may be the first member in {[(Zr6Z)X 12]X6}m- class with halides replaced by oxo- and hydroxyl groups and with an increased oxidation state of Zr. It is predicted to bear application potentials directed by both families. This work could suggest a direction in which the preparation of Zr-C cluster-assembled materials in a liquid environment may be eventually fulfilled. 1,3-Bis(diethylphosphino)propane (depp) protected small gold clusters are studied via multiple techniques, including Electrospray Ionization Mass Spectrometry (ESI-MS), Ultraviolet-Visible Spectroscopy (Uv-Vis), Nuclear Magnetic Resonance (NMR) for solution phase and Transmission Electron Microscopy (TEM) for the condensed phase. In particular, undeca-, dodeca- and trideca-gold clusters protected by depp and halogen ligands, i.e. [Au11-13(depp) 4Cl2-4]+, are found to be all predominant and persist in solution for months, while they gradually and spontaneously grow into a monomial trideca-gold clusters series. The unique preferred ligand combination, depp along with Cl, is discussed in terms of the ligand-core interaction and the closed-shell electronic configurations of the Au n (n = 11-13) cores, which enables them to serve as building units for larger cluster-assembled nanoparticles and form Self-Assembled Arrays (SAAs), as discovered by TEM measurements. Such spontaneous-growth behavior and the resultant SAAs observations are correlated by icosahedra-close-packing modes of clusters, following "magic numbers" rules. ˜7 shells of such cluster packing are proposed to be in the SAAs.

SOMFlow: Guided Exploratory Cluster Analysis with Self-Organizing Maps and Analytic Provenance.

PubMed

Sacha, Dominik; Kraus, Matthias; Bernard, Jurgen; Behrisch, Michael; Schreck, Tobias; Asano, Yuki; Keim, Daniel A

2018-01-01

Clustering is a core building block for data analysis, aiming to extract otherwise hidden structures and relations from raw datasets, such as particular groups that can be effectively related, compared, and interpreted. A plethora of visual-interactive cluster analysis techniques has been proposed to date, however, arriving at useful clusterings often requires several rounds of user interactions to fine-tune the data preprocessing and algorithms. We present a multi-stage Visual Analytics (VA) approach for iterative cluster refinement together with an implementation (SOMFlow) that uses Self-Organizing Maps (SOM) to analyze time series data. It supports exploration by offering the analyst a visual platform to analyze intermediate results, adapt the underlying computations, iteratively partition the data, and to reflect previous analytical activities. The history of previous decisions is explicitly visualized within a flow graph, allowing to compare earlier cluster refinements and to explore relations. We further leverage quality and interestingness measures to guide the analyst in the discovery of useful patterns, relations, and data partitions. We conducted two pair analytics experiments together with a subject matter expert in speech intonation research to demonstrate that the approach is effective for interactive data analysis, supporting enhanced understanding of clustering results as well as the interactive process itself.

Evaluating effective pair and multisite interactions for Ni-Mo system

NASA Astrophysics Data System (ADS)

Banerjee, Rumu H.; Arya, A.; Banerjee, S.

2018-04-01

Cluster expansion (CE) method was used to calculate the energies of various Ni-Mo phases. The clusters comprising of few nearest neighbours can describe any phase of Ni-Mo system by suitable choice of effective pair and multisite interaction parameters (ECI). The ECIs were evaluated in present study by fitting the ground state energies obtained by first principle calculations. The ECIs evaluated for Ni-Mo system were mostly pair clusters followed by triplets and quadruplet clusters with cluster diameters in the range 2.54 - 10.20 Å. The ECI values diminished for multi-body (triplets and quadruplets) clusters as compared to 2-point or pair clusters indicating a good convergence of CE model. With these ECIs the predicted energies of all the Ni-Mo structures across the Mo concentration range 0-100 at% were obtained. The quantitative error in the energies calculated by CE approach and first principle is very small (< 0.026 meV/atom). The appreciable values of 2-point ECIs upto 4th nearest neighbour reveal that two body interactions are dominant in the case of Ni-Mo system. These ECIs are compared with the reported values of compositional dependent effective pair interactions evaluated by first principle as well as by Monte Carlo method.

Probing dark matter physics with galaxy clusters

NASA Astrophysics Data System (ADS)

Dalal, Neal

2016-10-01

We propose a theoretical investigation of the effects of a class of dark matter (DM) self-interactions on the properties of galaxy clusters and their host dark matter halos. Recent work using HST has claimed the detection of a particular form of DM self-interaction, which can lead to observable displacements between satellite galaxies within clusters and the DM subhalos hosting them. This form of self-interaction is highly anisotropic, favoring forward scattering with low momentum transfer, unlike isotropically scattering self-interacting dark matter (SIDM) models. This class of models has not been simulated numerically, clouding the interpretation of the claimed offsets between galaxies and lensing peaks observed by HST. We propose to perform high resolution simulations of cosmological structure formation for this class of SIDM model, focusing on three observables accessible to existing HST observations of clusters. First, we will quantify the extent to which offsets between baryons and DM can arise in these models, as a function of the cross section. Secondly, we will also quantify the effects of this type of DM self-interaction on halo concentrations, to determine the range of cross-sections allowed by existing stringent constraints from HST. Finally we will compute the so-called splashback feature in clusters, specifically focusing on whether SIDM can resolve the current discrepancy between observed values of splashback radii in clusters compared to theoretical predictions for CDM. The proposed investigations will add value to all existing deep HST observations of galaxy clusters by allowing them to probe dark matter physics in three independent ways.

Clustering of Cyclodextrin-Functionalized Microbeads by an Amphiphilic Biopolymer: Real-Time Observation of Structures Resembling Blood Clots.

PubMed

Arya, Chandamany; Saez Cabesas, Camila A; Huang, Hubert; Raghavan, Srinivasa R

2017-10-25

Colloidal particles can be induced to cluster by adding polymers in a process called bridging flocculation. For bridging to occur, the polymer must bind strongly to the surfaces of adjacent particles, such as via electrostatic interactions. Here, we introduce a new system where bridging occurs due to specific interactions between the side chains of an amphiphilic polymer and supramolecules on the particle surface. The polymer is a hydrophobically modified chitosan (hmC) while the particles are uniform polymeric microbeads (∼160 μm in diameter) made by a microfluidic technique and functionalized on their surface by α-cyclodextrins (CDs). The CDs have hydrophobic binding pockets that can capture the n-alkyl hydrophobes present along the hmC chains. Clustering of CD-coated microbeads in water by hmC is visualized in real time using optical microscopy. Interestingly, the clustering follows two distinct stages: first, the microbeads are bridged into clusters by hmC chains, which occurs by the interaction of individual chains with the CDs on adjacent particles. Thereafter, additional hmC from the solution adsorbs onto the surfaces of the microbeads and an hmC "mesh" grows around the clusters. This growing nanostructured mesh can trap surrounding microsized objects and sequester them within the overall cluster. Such clustering is reminiscent of blood clotting where blood platelets initially cluster at a wound site, whereupon they induce growth of a protein (fibrin) mesh around the clusters, which entraps other passive cells. Clustering does not occur with the native chitosan (lacking hydrophobes) or with the bare particles (lacking CDs); these results confirm that the clustering is indeed due to hydrophobic interactions between the hmC and the CDs. Microbead clustering via amphiphilic biopolymers could be applicable in embolization, which is a surgical technique used to block blood flow to a particular area of the body, or in agglutination assays.

Interaction mining and skill-dependent recommendations for multi-objective team composition

PubMed Central

Dorn, Christoph; Skopik, Florian; Schall, Daniel; Dustdar, Schahram

2011-01-01

Web-based collaboration and virtual environments supported by various Web 2.0 concepts enable the application of numerous monitoring, mining and analysis tools to study human interactions and team formation processes. The composition of an effective team requires a balance between adequate skill fulfillment and sufficient team connectivity. The underlying interaction structure reflects social behavior and relations of individuals and determines to a large degree how well people can be expected to collaborate. In this paper we address an extended team formation problem that does not only require direct interactions to determine team connectivity but additionally uses implicit recommendations of collaboration partners to support even sparsely connected networks. We provide two heuristics based on Genetic Algorithms and Simulated Annealing for discovering efficient team configurations that yield the best trade-off between skill coverage and team connectivity. Our self-adjusting mechanism aims to discover the best combination of direct interactions and recommendations when deriving connectivity. We evaluate our approach based on multiple configurations of a simulated collaboration network that features close resemblance to real world expert networks. We demonstrate that our algorithm successfully identifies efficient team configurations even when removing up to 40% of experts from various social network configurations. PMID:22298939

Hydrophobicity within the three-dimensional Mercedes-Benz model: potential of mean force.

PubMed

Dias, Cristiano L; Hynninen, Teemu; Ala-Nissila, Tapio; Foster, Adam S; Karttunen, Mikko

2011-02-14

We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.

Hydrophobicity within the three-dimensional Mercedes-Benz model: Potential of mean force

NASA Astrophysics Data System (ADS)

Dias, Cristiano L.; Hynninen, Teemu; Ala-Nissila, Tapio; Foster, Adam S.; Karttunen, Mikko

2011-02-01

We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.

Tracing catchment fine sediment sources using the new SIFT (SedIment Fingerprinting Tool) open source software.

PubMed

Pulley, S; Collins, A L

2018-09-01

The mitigation of diffuse sediment pollution requires reliable provenance information so that measures can be targeted. Sediment source fingerprinting represents one approach for supporting these needs, but recent methodological developments have resulted in an increasing complexity of data processing methods rendering the approach less accessible to non-specialists. A comprehensive new software programme (SIFT; SedIment Fingerprinting Tool) has therefore been developed which guides the user through critical data analysis decisions and automates all calculations. Multiple source group configurations and composite fingerprints are identified and tested using multiple methods of uncertainty analysis. This aims to explore the sediment provenance information provided by the tracers more comprehensively than a single model, and allows for model configurations with high uncertainties to be rejected. This paper provides an overview of its application to an agricultural catchment in the UK to determine if the approach used can provide a reduction in uncertainty and increase in precision. Five source group classifications were used; three formed using a k-means cluster analysis containing 2, 3 and 4 clusters, and two a-priori groups based upon catchment geology. Three different composite fingerprints were used for each classification and bi-plots, range tests, tracer variability ratios and virtual mixtures tested the reliability of each model configuration. Some model configurations performed poorly when apportioning the composition of virtual mixtures, and different model configurations could produce different sediment provenance results despite using composite fingerprints able to discriminate robustly between the source groups. Despite this uncertainty, dominant sediment sources were identified, and those in close proximity to each sediment sampling location were found to be of greatest importance. This new software, by integrating recent methodological developments in tracer data processing, guides users through key steps. Critically, by applying multiple model configurations and uncertainty assessment, it delivers more robust solutions for informing catchment management of the sediment problem than many previously used approaches. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Mechanical and Metabolic Responses to Traditional and Cluster Set Configurations in the Bench Press Exercise.

PubMed

García-Ramos, Amador; González-Hernández, Jorge M; Baños-Pelegrín, Ezequiel; Castaño-Zambudio, Adrián; Capelo-Ramírez, Fernando; Boullosa, Daniel; Haff, Guy G; Jiménez-Reyes, Pedro

2017-10-20

García-Ramos, A, González-Hernández, JM, Baños-Pelegrín, E, Castaño-Zambudio, A, Capelo-Ramírez, F, Boullosa, D, Haff, GG, and Jiménez-Reyes, P. Mechanical and metabolic responses to traditional and cluster set configurations in the bench press exercise. J Strength Cond Res XX(X): 000-000, 2017-This study aimed to compare mechanical and metabolic responses between traditional (TR) and cluster (CL) set configurations in the bench press exercise. In a counterbalanced randomized order, 10 men were tested with the following protocols (sets × repetitions [inter-repetition rest]): TR1: 3 × 10 (0-second), TR2: 6 × 5 (0-second), CL5: 3 × 10 (5-second), CL10: 3 × 10 (10-second), and CL15: 3 × 10 (15-second). The number of repetitions (30), interset rest (5 minutes), and resistance applied (10 repetition maximum) were the same for all set configurations. Movement velocity and blood lactate concentration were used to assess the mechanical and metabolic responses, respectively. The comparison of the first and last set of the training session revealed a significant decrease in movement velocity for TR1 (Effect size [ES]: -0.92), CL10 (ES: -0.85), and CL15 (ES: -1.08) (but not for TR2 [ES: -0.38] and CL5 [ES: -0.37]); while blood lactate concentration was significantly increased for TR1 (ES: 1.11), TR2 (ES: 0.90), and CL5 (ES: 1.12) (but not for CL10 [ES: 0.03] and CL15 [ES: -0.43]). Based on velocity loss, set configurations were ranked as follows: TR1 (-39.3 ± 7.3%) > CL5 (-20.2 ± 14.7%) > CL10 (-12.9 ± 4.9%), TR2 (-10.3 ± 5.3%), and CL15 (-10.0 ± 2.3%). The set configurations were ranked as follows based on the lactate concentration: TR1 (7.9 ± 1.1 mmol·L) > CL5 (5.8 ± 0.9 mmol·L) > TR2 (4.2 ± 0.7 mmol·L) > CL10 (3.5 ± 0.4 mmol·L) and CL15 (3.4 ± 0.7 mmol·L). These results support the use of TR2, CL10, and CL15 for the maintenance of high mechanical outputs, while CL10 and CL15 produce less metabolic stress than TR2.

Making sense of the conflicting magic numbers in WSi{sub n} clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abreu, Marissa Baddick; Reber, Arthur C.; Khanna, Shiv N.

2015-08-21

First principles studies on the geometric structure, stability, and electronic structure of WSi{sub n} clusters, n = 6-16, have been carried out to show that the observed differing “magic sizes” for WSi{sub n} clusters are associated with the nature of the growth processes. The WSi{sub 12} cluster, observed as a magic species in experiments reacting transition metal ions with silane, is not stable due to a filled shell of 18 electrons, as previously proposed, but due to its atomic structure that arrests further growth because of an endohedral transition metal site. In fact, it is found that all of thesemore » clusters, n = 6-16, have filled 5d shells except for WSi{sub 12}, which has a 5d{sup 8} configuration that is caused by crystal field splitting. The stability of WSi{sub 15}{sup +}, observed as highly stable in clusters generated by vaporizing silicon and metal carbonyls, is shown to be associated with a combination of geometric and electronic features. The findings are compared with previous results on CrSi{sub n} clusters.« less

Atomic structure considerations for the low-temperature opacity of Sn

DOE PAGES

Colgan, J.; Kilcrease, D. P.; Abdallah, J.; ...

2017-03-31

Here, we have begun a preliminary investigation into the opacity of Sn at low temperatures (< 50 eV). The emissivity and opacity of Sn is a crucial factor in determining the utility of Sn in EUV lithography, with numerous industrial implications. To this end, we have been exploring the accuracy of some approximations used in opacity models for the relevant ion stages of Sn (neutral through ~ 18 times ionized). We also find that the use of intermediate-coupling, as compared to full configuration-interaction, is not adequate to obtain accurate line positions of the important bound-bound transitions in Sn. One requiresmore » full configuration-interaction to properly describe the strong mixing between the various n=4 sub-shells that give rise to the Δn= 0 transitions that dominate the opacity spectrum at low temperatures. Furthermore, since calculations that include full configuration-interaction for large numbers of configurations quickly become computationally prohibitive, we have explored hybrid calculations, in which full configuration-interaction is retained for the most important transitions, while intermediate-coupling is employed for all other transitions. After extensive exploration of the atomic structure properties, local-thermodynamic-equilibrium (LTE) opacities are generated using the ATOMIC code at selected temperatures and densities and compared to experiment.« less

Atomic structure considerations for the low-temperature opacity of Sn

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colgan, J.; Kilcrease, D. P.; Abdallah, J.

Here, we have begun a preliminary investigation into the opacity of Sn at low temperatures (< 50 eV). The emissivity and opacity of Sn is a crucial factor in determining the utility of Sn in EUV lithography, with numerous industrial implications. To this end, we have been exploring the accuracy of some approximations used in opacity models for the relevant ion stages of Sn (neutral through ~ 18 times ionized). We also find that the use of intermediate-coupling, as compared to full configuration-interaction, is not adequate to obtain accurate line positions of the important bound-bound transitions in Sn. One requiresmore » full configuration-interaction to properly describe the strong mixing between the various n=4 sub-shells that give rise to the Δn= 0 transitions that dominate the opacity spectrum at low temperatures. Furthermore, since calculations that include full configuration-interaction for large numbers of configurations quickly become computationally prohibitive, we have explored hybrid calculations, in which full configuration-interaction is retained for the most important transitions, while intermediate-coupling is employed for all other transitions. After extensive exploration of the atomic structure properties, local-thermodynamic-equilibrium (LTE) opacities are generated using the ATOMIC code at selected temperatures and densities and compared to experiment.« less

Intelligent nanomedicine integrating diagnosis and therapy

NASA Technical Reports Server (NTRS)

Li, Na (Inventor); Tan, Winny (Inventor)

2012-01-01

A method of controlling the activity of a biologically active compound. The method concerns an oligonucleotide-based compound, comprising a hairpin-forming oligonucleotide, an effector moiety physically associated with the oligonucleotide, where the effector moiety possesses a biological activity, and a regulating moiety physically associated with the oligonucleotide, where the regulating moiety controls the biological activity of the effector moiety by interacting with the effector moiety. The oligonucleotide can assume a hairpin configuration, where the effector and regulating moieties interact, or an open configuration, where the effector and regulating moieties fail to interact. Depending on the nature of the effector and regulating moieties, either configuration can result in the expression of the biological activity of the effector moiety.

Fluxoids configurations in finite superconducting networks

NASA Astrophysics Data System (ADS)

Sharon, Omri J.; Haham, Noam; Shaulov, Avner A.; Yeshurun, Yosef

2017-12-01

Analysis of superconducting ladders consisting of rectangular loops, yields an Ising like expression for the total energy of the ladders as a function of the loops vorticities and the applied magnetic field. This expression shows that fluxoids can be treated as repulsively interacting objects driven towards the ladder center by the applied field. Distinctive repulsive interactions between fluxoids are obtained depending on the ratio l between the loops length and the common width of adjacent loops. A 'short range' and a 'long range' interactions obtained for l ≳ 1 and l ≪ 1, respectively, give rise to remarkably different fluxoid configurations. The different configurations of fluxoids in different types of ladders are illustrated by simulations.

Application of clustering methods: Regularized Markov clustering (R-MCL) for analyzing dengue virus similarity

NASA Astrophysics Data System (ADS)

Lestari, D.; Raharjo, D.; Bustamam, A.; Abdillah, B.; Widhianto, W.

2017-07-01

Dengue virus consists of 10 different constituent proteins and are classified into 4 major serotypes (DEN 1 - DEN 4). This study was designed to perform clustering against 30 protein sequences of dengue virus taken from Virus Pathogen Database and Analysis Resource (VIPR) using Regularized Markov Clustering (R-MCL) algorithm and then we analyze the result. By using Python program 3.4, R-MCL algorithm produces 8 clusters with more than one centroid in several clusters. The number of centroid shows the density level of interaction. Protein interactions that are connected in a tissue, form a complex protein that serves as a specific biological process unit. The analysis of result shows the R-MCL clustering produces clusters of dengue virus family based on the similarity role of their constituent protein, regardless of serotypes.

Solving the scalability issue in quantum-based refinement: Q|R#1.

PubMed

Zheng, Min; Moriarty, Nigel W; Xu, Yanting; Reimers, Jeffrey R; Afonine, Pavel V; Waller, Mark P

2017-12-01

Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately as n m , where n is the number of atoms and m (≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package called Q|R, this issue is referred to as Q|R#1. A divide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1. Firstly, the atomic model of a crystal structure is analyzed to detect noncovalent interactions between residues, and the results of the analysis are represented as an interaction graph. Secondly, a graph-clustering algorithm is used to partition the interaction graph into a set of clusters in such a way as to minimize disruption to the noncovalent interaction network. Thirdly, the environment surrounding each individual cluster is analyzed and any residue that is interacting with a particular cluster is assigned to the buffer region of that particular cluster. A fragment is defined as a cluster plus its buffer region. The gradients for all atoms from each of the fragments are computed, and only the gradients from each cluster are combined to create the total gradients. A quantum-based refinement is carried out using the total gradients as chemical restraints. In order to validate this interaction graph-based fragmentation approach in Q|R, the entire atomic model of an amyloid cross-β spine crystal structure (PDB entry 2oNA) was refined.

First-Principles Study of Thermodynamic and Magnetic Properties of Alloys

NASA Astrophysics Data System (ADS)

Zhuravlev, Ivan

The standard theoretical framework for predicting phase diagrams and other thermodynamic properties of alloys requires an adequate representation of the formation enthalpy. An important part of the formation enthalpy in size-mismatched alloys comes from atomic relaxations. The harmonic Kanzaki-Krivoglaz-Khachaturyan model of strain-induced interaction is generalized to concentrated size-mismatched alloys and adapted to first-principles calculations. The configuration dependence of both Kanzaki forces and force constants is represented by real-space cluster expansions that can be constructed based on the calculated forces. Developed configuration-dependent lattice deformation model is implemented for the fcc lattice and applied to Cu1-x Aux and Fe1-x Ptx alloys for concentrations x = 0.25, 0.5, and 0.75. The model is further adapted to concentration wave analysis and Monte Carlo. Good agreement with experiment is found for all systems except CuAu3 and FePt3. The structural and ordering energetics are studied in Au-Fe alloys by combining DFT calculations with effective Hamiltonian techniques: a cluster expansion with structural filters, and CLDM. The phase separation tendency in Au-Fe persists even if the fcc-bcc decomposition is suppressed. The relative stability of disordered bcc and fcc phases observed in nanoparticles is reproduced, but the fully ordered L10 AuFe, L12 Au3Fe, and L1 2 AuFe3 structures are unstable in DFT. Effects of magnetism on the chemical ordering are also discussed. Magnetocrystalline anisotropy is one of the key properties of a magnetic material. Understanding of its temperature and concentration dependence is a challenging theoretical problem with implications for the design of better materials for permanent magnets and other applications. The origins of the anomalous temperature dependence of magnetocrystalline anisotropy in (Fe 1-xCox)2B alloys are elucidated using first-principles calculations within the disordered local moment model. Excellent agreement with experimental data is obtained. Electronic structure calculations are used to examine the magnetic properties of Fe2P-based alloys and the mechanisms through which the Curie temperature and magnetocrystalline anisotropy can be optimized for specific applications. It is found that at elevated temperatures the magnetic interaction in pure Fe2P develops a pronounced two-dimensional character. Co-alloying of Fe2P with Co (or Ni) and Si is suggested as a strategy for maximizing the magnetocrystalline anisotropy above room temperature.