Communication: A simplified coupled-cluster Lagrangian for polarizable embedding.

PubMed

Krause, Katharina; Klopper, Wim

2016-01-28

A simplified coupled-cluster Lagrangian, which is linear in the Lagrangian multipliers, is proposed for the coupled-cluster treatment of a quantum mechanical system in a polarizable environment. In the simplified approach, the amplitude equations are decoupled from the Lagrangian multipliers and the energy obtained from the projected coupled-cluster equation corresponds to a stationary point of the Lagrangian.

Communication: A simplified coupled-cluster Lagrangian for polarizable embedding

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

Krause, Katharina; Klopper, Wim, E-mail: klopper@kit.edu

A simplified coupled-cluster Lagrangian, which is linear in the Lagrangian multipliers, is proposed for the coupled-cluster treatment of a quantum mechanical system in a polarizable environment. In the simplified approach, the amplitude equations are decoupled from the Lagrangian multipliers and the energy obtained from the projected coupled-cluster equation corresponds to a stationary point of the Lagrangian.

Synchronization as Aggregation: Cluster Kinetics of Pulse-Coupled Oscillators.

PubMed

O'Keeffe, Kevin P; Krapivsky, P L; Strogatz, Steven H

2015-08-07

We consider models of identical pulse-coupled oscillators with global interactions. Previous work showed that under certain conditions such systems always end up in sync, but did not quantify how small clusters of synchronized oscillators progressively coalesce into larger ones. Using tools from the study of aggregation phenomena, we obtain exact results for the time-dependent distribution of cluster sizes as the system evolves from disorder to synchrony.

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

Gomez, John A.; Henderson, Thomas M.; Scuseria, Gustavo E.

Restricted single-reference coupled cluster theory truncated to single and double excitations accurately describes weakly correlated systems, but often breaks down in the presence of static or strong correlation. Good coupled cluster energies in the presence of degeneracies can be obtained by using a symmetry-broken reference, such as unrestricted Hartree-Fock, but at the cost of good quantum numbers. A large body of work has shown that modifying the coupled cluster ansatz allows for the treatment of strong correlation within a single-reference, symmetry-adapted framework. The recently introduced singlet-paired coupled cluster doubles (CCD0) method is one such model, which recovers correct behavior formore » strong correlation without requiring symmetry breaking in the reference. Here, we extend singlet-paired coupled cluster for application to open shells via restricted open-shell singlet-paired coupled cluster singles and doubles (ROCCSD0). The ROCCSD0 approach retains the benefits of standard coupled cluster theory and recovers correct behavior for strongly correlated, open-shell systems using a spin-preserving ROHF reference.« less

The Mössbauer Parameters of the Proximal Cluster of Membrane-Bound Hydrogenase Revisited: A Density Functional Theory Study.

PubMed

Tabrizi, Shadan Ghassemi; Pelmenschikov, Vladimir; Noodleman, Louis; Kaupp, Martin

2016-01-12

An unprecedented [4Fe-3S] cluster proximal to the regular [NiFe] active site has recently been found to be responsible for the ability of membrane-bound hydrogenases (MBHs) to oxidize dihydrogen in the presence of ambient levels of oxygen. Starting from proximal cluster models of a recent DFT study on the redox-dependent structural transformation of the [4Fe-3S] cluster, (57)Fe Mössbauer parameters (electric field gradients, isomer shifts, and nuclear hyperfine couplings) were calculated using DFT. Our results revise the previously reported correspondence of Mössbauer signals and iron centers in the [4Fe-3S](3+) reduced-state proximal cluster. Similar conflicting assignments are also resolved for the [4Fe-3S](5+) superoxidized state with particular regard to spin-coupling in the broken-symmetry DFT calculations. Calculated (57)Fe hyperfine coupling (HFC) tensors expose discrepancies in the experimental set of HFC tensors and substantiate the need for additional experimental work on the magnetic properties of the MBH proximal cluster in its reduced and superoxidized redox states.

Cluster dynamics of pulse coupled oscillators

NASA Astrophysics Data System (ADS)

O'Keeffe, Kevin; Strogatz, Steven; Krapivsky, Paul

2015-03-01

We study the dynamics of networks of pulse coupled oscillators. Much attention has been devoted to the ultimate fate of the system: which conditions lead to a steady state in which all the oscillators are firing synchronously. But little is known about how synchrony builds up from an initially incoherent state. The current work addresses this question. Oscillators start to synchronize by forming clusters of different sizes that fire in unison. First pairs of oscillators, then triplets and so on. These clusters progressively grow by coalescing with others, eventually resulting in the fully synchronized state. We study the mean field model in which the coupling between oscillators is all to all. We use probabilistic arguments to derive a recursive set of evolution equations for these clusters. Using a generating function formalism, we derive simple equations for the moments of these clusters. Our results are in good agreement simulation. We then numerically explore the effects of non-trivial connectivity. Our results have potential application to ultra-low power ``impulse radio'' & sensor networks.

X-ray aspects of the DAFT/FADA clusters

NASA Astrophysics Data System (ADS)

Guennou, L.; Durret, F.; Lima Neto, G. B.; Adami, C.

2012-12-01

We have undertaken the DAFT/FADA survey with the aim of applying constraints on dark energy based on weak lensing tomography as well as obtaining homogeneous and high quality data for a sample of 91 massive clusters in the redshift range [0.4,0.9] for which there are HST archive data. We have analysed the XMM-Newton data available for 42 of these clusters to derive their X-ray temperatures and luminosities and search for substructures. This study was coupled with a dynamical analysis for the 26 clusters having at least 30 spectroscopic galaxy redshifts in the cluster range. We present preliminary results on the coupled X-ray and dynamical analyses of these clusters.

Stochastic coupled cluster theory: Efficient sampling of the coupled cluster expansion

NASA Astrophysics Data System (ADS)

Scott, Charles J. C.; Thom, Alex J. W.

2017-09-01

We consider the sampling of the coupled cluster expansion within stochastic coupled cluster theory. Observing the limitations of previous approaches due to the inherently non-linear behavior of a coupled cluster wavefunction representation, we propose new approaches based on an intuitive, well-defined condition for sampling weights and on sampling the expansion in cluster operators of different excitation levels. We term these modifications even and truncated selections, respectively. Utilising both approaches demonstrates dramatically improved calculation stability as well as reduced computational and memory costs. These modifications are particularly effective at higher truncation levels owing to the large number of terms within the cluster expansion that can be neglected, as demonstrated by the reduction of the number of terms to be sampled when truncating at triple excitations by 77% and hextuple excitations by 98%.

Influences of adding negative couplings between cliques of Kuramoto-like oscillators

NASA Astrophysics Data System (ADS)

Yang, Li-xin; Lin, Xiao-lin; Jiang, Jun

2018-06-01

We study the dynamics in a clustered network of coupled oscillators by considering positive and negative coupling schemes. Second order oscillators can be interpreted as a model of consumers and generators working in a power network. Numerical results indicate that coupling strategies play an important role in the synchronizability of the clustered power network. It is found that the synchronizability can be enhanced as the positive intragroup connections increase. Meanwhile, when the intragroup interactions are positive and the probability p that two nodes belonging to different clusters are connected is increased, the synchronization has better performance. Besides, when the intragroup connections are negative, it is observed that the power network has poor synchronizability as the probability p increases. Our simulation results can help us understand the collective behavior of the power network with positive and negative couplings.

Symmetry, Hopf bifurcation, and the emergence of cluster solutions in time delayed neural networks.

PubMed

Wang, Zhen; Campbell, Sue Ann

2017-11-01

We consider the networks of N identical oscillators with time delayed, global circulant coupling, modeled by a system of delay differential equations with Z N symmetry. We first study the existence of Hopf bifurcations induced by the coupling time delay and then use symmetric Hopf bifurcation theory to determine how these bifurcations lead to different patterns of symmetric cluster oscillations. We apply our results to a case study: a network of FitzHugh-Nagumo neurons with diffusive coupling. For this model, we derive the asymptotic stability, global asymptotic stability, absolute instability, and stability switches of the equilibrium point in the plane of coupling time delay (τ) and excitability parameter (a). We investigate the patterns of cluster oscillations induced by the time delay and determine the direction and stability of the bifurcating periodic orbits by employing the multiple timescales method and normal form theory. We find that in the region where stability switching occurs, the dynamics of the system can be switched from the equilibrium point to any symmetric cluster oscillation, and back to equilibrium point as the time delay is increased.

Relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian: Relativistic pair correlation energies of the Xe atom

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

Eliav, E.; Kaldor, U.; Ishikawa, Y.

1994-12-31

Relativistic pair correlation energies of Xe were computed by employing a recently developed relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian. The matrix Dirac-Fock-Breit SCF and relativistic coupled cluster calculations were performed by means of expansion in basis sets of well-tempered Gaussian spinors. A detailed study of the pair correlation energies in Xe is performed, in order to investigate the effects of the low-frequency Breit interaction on the correlation energies of Xe. Nonadditivity of correlation and relativistic (particularly Breit) effects is discussed.

Excitons in Potassium Bromide: A Study using Embedded Time-dependent Density Functional Theory and Equation-of-Motion Coupled Cluster Methods

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

Govind, Niranjan; Sushko, Petr V.; Hess, Wayne P.

2009-03-05

We present a study of the electronic excitations in insulating materials using an embedded- cluster method. The excited states of the embedded cluster are studied systematically using time-dependent density functional theory (TDDFT) and high-level equation-of-motion coupled cluster (EOMCC) methods. In particular, we have used EOMCC models with singles and doubles (EOMCCSD) and two approaches which account for the e®ect of triply excited con¯gurations in non-iterative and iterative fashions. We present calculations of the lowest surface excitations of the well-studied potassium bromide (KBr) system and compare our results with experiment. The bulk-surface exciton shift is also calculated at the TDDFT levelmore » and compared with experiment.« less

Coarse-Grained Clustering Dynamics of Heterogeneously Coupled Neurons.

PubMed

Moon, Sung Joon; Cook, Katherine A; Rajendran, Karthikeyan; Kevrekidis, Ioannis G; Cisternas, Jaime; Laing, Carlo R

2015-12-01

The formation of oscillating phase clusters in a network of identical Hodgkin-Huxley neurons is studied, along with their dynamic behavior. The neurons are synaptically coupled in an all-to-all manner, yet the synaptic coupling characteristic time is heterogeneous across the connections. In a network of N neurons where this heterogeneity is characterized by a prescribed random variable, the oscillatory single-cluster state can transition-through [Formula: see text] (possibly perturbed) period-doubling and subsequent bifurcations-to a variety of multiple-cluster states. The clustering dynamic behavior is computationally studied both at the detailed and the coarse-grained levels, and a numerical approach that can enable studying the coarse-grained dynamics in a network of arbitrarily large size is suggested. Among a number of cluster states formed, double clusters, composed of nearly equal sub-network sizes are seen to be stable; interestingly, the heterogeneity parameter in each of the double-cluster components tends to be consistent with the random variable over the entire network: Given a double-cluster state, permuting the dynamical variables of the neurons can lead to a combinatorially large number of different, yet similar "fine" states that appear practically identical at the coarse-grained level. For weak heterogeneity we find that correlations rapidly develop, within each cluster, between the neuron's "identity" (its own value of the heterogeneity parameter) and its dynamical state. For single- and double-cluster states we demonstrate an effective coarse-graining approach that uses the Polynomial Chaos expansion to succinctly describe the dynamics by these quickly established "identity-state" correlations. This coarse-graining approach is utilized, within the equation-free framework, to perform efficient computations of the neuron ensemble dynamics.

Distinct collective states due to trade-off between attractive and repulsive couplings

NASA Astrophysics Data System (ADS)

Sathiyadevi, K.; Chandrasekar, V. K.; Senthilkumar, D. V.; Lakshmanan, M.

2018-03-01

We investigate the effect of repulsive coupling together with an attractive coupling in a network of nonlocally coupled oscillators. To understand the complex interaction between these two couplings we introduce a control parameter in the repulsive coupling which plays a crucial role in inducing distinct complex collective patterns. In particular, we show the emergence of various cluster chimera death states through a dynamically distinct transition route, namely the oscillatory cluster state and coherent oscillation death state as a function of the repulsive coupling in the presence of the attractive coupling. In the oscillatory cluster state, the oscillators in the network are grouped into two distinct dynamical states of homogeneous and inhomogeneous oscillatory states. Further, the network of coupled oscillators follow the same transition route in the entire coupling range. Depending upon distinct coupling ranges, the system displays different number of clusters in the death state and oscillatory state. We also observe that the number of coherent domains in the oscillatory cluster state exponentially decreases with increase in coupling range and obeys a power-law decay. Additionally, we show analytical stability for observed solitary state, synchronized state, and incoherent oscillation death state.

Development and Application of Single-Referenced Perturbation and Coupled-Cluster Theories for Excited Electronic States

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

Recent work on the development of single-reference perturbation theories for the study of excited electronic states will be discussed. The utility of these methods will be demonstrated by comparison to linear-response coupled-cluster excitation energies. Results for some halogen molecules of interest in stratospheric chemistry will be presented.

Experimental observation of chimera and cluster states in a minimal globally coupled network

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Bansal, Kanika; Murphy, Thomas E.; Roy, Rajarshi

2016-09-01

A "chimera state" is a dynamical pattern that occurs in a network of coupled identical oscillators when the symmetry of the oscillator population is broken into synchronous and asynchronous parts. We report the experimental observation of chimera and cluster states in a network of four globally coupled chaotic opto-electronic oscillators. This is the minimal network that can support chimera states, and our study provides new insight into the fundamental mechanisms underlying their formation. We use a unified approach to determine the stability of all the observed partially synchronous patterns, highlighting the close relationship between chimera and cluster states as belonging to the broader phenomenon of partial synchronization. Our approach is general in terms of network size and connectivity. We also find that chimera states often appear in regions of multistability between global, cluster, and desynchronized states.

X-ray and optical substructures of the DAFT/FADA survey clusters

NASA Astrophysics Data System (ADS)

Guennou, L.; Durret, F.; Adami, C.; Lima Neto, G. B.

2013-04-01

We have undertaken the DAFT/FADA survey with the double aim of setting constraints on dark energy based on weak lensing tomography and of obtaining homogeneous and high quality data for a sample of 91 massive clusters in the redshift range 0.4-0.9 for which there were HST archive data. We have analysed the XMM-Newton data available for 42 of these clusters to derive their X-ray temperatures and luminosities and search for substructures. Out of these, a spatial analysis was possible for 30 clusters, but only 23 had deep enough X-ray data for a really robust analysis. This study was coupled with a dynamical analysis for the 26 clusters having at least 30 spectroscopic galaxy redshifts in the cluster range. Altogether, the X-ray sample of 23 clusters and the optical sample of 26 clusters have 14 clusters in common. We present preliminary results on the coupled X-ray and dynamical analyses of these 14 clusters.

Communication: Relativistic Fock-space coupled cluster study of small building blocks of larger uranium complexes.

PubMed

Tecmer, Paweł; Gomes, André Severo Pereira; Knecht, Stefan; Visscher, Lucas

2014-07-28

We present a study of the electronic structure of the [UO2](+), [UO2](2 +), [UO2](3 +), NUO, [NUO](+), [NUO](2 +), [NUN](-), NUN, and [NUN](+) molecules with the intermediate Hamiltonian Fock-space coupled cluster method. The accuracy of mean-field approaches based on the eXact-2-Component Hamiltonian to incorporate spin-orbit coupling and Gaunt interactions are compared to results obtained with the Dirac-Coulomb Hamiltonian. Furthermore, we assess the reliability of calculations employing approximate density functionals in describing electronic spectra and quantities useful in rationalizing Uranium (VI) species reactivity (hardness, electronegativity, and electrophilicity).

Communication: Relativistic Fock-space coupled cluster study of small building blocks of larger uranium complexes

NASA Astrophysics Data System (ADS)

Tecmer, Paweł; Severo Pereira Gomes, André; Knecht, Stefan; Visscher, Lucas

2014-07-01

We present a study of the electronic structure of the [UO2]+, [UO2]2 +, [UO2]3 +, NUO, [NUO]+, [NUO]2 +, [NUN]-, NUN, and [NUN]+ molecules with the intermediate Hamiltonian Fock-space coupled cluster method. The accuracy of mean-field approaches based on the eXact-2-Component Hamiltonian to incorporate spin-orbit coupling and Gaunt interactions are compared to results obtained with the Dirac-Coulomb Hamiltonian. Furthermore, we assess the reliability of calculations employing approximate density functionals in describing electronic spectra and quantities useful in rationalizing Uranium (VI) species reactivity (hardness, electronegativity, and electrophilicity).

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-01

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra.

PubMed

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-07

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

PubMed

Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

2011-01-21

A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics.

Experimental observation of chimera and cluster states in a minimal globally coupled network

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

Hart, Joseph D.; Department of Physics, University of Maryland, College Park, Maryland 20742; Bansal, Kanika

A “chimera state” is a dynamical pattern that occurs in a network of coupled identical oscillators when the symmetry of the oscillator population is broken into synchronous and asynchronous parts. We report the experimental observation of chimera and cluster states in a network of four globally coupled chaotic opto-electronic oscillators. This is the minimal network that can support chimera states, and our study provides new insight into the fundamental mechanisms underlying their formation. We use a unified approach to determine the stability of all the observed partially synchronous patterns, highlighting the close relationship between chimera and cluster states as belongingmore » to the broader phenomenon of partial synchronization. Our approach is general in terms of network size and connectivity. We also find that chimera states often appear in regions of multistability between global, cluster, and desynchronized states.« less

Multifrequency multi-qubit entanglement based on plasmonic hot spots

PubMed Central

Ren, Jun; Wu, Tong; Zhang, Xiangdong

2015-01-01

The theoretical method to study strong coupling between an ensemble of quantum emitters (QEs) and surface plasmons excited by the nanoparticle cluster has been presented by using a rigorous first-principles electromagnetic Green’s tensor technique. We have demonstrated that multi-qubit entanglements for two-level QEs can be produced at different coupling resonance frequencies, when they locate in the hot spots of the metallic nanoparticle cluster. The duration of quantum beats for such an entanglement can reach two orders longer than that for the entanglement in a photonic cavity. The phenomenon originates from collective coupling resonance excitation of the cluster. At the frequency of single scattering resonance, the entanglement cannot be produced although the single QE spontaneous decay rate is very big. PMID:26350051

Applying the Coupled-Cluster Ansatz to Solids and Surfaces in the Thermodynamic Limit

NASA Astrophysics Data System (ADS)

Gruber, Thomas; Liao, Ke; Tsatsoulis, Theodoros; Hummel, Felix; Grüneis, Andreas

2018-04-01

Modern electronic structure theories can predict and simulate a wealth of phenomena in surface science and solid-state physics. In order to allow for a direct comparison with experiment, such ab initio predictions have to be made in the thermodynamic limit, substantially increasing the computational cost of many-electron wave-function theories. Here, we present a method that achieves thermodynamic limit results for solids and surfaces using the "gold standard" coupled cluster ansatz of quantum chemistry with unprecedented efficiency. We study the energy difference between carbon diamond and graphite crystals, adsorption energies of water on h -BN, as well as the cohesive energy of the Ne solid, demonstrating the increased efficiency and accuracy of coupled cluster theory for solids and surfaces.

Coupled Cluster Studies of Ionization Potentials and Electron Affinities of Single-Walled Carbon Nanotubes

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

Peng, Bo; Govind, Niranjan; Aprà, Edoardo

In this paper we apply equation-of-motion coupled cluster (EOMCC) methods in studies of vertical ionization potentials (IP) and electron affinities (EA) for sin- gled walled carbon nanotubes. EOMCC formulations for ionization potentials and electron affinities employing excitation manifolds spanned by single and double ex- citations (IP/EA-EOMCCSD) are used to study IPs and EAs of nanotubes as a function of nanotube length. Several armchair nanotubes corresponding to C20nH20 models with n = 2 - 6 have been used in benchmark calculations. In agreement with previous studies, we demonstrate that the electronegativity of C20nH20 systems remains, to a large extent, independent ofmore » nanotube length. We also compare IP/EA- EOMCCSD results with those obtained with the coupled cluster models with single and double excitations corrected by perturbative triples, CCSD(T), and density func- tional theory (DFT) using global and range-separated hybrid exchange-correlation functionals.« less

Orbital-ordering-driven multiferroicity and magnetoelectric coupling in GeV₄S₈.

PubMed

Singh, Kiran; Simon, Charles; Cannuccia, Elena; Lepetit, Marie-Bernadette; Corraze, Benoit; Janod, Etienne; Cario, Laurent

2014-09-26

We report here the discovery of multiferroicity and large magnetoelectric coupling in the type I orbital order system GeV₄S₈. Our study demonstrates that this clustered compound displays a para-ferroelectric transition at 32 K. This transition originates from an orbital ordering which reorganizes the charge within the transition metal clusters. Below the antiferromagnetic transition at 17 K, the application of a magnetic field significantly affects the ferroelectric polarization, revealing thus a large magnetoelectric coupling. Our study suggests that the application of a magnetic field induces a metamagnetic transition which significantly affects the ferroelectric polarization thanks to an exchange striction phenomenon.

Cluster synchronization in networks of neurons with chemical synapses

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

Juang, Jonq, E-mail: jjuang@math.nctu.edu.tw; Liang, Yu-Hao, E-mail: moonsea.am96g@g2.nctu.edu.tw

2014-03-15

In this work, we study the cluster synchronization of chemically coupled and generally formulated networks which are allowed to be nonidentical. The sufficient condition for the existence of stably synchronous clusters is derived. Specifically, we only need to check the stability of the origins of m decoupled linear systems. Here, m is the number of subpopulations. Examples of nonidentical networks such as Hindmarsh-Rose (HR) neurons with various choices of parameters in different subpopulations, or HR neurons in one subpopulation and FitzHugh-Nagumo neurons in the other subpopulation are provided. Explicit threshold for the coupling strength that guarantees the stably cluster synchronizationmore » can be obtained.« less

Are trinuclear superhalogens promising candidates for building blocks of novel magnetic materials? A theoretical prospect from combined broken-symmetry density functional theory and ab initio study.

PubMed

Yu, Yang; Li, Chen; Yin, Bing; Li, Jian-Li; Huang, Yuan-He; Wen, Zhen-Yi; Jiang, Zhen-Yi

2013-08-07

The structures, relative stabilities, vertical electron detachment energies, and magnetic properties of a series of trinuclear clusters are explored via combined broken-symmetry density functional theory and ab initio study. Several exchange-correlation functionals are utilized to investigate the effects of different halogen elements and central atoms on the properties of the clusters. These clusters are shown to possess stronger superhalogen properties than previously reported dinuclear superhalogens. The calculated exchange coupling constants indicate the antiferromagnetic coupling between the transition metal ions. Spin density analysis demonstrates the importance of spin delocalization in determining the strengths of various couplings. Spin frustration is shown to occur in some of the trinuclear superhalogens. The coexistence of strong superhalogen properties and spin frustration implies the possibility of trinuclear superhalogens working as the building block of new materials of novel magnetic properties.

Computational Studies of Magnetically Doped Semiconductor Nanoclusters

NASA Astrophysics Data System (ADS)

Gutsev, Lavrenty Gennady

Spin-polarized unrestricted density functional theory is used to calculate the molecular properties of magnetic semiconductor quantum dots doped with 3d-metal atoms. We calculate total energies of the low spin antiferromagnetically coupled states using a spin-flipping algorithm leading to the broken-symmetry states. Given the novel nature of the materials studied, we simulate experimental observables such as hyperfine couplings, ionization/ energies, electron affinities, first and second order polarizabilities, band gaps and exchange coupling constants. Specifically, we begin our investigation with pure clusters of (CdSe )16 and demonstrate the dependence of molecular observables on geometrical structures. We also show that the many isomers of this cluster are energetically quite closely spaced, and thus it would be necessary to employ a battery of tests to experimentally distinguish them. Next, we discuss Mn-doping into the cage (CdSe)9 cluster as well as the zinc-blende stacking type cluster (CdSe)36. We show that the local exchange coupling mechanism is ligand-mediated superexchange and simulate the isotropic hyperfine constants. Finally, we discuss a novel study where (CdSe)9 is doped with Mn or Fe up to a full replacement of all the Cd's and discuss the transition points for the magnetic behavior and specifically the greatly differing band-gap shifts. We also outline an unexpected pattern in the polarizability of the material as metals are added and compare our results with the results from theoretical studies of the bulk material.

Antiferromagnetic exchange coupling measurements on single Co clusters

NASA Astrophysics Data System (ADS)

Wernsdorfer, W.; Leroy, D.; Portemont, C.; Brenac, A.; Morel, R.; Notin, L.; Mailly, D.

2009-03-01

We report on single-cluster measurements of the angular dependence of the low-temperature ferromagnetic core magnetization switching field in exchange-coupled Co/CoO core-shell clusters (4 nm) using a micro-bridge DC superconducting quantum interference device (μ-SQUID). It is observed that the coupling with the antiferromagnetic shell induces modification in the switching field for clusters with intrinsic uniaxial anisotropy depending on the direction of the magnetic field applied during the cooling. Using a modified Stoner-Wohlfarth model, it is shown that the core interacts with two weakly coupled and asymmetrical antiferromagnetic sublattices. Ref.: C. Portemont, R. Morel, W. Wernsdorfer, D. Mailly, A. Brenac, and L. Notin, Phys. Rev. B 78, 144415 (2008)

Electrostatic effects on clustering and ion dynamics in ionomer melts

NASA Astrophysics Data System (ADS)

Ma, Boran; Nguyen, Trung; Pryamitsyn, Victor; Olvera de La Cruz, Monica

An understanding of the relationships between ionomer chain morphology, dynamics and counter-ion mobility is a key factor in the design of ion conducting membranes for battery applications. In this study, we investigate the influence of electrostatic coupling between randomly charged copolymers (ionomers) and counter ions on the structural and dynamic features of a model system of ionomer melts. Using coarse-grained molecular dynamics (CGMD) simulations, we found that variations in electrostatic coupling strength (Γ) remarkably affect the formation of ion-counter ion clusters, ion mobility, and polymer dynamics for a range of charged monomer fractions. Specifically, an increase in Γ leads to larger ionic cluster sizes and reduced polymer and ion mobility. Analysis of the distribution of the radius of gyration of the clusters further reveals that the fractal dimension of the ion clusters is nearly independent from Γ for all the cases studied. Finally, at sufficiently high values of Γ, we observed arrested heterogeneous ions mobility, which is correlated with an increase in ion cluster size. These findings provide insight into the role of electrostatics in governing the nanostructures formed by ionomers.

Dynamics of a network of phase oscillators with plastic couplings

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

Nekorkin, V. I.; Kasatkin, D. V.; Moscow Institute of Physics and Technology

The processes of synchronization and phase cluster formation are investigated in a complex network of dynamically coupled phase oscillators. Coupling weights evolve dynamically depending on the phase relations between the oscillators. It is shown that the network exhibits several types of behavior: the globally synchronized state, two-cluster and multi-cluster states, different synchronous states with a fixed phase relationship between the oscillators and chaotic desynchronized state.

Predictive coupled-cluster isomer orderings for some Si{sub n}C{sub m} (m, n ≤ 12) clusters: A pragmatic comparison between DFT and complete basis limit coupled-cluster benchmarks

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

Byrd, Jason N., E-mail: byrd.jason@ensco.com; ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940; Lutz, Jesse J., E-mail: jesse.lutz.ctr@afit.edu

The accurate determination of the preferred Si{sub 12}C{sub 12} isomer is important to guide experimental efforts directed towards synthesizing SiC nano-wires and related polymer structures which are anticipated to be highly efficient exciton materials for the opto-electronic devices. In order to definitively identify preferred isomeric structures for silicon carbon nano-clusters, highly accurate geometries, energies, and harmonic zero point energies have been computed using coupled-cluster theory with systematic extrapolation to the complete basis limit for set of silicon carbon clusters ranging in size from SiC{sub 3} to Si{sub 12}C{sub 12}. It is found that post-MBPT(2) correlation energy plays a significant rolemore » in obtaining converged relative isomer energies, suggesting that predictions using low rung density functional methods will not have adequate accuracy. Utilizing the best composite coupled-cluster energy that is still computationally feasible, entailing a 3-4 SCF and coupled-cluster theory with singles and doubles extrapolation with triple-ζ (T) correlation, the closo Si{sub 12}C{sub 12} isomer is identified to be the preferred isomer in the support of previous calculations [X. F. Duan and L. W. Burggraf, J. Chem. Phys. 142, 034303 (2015)]. Additionally we have investigated more pragmatic approaches to obtaining accurate silicon carbide isomer energies, including the use of frozen natural orbital coupled-cluster theory and several rungs of standard and double-hybrid density functional theory. Frozen natural orbitals as a way to compute post-MBPT(2) correlation energy are found to be an excellent balance between efficiency and accuracy.« less

Title: Chimeras in small, globally coupled networks: Experiments and stability analysis

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Bansal, Kanika; Murphy, Thomas E.; Roy, Rajarshi

Since the initial observation of chimera states, there has been much discussion of the conditions under which these states emerge. The emphasis thus far has mainly been to analyze large networks of coupled oscillators; however, recent studies have begun to focus on the opposite limit: what is the smallest system of coupled oscillators in which chimeras can exist? We experimentally observe chimeras and other partially synchronous patterns in a network of four globally-coupled chaotic opto-electronic oscillators. By examining the equations of motion, we demonstrate that symmetries in the network topology allow a variety of synchronous states to exist, including cluster synchronous states and a chimera state. Using the group theoretical approach recently developed for analyzing cluster synchronization, we show how to derive the variational equations for these synchronous patterns and calculate their linear stability. The stability analysis gives good agreement with our experimental results. Both experiments and simulations suggest that these chimera states often appear in regions of multistability between global, cluster, and desynchronized states.

Chimera states in nonlocally coupled phase oscillators with biharmonic interaction

NASA Astrophysics Data System (ADS)

Cheng, Hongyan; Dai, Qionglin; Wu, Nianping; Feng, Yuee; Li, Haihong; Yang, Junzhong

2018-03-01

Chimera states, which consist of coexisting domains of coherent and incoherent parts, have been observed in a variety of systems. Most of previous works on chimera states have taken into account specific form of interaction between oscillators, for example, sinusoidal coupling or diffusive coupling. Here, we investigate chimera dynamics in nonlocally coupled phase oscillators with biharmonic interaction. We find novel chimera states with features such as that oscillators in the same coherent cluster may split into two groups with a phase difference around π/2 and that oscillators in adjacent coherent clusters may have a phase difference close to π/2. The different impacts of the coupling ranges in the first and the second harmonic interactions on chimera dynamics are investigated based on the synchronous dynamics in globally coupled phase oscillators. Our study suggests a new direction in the field of chimera dynamics.

Event-based cluster synchronization of coupled genetic regulatory networks

NASA Astrophysics Data System (ADS)

Yue, Dandan; Guan, Zhi-Hong; Li, Tao; Liao, Rui-Quan; Liu, Feng; Lai, Qiang

2017-09-01

In this paper, the cluster synchronization of coupled genetic regulatory networks with a directed topology is studied by using the event-based strategy and pinning control. An event-triggered condition with a threshold consisting of the neighbors' discrete states at their own event time instants and a state-independent exponential decay function is proposed. The intra-cluster states information and extra-cluster states information are involved in the threshold in different ways. By using the Lyapunov function approach and the theories of matrices and inequalities, we establish the cluster synchronization criterion. It is shown that both the avoidance of continuous transmission of information and the exclusion of the Zeno behavior are ensured under the presented triggering condition. Explicit conditions on the parameters in the threshold are obtained for synchronization. The stability criterion of a single GRN is also given under the reduced triggering condition. Numerical examples are provided to validate the theoretical results.

Structure, stability, and properties of the trans peroxo nitrate radical: the importance of nondynamic correlation.

PubMed

Dutta, Achintya Kumar; Dar, Manzoor; Vaval, Nayana; Pal, Sourav

2014-02-27

We report a comparative single-reference and multireference coupled-cluster investigation on the structure, potential energy surface, and IR spectroscopic properties of the trans peroxo nitrate radical, one of the key intermediates in stratospheric NOX chemistry. The previous single-reference ab initio studies predicted an unbound structure for the trans peroxo nitrate radical. However, our Fock space multireference coupled-cluster calculation confirms a bound structure for the trans peroxo nitrate radical, in accordance with the experimental results reported earlier. Further, the analysis of the potential energy surface in FSMRCC method indicates a well-behaved minima, contrary to the shallow minima predicted by the single-reference coupled-cluster method. The harmonic force field analysis, of various possible isomers of peroxo nitrate also reveals that only the trans structure leads to the experimentally observed IR peak at 1840 cm(-1). The present study highlights the critical importance of nondynamic correlation in predicting the structure and properties of high-energy stratospheric NOx radicals.

Spectroscopic and electric properties of the LiCs molecule: a coupled cluster study including higher excitations

NASA Astrophysics Data System (ADS)

Sørensen, L. K.; Fleig, T.; Olsen, J.

2009-08-01

Aimed at obtaining complete and highly accurate potential energy surfaces for molecules containing heavy elements, we present a new general-order coupled cluster method which can be applied in the framework of the spin-free Dirac formalism. As an initial application we present a systematic study of electron correlation and relativistic effects on the spectroscopic and electric properties of the LiCs molecule in its electronic ground state. In particular, we closely investigate the importance of excitations higher than coupled cluster doubles, spin-free and spin-dependent relativistic effects and the correlation of outer-core electrons on the equilibrium bond length, the harmonic vibrational frequency, the dissociation energy, the dipole moment and the static electric dipole polarizability. We demonstrate that our new implementation allows for highly accurate calculations not only in the bonding region but also along the complete potential curve. The quality of our results is demonstrated by a vibrational analysis where an almost complete set of vibrational levels has been calculated accurately.

Approximate solution of coupled cluster equations: application to the coupled cluster doubles method and non-covalent interacting systems.

PubMed

Smiga, Szymon; Fabiano, Eduardo

2017-11-15

We have developed a simplified coupled cluster (SCC) methodology, using the basic idea of scaled MP2 methods. The scheme has been applied to the coupled cluster double equations and implemented in three different non-iterative variants. This new method (especially the SCCD[3] variant, which utilizes a spin-resolved formalism) has been found to be very efficient and to yield an accurate approximation of the reference CCD results for both total and interaction energies of different atoms and molecules. Furthermore, we demonstrate that the equations determining the scaling coefficients for the SCCD[3] approach can generate non-empirical SCS-MP2 scaling coefficients which are in good agreement with previous theoretical investigations.

Stability and Noise-induced Transitions in an Ensemble of Nonlocally Coupled Chaotic Maps

NASA Astrophysics Data System (ADS)

Bukh, Andrei V.; Slepnev, Andrei V.; Anishchenko, Vadim S.; Vadivasova, Tatiana E.

2018-05-01

The influence of noise on chimera states arising in ensembles of nonlocally coupled chaotic maps is studied. There are two types of chimera structures that can be obtained in such ensembles: phase and amplitude chimera states. In this work, a series of numerical experiments is carried out to uncover the impact of noise on both types of chimeras. The noise influence on a chimera state in the regime of periodic dynamics results in the transition to chaotic dynamics. At the same time, the transformation of incoherence clusters of the phase chimera to incoherence clusters of the amplitude chimera occurs. Moreover, it is established that the noise impact may result in the appearance of a cluster with incoherent behavior in the middle of a coherence cluster.

Statistical analysis of activation and reaction energies with quasi-variational coupled-cluster theory

NASA Astrophysics Data System (ADS)

Black, Joshua A.; Knowles, Peter J.

2018-06-01

The performance of quasi-variational coupled-cluster (QV) theory applied to the calculation of activation and reaction energies has been investigated. A statistical analysis of results obtained for six different sets of reactions has been carried out, and the results have been compared to those from standard single-reference methods. In general, the QV methods lead to increased activation energies and larger absolute reaction energies compared to those obtained with traditional coupled-cluster theory.

Coupled-cluster computations of atomic nuclei

NASA Astrophysics Data System (ADS)

Hagen, G.; Papenbrock, T.; Hjorth-Jensen, M.; Dean, D. J.

2014-09-01

In the past decade, coupled-cluster theory has seen a renaissance in nuclear physics, with computations of neutron-rich and medium-mass nuclei. The method is efficient for nuclei with product-state references, and it describes many aspects of weakly bound and unbound nuclei. This report reviews the technical and conceptual developments of this method in nuclear physics, and the results of coupled-cluster calculations for nucleonic matter, and for exotic isotopes of helium, oxygen, calcium, and some of their neighbors.

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

Combining symmetry collective states with coupled-cluster theory: Lessons from the Agassi model Hamiltonian

NASA Astrophysics Data System (ADS)

Hermes, Matthew R.; Dukelsky, Jorge; Scuseria, Gustavo E.

2017-06-01

The failures of single-reference coupled-cluster theory for strongly correlated many-body systems is flagged at the mean-field level by the spontaneous breaking of one or more physical symmetries of the Hamiltonian. Restoring the symmetry of the mean-field determinant by projection reveals that coupled-cluster theory fails because it factorizes high-order excitation amplitudes incorrectly. However, symmetry-projected mean-field wave functions do not account sufficiently for dynamic (or weak) correlation. Here we pursue a merger of symmetry projection and coupled-cluster theory, following previous work along these lines that utilized the simple Lipkin model system as a test bed [J. Chem. Phys. 146, 054110 (2017), 10.1063/1.4974989]. We generalize the concept of a symmetry-projected mean-field wave function to the concept of a symmetry projected state, in which the factorization of high-order excitation amplitudes in terms of low-order ones is guided by symmetry projection and is not exponential, and combine them with coupled-cluster theory in order to model the ground state of the Agassi Hamiltonian. This model has two separate channels of correlation and two separate physical symmetries which are broken under strong correlation. We show how the combination of symmetry collective states and coupled-cluster theory is effective in obtaining correlation energies and order parameters of the Agassi model throughout its phase diagram.

Communication: Biological applications of coupled-cluster frozen-density embedding

NASA Astrophysics Data System (ADS)

Heuser, Johannes; Höfener, Sebastian

2018-04-01

We report the implementation of the Laplace-transform scaled opposite-spin (LT-SOS) resolution-of-the-identity second-order approximate coupled-cluster singles and doubles (RICC2) combined with frozen-density embedding for excitation energies and molecular properties. In the present work, we furthermore employ the Hartree-Fock density for the interaction energy leading to a simplified Lagrangian which is linear in the Lagrangian multipliers. This approximation has the key advantage of a decoupling of the coupled-cluster amplitude and multipliers, leading also to a significant reduction in computation time. Using the new simplified Lagrangian in combination with efficient wavefunction models such as RICC2 or LT-SOS-RICC2 and density-functional theory (DFT) for the environment molecules (CC2-in-DFT) enables the efficient study of biological applications such as the rhodopsin and visual cone pigments using ab initio methods as routine applications.

An efficient matrix-matrix multiplication based antisymmetric tensor contraction engine for general order coupled cluster.

PubMed

Hanrath, Michael; Engels-Putzka, Anna

2010-08-14

In this paper, we present an efficient implementation of general tensor contractions, which is part of a new coupled-cluster program. The tensor contractions, used to evaluate the residuals in each coupled-cluster iteration are particularly important for the performance of the program. We developed a generic procedure, which carries out contractions of two tensors irrespective of their explicit structure. It can handle coupled-cluster-type expressions of arbitrary excitation level. To make the contraction efficient without loosing flexibility, we use a three-step procedure. First, the data contained in the tensors are rearranged into matrices, then a matrix-matrix multiplication is performed, and finally the result is backtransformed to a tensor. The current implementation is significantly more efficient than previous ones capable of treating arbitrary high excitations.

Using Hyperfine Electron Paramagnetic Resonance Spectroscopy to Define the Proton-Coupled Electron Transfer Reaction at Fe-S Cluster N2 in Respiratory Complex I.

PubMed

Le Breton, Nolwenn; Wright, John J; Jones, Andrew J Y; Salvadori, Enrico; Bridges, Hannah R; Hirst, Judy; Roessler, Maxie M

2017-11-15

Energy-transducing respiratory complex I (NADH:ubiquinone oxidoreductase) is one of the largest and most complicated enzymes in mammalian cells. Here, we used hyperfine electron paramagnetic resonance (EPR) spectroscopic methods, combined with site-directed mutagenesis, to determine the mechanism of a single proton-coupled electron transfer reaction at one of eight iron-sulfur clusters in complex I, [4Fe-4S] cluster N2. N2 is the terminal cluster of the enzyme's intramolecular electron-transfer chain and the electron donor to ubiquinone. Because of its position and pH-dependent reduction potential, N2 has long been considered a candidate for the elusive "energy-coupling" site in complex I at which energy generated by the redox reaction is used to initiate proton translocation. Here, we used hyperfine sublevel correlation (HYSCORE) spectroscopy, including relaxation-filtered hyperfine and single-matched resonance transfer (SMART) HYSCORE, to detect two weakly coupled exchangeable protons near N2. We assign the larger coupling with A( 1 H) = [-3.0, -3.0, 8.7] MHz to the exchangeable proton of a conserved histidine and conclude that the histidine is hydrogen-bonded to N2, tuning its reduction potential. The histidine protonation state responds to the cluster oxidation state, but the two are not coupled sufficiently strongly to catalyze a stoichiometric and efficient energy transduction reaction. We thus exclude cluster N2, despite its proton-coupled electron transfer chemistry, as the energy-coupling site in complex I. Our work demonstrates the capability of pulse EPR methods for providing detailed information on the properties of individual protons in even the most challenging of energy-converting enzymes.

Macroscopic Magnetic Coupling Effect: The Physical Origination of a High-Temperature Superconducting Flux Pump

NASA Astrophysics Data System (ADS)

Wang, Wei; Coombs, Tim

2018-04-01

We have uncovered at the macroscopic scale a magnetic coupling phenomenon in a superconducting YBa2Cu3O7 -δ (YBCO) film, which physically explains the mechanism of the high-temperature superconducting flux pump. The coupling occurs between the applied magnetic poles and clusters of vortices induced in the YBCO film, with each cluster containing millions of vortices. The coupling energy is verified to originate from the inhomogeneous field of the magnetic poles, which reshapes the vortex distribution, aggregates millions of vortices into a single cluster, and accordingly moves with the poles. A contrast study is designed to verify that, to provide the effective coupling energy, the applied wavelength must be short while the field amplitude must be strong, i.e., local-field inhomogeneity is the crucial factor. This finding broadens our understanding of the collective vortex behavior in an applied magnetic field with strong local inhomogeneity. Moreover, this phenomenon largely increases the controlled vortex flow rate by several orders of magnitude compared with existing methods, providing motivation for and physical support to a new branch of wireless superconducting dc power sources, i.e., the high-temperature superconducting flux pump.

Assessing the distinguishable cluster approximation based on the triple bond-breaking in the nitrogen molecule

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

Rishi, Varun; Perera, Ajith; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu

2016-03-28

Obtaining the correct potential energy curves for the dissociation of multiple bonds is a challenging problem for ab initio methods which are affected by the choice of a spin-restricted reference function. Coupled cluster (CC) methods such as CCSD (coupled cluster singles and doubles model) and CCSD(T) (CCSD + perturbative triples) correctly predict the geometry and properties at equilibrium but the process of bond dissociation, particularly when more than one bond is simultaneously broken, is much more complicated. New modifications of CC theory suggest that the deleterious role of the reference function can be diminished, provided a particular subset of termsmore » is retained in the CC equations. The Distinguishable Cluster (DC) approach of Kats and Manby [J. Chem. Phys. 139, 021102 (2013)], seemingly overcomes the deficiencies for some bond-dissociation problems and might be of use in quasi-degenerate situations in general. DC along with other approximate coupled cluster methods such as ACCD (approximate coupled cluster doubles), ACP-D45, ACP-D14, 2CC, and pCCSD(α, β) (all defined in text) falls under a category of methods that are basically obtained by the deletion of some quadratic terms in the double excitation amplitude equation for CCD/CCSD (coupled cluster doubles model/coupled cluster singles and doubles model). Here these approximate methods, particularly those based on the DC approach, are studied in detail for the nitrogen molecule bond-breaking. The N{sub 2} problem is further addressed with conventional single reference methods but based on spatial symmetry-broken restricted Hartree–Fock (HF) solutions to assess the use of these references for correlated calculations in the situation where CC methods using fully symmetry adapted SCF solutions fail. The distinguishable cluster method is generalized: 1) to different orbitals for different spins (unrestricted HF based DCD and DCSD), 2) by adding triples correction perturbatively (DCSD(T)) and iteratively (DCSDT-n), and 3) via an excited state approximation through the equation of motion (EOM) approach (EOM-DCD, EOM-DCSD). The EOM-CC method is used to identify lower-energy CC solutions to overcome singularities in the CC potential energy curves. It is also shown that UHF based CC and DC methods behave very similarly in bond-breaking of N{sub 2}, and that using spatially broken but spin preserving SCF references makes the CCSD solutions better than those for DCSD.« less

Cluster-modified function projective synchronisation of complex networks with asymmetric coupling

NASA Astrophysics Data System (ADS)

Wang, Shuguo

2018-02-01

This paper investigates the cluster-modified function projective synchronisation (CMFPS) of a generalised linearly coupled network with asymmetric coupling and nonidentical dynamical nodes. A novel synchronisation scheme is proposed to achieve CMFPS in community networks. We use adaptive control method to derive CMFPS criteria based on Lyapunov stability theory. Each cluster of networks is synchronised with target system by state transformation with scaling function matrix. Numerical simulation results are presented finally to illustrate the effectiveness of this method.

Coupling of Acoustic Cavitation with Dem-Based Particle Solvers for Modeling De-agglomeration of Particle Clusters in Liquid Metals

NASA Astrophysics Data System (ADS)

Manoylov, Anton; Lebon, Bruno; Djambazov, Georgi; Pericleous, Koulis

2017-11-01

The aerospace and automotive industries are seeking advanced materials with low weight yet high strength and durability. Aluminum and magnesium-based metal matrix composites with ceramic micro- and nano-reinforcements promise the desirable properties. However, larger surface-area-to-volume ratio in micro- and especially nanoparticles gives rise to van der Waals and adhesion forces that cause the particles to agglomerate in clusters. Such clusters lead to adverse effects on final properties, no longer acting as dislocation anchors but instead becoming defects. Also, agglomeration causes the particle distribution to become uneven, leading to inconsistent properties. To break up clusters, ultrasonic processing may be used via an immersed sonotrode, or alternatively via electromagnetic vibration. This paper combines a fundamental study of acoustic cavitation in liquid aluminum with a study of the interaction forces causing particles to agglomerate, as well as mechanisms of cluster breakup. A non-linear acoustic cavitation model utilizing pressure waves produced by an immersed horn is presented, and then applied to cavitation in liquid aluminum. Physical quantities related to fluid flow and quantities specific to the cavitation solver are passed to a discrete element method particles model. The coupled system is then used for a detailed study of clusters' breakup by cavitation.

Pattern formation for NO+N H3 on Pt(100): Two-dimensional numerical results

NASA Astrophysics Data System (ADS)

Uecker, Hannes

2005-01-01

The Lombardo-Fink-Imbihl model of the NO+NH3 reaction on a Pt(100) surface consists of seven coupled ordinary differential equations (ODE) and shows stable relaxation oscillations with sharp transitions in the relevant temperature range. Here we study numerically the effect of coupling of these oscillators by surface diffusion in two dimensions. We find different types of patterns, in particular phase clusters and standing waves. In models of related surface reactions such clustered solutions are known to exist only under a global coupling through the gas phase. This global coupling is replaced here by relatively fast diffusion of two variables which are kinetically slaved in the ODE. We also compare our simulations with experimental results and discuss some shortcomings of the model.

Cluster Formation of Anchored Proteins Induced by Membrane-Mediated Interaction

PubMed Central

Li, Shuangyang; Zhang, Xianren; Wang, Wenchuan

2010-01-01

Abstract Computer simulations were used to study the cluster formation of anchored proteins in a membrane. The rate and extent of clustering was found to be dependent upon the hydrophobic length of the anchored proteins embedded in the membrane. The cluster formation mechanism of anchored proteins in our work was ascribed to the different local perturbations on the upper and lower monolayers of the membrane and the intermonolayer coupling. Simulation results demonstrated that only when the penetration depth of anchored proteins was larger than half the membrane thickness, could the structure of the lower monolayer be significantly deformed. Additionally, studies on the local structures of membranes indicated weak perturbation of bilayer thickness for a shallowly inserted protein, while there was significant perturbation for a more deeply inserted protein. The origin of membrane-mediated protein-protein interaction is therefore due to the local perturbation of the membrane thickness, and the entropy loss—both of which are caused by the conformation restriction on the lipid chains and the enhanced intermonolayer coupling for a deeply inserted protein. Finally, in this study we addressed the difference of cluster formation mechanisms between anchored proteins and transmembrane proteins. PMID:20513399

Relativistic coupled-cluster calculations of the 173Yb nuclear quadrupole coupling constant for the YbF molecule

NASA Astrophysics Data System (ADS)

Pašteka, L. F.; Mawhorter, R. J.; Schwerdtfeger, P.

2016-04-01

We report calculations on the q(Yb) electric field gradient (EFG) for the X2Σ+ and A2Π1/2 electronic states of the ytterbium monofluoride (YbF) molecule at the molecular mean-field Dirac-Coulomb-Gaunt as well as scalar-relativistic coupled-cluster levels of theory using large uncontracted basis sets. Vibrational contributions are included in the final results. Our estimated nuclear quadrupole coupling constants of -3386(78) MHz and -2083(153) MHz for the X2Σ+ and A2Π1/2 states of 173YbF are in stark contrast to the only available experimental results (-2050(170) MHz and -1090(160) MHz) respectively, where the only similarity is the difference between the two values. Perturbative triple contributions in the coupled cluster treatment are significant and point towards the necessity to go to higher order in the coupled-cluster treatment in future calculations. We also present density functional calculations which show rather large variations for the Yb EFG with different functionals used; the best result was obtained using the CAM-B3LYP* functional.

Communication: Spin densities within a unitary group based spin-adapted open-shell coupled-cluster theory: Analytic evaluation of isotropic hyperfine-coupling constants for the combinatoric open-shell coupled-cluster scheme

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

Datta, Dipayan, E-mail: datta.dipayan@gmail.com; Gauss, Jürgen, E-mail: gauss@uni-mainz.de

We report analytical calculations of isotropic hyperfine-coupling constants in radicals using a spin-adapted open-shell coupled-cluster theory, namely, the unitary group based combinatoric open-shell coupled-cluster (COSCC) approach within the singles and doubles approximation. A scheme for the evaluation of the one-particle spin-density matrix required in these calculations is outlined within the spin-free formulation of the COSCC approach. In this scheme, the one-particle spin-density matrix for an open-shell state with spin S and M{sub S} = + S is expressed in terms of the one- and two-particle spin-free (charge) density matrices obtained from the Lagrangian formulation that is used for calculating themore » analytic first derivatives of the energy. Benchmark calculations are presented for NO, NCO, CH{sub 2}CN, and two conjugated π-radicals, viz., allyl and 1-pyrrolyl in order to demonstrate the performance of the proposed scheme.« less

A four-component Fock-space coupled cluster investigation of the HM(CO)5, (M = Mn, Re) photoelectron spectra

NASA Astrophysics Data System (ADS)

Nikoobakht, Behnam; Siebert, Max; Pernpointner, Markus

2015-11-01

In this work, we readdress the photoelectron spectra of the HM(CO)5, (M=Mn, Re) carbonyl complexes by applying four-component Fock-space coupled cluster (FSCC) methods for their calculation in order to extend earlier studies based on less demanding approaches. The final-state characterisation was based on group theoretical considerations of the contributing orbitals and allowed for an unambiguous assignment. Energy level diagrams show the effect of spin-orbit (SO) coupling starting from scalar relativistic results and for the heavy representative HRe(CO)5 nonadditivity effects of SO and electron correlation can be observed requiring a consistent treatment of both contributions.

Acculturation Stress, Drinking, and Intimate Partner Violence among Hispanic Couples in the U.S

ERIC Educational Resources Information Center

Caetano, Raul; Ramisetty-Mikler, Suhasini; Caetano Vaeth, Patrice A.; Harris, T. Robert

2007-01-01

This article examines the cross-sectional association between acculturation, acculturation stress, drinking, and intimate partner violence (IPV) among Hispanic couples in the U.S. The data being analyzed come from a multi-cluster random household sample of couples interviewed as part of the second wave of a 5-year national longitudinal study. The…

Development of New Open-Shell Perturbation and Coupled-Cluster Theories Based on Symmetric Spin Orbitals

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Arnold, James O. (Technical Monitor)

1994-01-01

A new spin orbital basis is employed in the development of efficient open-shell coupled-cluster and perturbation theories that are based on a restricted Hartree-Fock (RHF) reference function. The spin orbital basis differs from the standard one in the spin functions that are associated with the singly occupied spatial orbital. The occupied orbital (in the spin orbital basis) is assigned the delta(+) = 1/square root of 2(alpha+Beta) spin function while the unoccupied orbital is assigned the delta(-) = 1/square root of 2(alpha-Beta) spin function. The doubly occupied and unoccupied orbitals (in the reference function) are assigned the standard alpha and Beta spin functions. The coupled-cluster and perturbation theory wave functions based on this set of "symmetric spin orbitals" exhibit much more symmetry than those based on the standard spin orbital basis. This, together with interacting space arguments, leads to a dramatic reduction in the computational cost for both coupled-cluster and perturbation theory. Additionally, perturbation theory based on "symmetric spin orbitals" obeys Brillouin's theorem provided that spin and spatial excitations are both considered. Other properties of the coupled-cluster and perturbation theory wave functions and models will be discussed.

A noniterative asymmetric triple excitation correction for the density-fitted coupled-cluster singles and doubles method: Preliminary applications

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

Bozkaya, Uğur, E-mail: ugrbzky@gmail.com

2016-04-14

An efficient implementation of the asymmetric triples correction for the coupled-cluster singles and doubles [ΛCCSD(T)] method [S. A. Kucharski and R. J. Bartlett, J. Chem. Phys. 108, 5243 (1998); T. D. Crawford and J. F. Stanton, Int. J. Quantum Chem. 70, 601 (1998)] with the density-fitting [DF-ΛCCSD(T)] approach is presented. The computational time for the DF-ΛCCSD(T) method is compared with that of ΛCCSD(T). Our results demonstrate that the DF-ΛCCSD(T) method provide substantially lower computational costs than ΛCCSD(T). Further application results show that the ΛCCSD(T) and DF-ΛCCSD(T) methods are very beneficial for the study of single bond breaking problems as wellmore » as noncovalent interactions and transition states. We conclude that ΛCCSD(T) and DF-ΛCCSD(T) are very promising for the study of challenging chemical systems, where the coupled-cluster singles and doubles with perturbative triples method fails.« less

Heterogeneous delays making parents synchronized: A coupled maps on Cayley tree model

NASA Astrophysics Data System (ADS)

Singh, Aradhana; Jalan, Sarika

2014-06-01

We study the phase synchronized clusters in the diffusively coupled maps on the Cayley tree networks for heterogeneous delay values. Cayley tree networks comprise of two parts: the inner nodes and the boundary nodes. We find that heterogeneous delays lead to various cluster states, such as; (a) cluster state consisting of inner nodes and boundary nodes, and (b) cluster state consisting of only boundary nodes. The former state may comprise of nodes from all the generations forming self-organized cluster or nodes from few generations yielding driven clusters depending upon on the parity of heterogeneous delay values. Furthermore, heterogeneity in delays leads to the lag synchronization between the siblings lying on the boundary by destroying the exact synchronization among them. The time lag being equal to the difference in the delay values. The Lyapunov function analysis sheds light on the destruction of the exact synchrony among the last generation nodes. To the end we discuss the relevance of our results with respect to their applications in the family business as well as in understanding the occurrence of genetic diseases.

From globally coupled maps to complex-systems biology

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

Kaneko, Kunihiko, E-mail: kaneko@complex.c.u-tokyo.ac.jp

Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

Correlation buildup during recrystallization in three-dimensional dusty plasma clusters

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

Schella, André; Mulsow, Matthias; Melzer, André

2014-05-15

The recrystallization process of finite three-dimensional dust clouds after laser heating is studied experimentally. The time-dependent Coulomb coupling parameter is presented, showing that the recrystallization starts with an exponential cooling phase where cooling is slower than damping by the neutral gas friction. At later times, the coupling parameter oscillates into equilibrium. It is found that a large fraction of cluster states after recrystallization experiments is in metastable states. The temporal evolution of the correlation buildup shows that correlation occurs on even slower time scale than cooling.

Near-Edge X-ray Absorption Fine Structure within Multilevel Coupled Cluster Theory.

PubMed

Myhre, Rolf H; Coriani, Sonia; Koch, Henrik

2016-06-14

Core excited states are challenging to calculate, mainly because they are embedded in a manifold of high-energy valence-excited states. However, their locality makes their determination ideal for local correlation methods. In this paper, we demonstrate the performance of multilevel coupled cluster theory in computing core spectra both within the core-valence separated and the asymmetric Lanczos implementations of coupled cluster linear response theory. We also propose a visualization tool to analyze the excitations using the difference between the ground-state and excited-state electron densities.

Complete characterization of the stability of cluster synchronization in complex dynamical networks.

PubMed

Sorrentino, Francesco; Pecora, Louis M; Hagerstrom, Aaron M; Murphy, Thomas E; Roy, Rajarshi

2016-04-01

Synchronization is an important and prevalent phenomenon in natural and engineered systems. In many dynamical networks, the coupling is balanced or adjusted to admit global synchronization, a condition called Laplacian coupling. Many networks exhibit incomplete synchronization, where two or more clusters of synchronization persist, and computational group theory has recently proved to be valuable in discovering these cluster states based on the topology of the network. In the important case of Laplacian coupling, additional synchronization patterns can exist that would not be predicted from the group theory analysis alone. Understanding how and when clusters form, merge, and persist is essential for understanding collective dynamics, synchronization, and failure mechanisms of complex networks such as electric power grids, distributed control networks, and autonomous swarming vehicles. We describe a method to find and analyze all of the possible cluster synchronization patterns in a Laplacian-coupled network, by applying methods of computational group theory to dynamically equivalent networks. We present a general technique to evaluate the stability of each of the dynamically valid cluster synchronization patterns. Our results are validated in an optoelectronic experiment on a five-node network that confirms the synchronization patterns predicted by the theory.

Spin-orbit splitted excited states using explicitly-correlated equation-of-motion coupled-cluster singles and doubles eigenvectors

NASA Astrophysics Data System (ADS)

Bokhan, Denis; Trubnikov, Dmitrii N.; Perera, Ajith; Bartlett, Rodney J.

2018-04-01

An explicitly-correlated method of calculation of excited states with spin-orbit couplings, has been formulated and implemented. Developed approach utilizes left and right eigenvectors of equation-of-motion coupled-cluster model, which is based on the linearly approximated explicitly correlated coupled-cluster singles and doubles [CCSD(F12)] method. The spin-orbit interactions are introduced by using the spin-orbit mean field (SOMF) approximation of the Breit-Pauli Hamiltonian. Numerical tests for several atoms and molecules show good agreement between explicitly-correlated results and the corresponding values, calculated in complete basis set limit (CBS); the highly-accurate excitation energies can be obtained already at triple- ζ level.

Projected Hartree-Fock theory as a polynomial of particle-hole excitations and its combination with variational coupled cluster theory

NASA Astrophysics Data System (ADS)

Qiu, Yiheng; Henderson, Thomas M.; Scuseria, Gustavo E.

2017-05-01

Projected Hartree-Fock theory provides an accurate description of many kinds of strong correlations but does not properly describe weakly correlated systems. Coupled cluster theory, in contrast, does the opposite. It therefore seems natural to combine the two so as to describe both strong and weak correlations with high accuracy in a relatively black-box manner. Combining the two approaches, however, is made more difficult by the fact that the two techniques are formulated very differently. In earlier work, we showed how to write spin-projected Hartree-Fock in a coupled-cluster-like language. Here, we fill in the gaps in that earlier work. Further, we combine projected Hartree-Fock and coupled cluster theory in a variational formulation and show how the combination performs for the description of the Hubbard Hamiltonian and for several small molecular systems.

Global cluster synchronization in nonlinearly coupled community networks with heterogeneous coupling delays.

PubMed

Tseng, Jui-Pin

2017-02-01

This investigation establishes the global cluster synchronization of complex networks with a community structure based on an iterative approach. The units comprising the network are described by differential equations, and can be non-autonomous and involve time delays. In addition, units in the different communities can be governed by different equations. The coupling configuration of the network is rather general. The coupling terms can be non-diffusive, nonlinear, asymmetric, and with heterogeneous coupling delays. Based on this approach, both delay-dependent and delay-independent criteria for global cluster synchronization are derived. We implement the present approach for a nonlinearly coupled neural network with heterogeneous coupling delays. Two numerical examples are given to show that neural networks can behave in a variety of new collective ways under the synchronization criteria. These examples also demonstrate that neural networks remain synchronized in spite of coupling delays between neurons across different communities; however, they may lose synchrony if the coupling delays between the neurons within the same community are too large, such that the synchronization criteria are violated. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Gap-junction coupling and ATP-sensitive potassium channels in human β -cell clusters: Effects on emergent dynamics

NASA Astrophysics Data System (ADS)

Loppini, A.; Pedersen, M. G.; Braun, M.; Filippi, S.

2017-09-01

The importance of gap-junction coupling between β cells in pancreatic islets is well established in mouse. Such ultrastructural connections synchronize cellular activity, confine biological heterogeneity, and enhance insulin pulsatility. Dysfunction of coupling has been associated with diabetes and altered β -cell function. However, the role of gap junctions between human β cells is still largely unexplored. By using patch-clamp recordings of β cells from human donors, we previously estimated electrical properties of these channels by mathematical modeling of pairs of human β cells. In this work we revise our estimate by modeling triplet configurations and larger heterogeneous clusters. We find that a coupling conductance in the range 0.005 -0.020 nS/pF can reproduce experiments in almost all the simulated arrangements. We finally explore the consequence of gap-junction coupling of this magnitude between β cells with mutant variants of the ATP-sensitive potassium channels involved in some metabolic disorders and diabetic conditions, translating studies performed on rodents to the human case. Our results are finally discussed from the perspective of therapeutic strategies. In summary, modeling of more realistic clusters with more than two β cells slightly lowers our previous estimate of gap-junction conductance and gives rise to patterns that more closely resemble experimental traces.

Phase diagram and quench dynamics of the cluster-XY spin chain

NASA Astrophysics Data System (ADS)

Montes, Sebastián; Hamma, Alioscia

2012-08-01

We study the complete phase space and the quench dynamics of an exactly solvable spin chain, the cluster-XY model. In this chain, the cluster term and the XY couplings compete to give a rich phase diagram. The phase diagram is studied by means of the quantum geometric tensor. We study the time evolution of the system after a critical quantum quench using the Loschmidt echo. The structure of the revivals after critical quantum quenches presents a nontrivial behavior depending on the phase of the initial state and the critical point.

Phase diagram and quench dynamics of the cluster-XY spin chain.

PubMed

Montes, Sebastián; Hamma, Alioscia

2012-08-01

We study the complete phase space and the quench dynamics of an exactly solvable spin chain, the cluster-XY model. In this chain, the cluster term and the XY couplings compete to give a rich phase diagram. The phase diagram is studied by means of the quantum geometric tensor. We study the time evolution of the system after a critical quantum quench using the Loschmidt echo. The structure of the revivals after critical quantum quenches presents a nontrivial behavior depending on the phase of the initial state and the critical point.

Typology of Couples Entering Alcohol Behavioral Couple Therapy: An Empirical Approach and Test of Predictive Validity on Treatment Response

PubMed Central

Ladd, Benjamin O.; McCrady, Barbara S.

2016-01-01

The current study aimed to examine whether classification of couples in which one partner has an alcohol problem is similar to that reported in the general couples literature. Typologies of couples seeking Alcohol Behavioral Couple Therapy (ABCT) were developed via hierarchical cluster analysis using behavioral codes of couple interactions during their first ABCT session. Four couples types based on in-session behavior were established reliably, labeled Avoider, Validator, Hostile, and Ambivalent-Detached. These couple types resembled couples types found in previous research. Couple type was associated with baseline relationship satisfaction, but not alcohol use. Results suggest heterogeneity in couples with alcohol problems presenting to treatment; further study is needed to investigate the function of alcohol within these different types. PMID:25808432

Coupled-cluster based R-matrix codes (CCRM): Recent developments

NASA Astrophysics Data System (ADS)

Sur, Chiranjib; Pradhan, Anil K.

2008-05-01

We report the ongoing development of the new coupled-cluster R-matrix codes (CCRM) for treating electron-ion scattering and radiative processes within the framework of the relativistic coupled-cluster method (RCC), interfaced with the standard R-matrix methodology. The RCC method is size consistent and in principle equivalent to an all-order many-body perturbation theory. The RCC method is one of the most accurate many-body theories, and has been applied for several systems. This project should enable the study of electron-interactions with heavy atoms/ions, utilizing not only high speed computing platforms but also improved theoretical description of the relativistic and correlation effects for the target atoms/ions as treated extensively within the RCC method. Here we present a comprehensive outline of the newly developed theoretical method and a schematic representation of the new suite of CCRM codes. We begin with the flowchart and description of various stages involved in this development. We retain the notations and nomenclature of different stages as analogous to the standard R-matrix codes.

Renormalized coupled cluster approaches in the cluster-in-molecule framework: predicting vertical electron binding energies of the anionic water clusters (H2O)(n)(-).

PubMed

Xu, Peng; Gordon, Mark S

2014-09-04

Anionic water clusters are generally considered to be extremely challenging to model using fragmentation approaches due to the diffuse nature of the excess electron distribution. The local correlation coupled cluster (CC) framework cluster-in-molecule (CIM) approach combined with the completely renormalized CR-CC(2,3) method [abbreviated CIM/CR-CC(2,3)] is shown to be a viable alternative for computing the vertical electron binding energies (VEBE). CIM/CR-CC(2,3) with the threshold parameter ζ set to 0.001, as a trade-off between accuracy and computational cost, demonstrates the reliability of predicting the VEBE, with an average percentage error of ∼15% compared to the full ab initio calculation at the same level of theory. The errors are predominantly from the electron correlation energy. The CIM/CR-CC(2,3) approach provides the ease of a black-box type calculation with few threshold parameters to manipulate. The cluster sizes that can be studied by high-level ab initio methods are significantly increased in comparison with full CC calculations. Therefore, the VEBE computed by the CIM/CR-CC(2,3) method can be used as benchmarks for testing model potential approaches in small-to-intermediate-sized water clusters.

Hydrodynamical simulations of coupled and uncoupled quintessence models - II. Galaxy clusters

NASA Astrophysics Data System (ADS)

Carlesi, Edoardo; Knebe, Alexander; Lewis, Geraint F.; Yepes, Gustavo

2014-04-01

We study the z = 0 properties of clusters (and large groups) of galaxies within the context of interacting and non-interacting quintessence cosmological models, using a series of adiabatic SPH simulations. Initially, we examine the average properties of groups and clusters, quantifying their differences in ΛCold Dark Matter (ΛCDM), uncoupled Dark Energy (uDE) and coupled Dark Energy (cDE) cosmologies. In particular, we focus upon radial profiles of the gas density, temperature and pressure, and we also investigate how the standard hydrodynamic equilibrium hypothesis holds in quintessence cosmologies. While we are able to confirm previous results about the distribution of baryons, we also find that the main discrepancy (with differences up to 20 per cent) can be seen in cluster pressure profiles. We then switch attention to individual structures, mapping each halo in quintessence cosmology to its ΛCDM counterpart. We are able to identify a series of small correlations between the coupling in the dark sector and halo spin, triaxiality and virialization ratio. When looking at spin and virialization of dark matter haloes, we find a weak (5 per cent) but systematic deviation in fifth force scenarios from ΛCDM.

Mechanisms contributing to cluster formation in the inferior olivary nucleus in brainstem slices from postnatal mice

PubMed Central

Kølvraa, Mathias; Müller, Felix C; Jahnsen, Henrik; Rekling, Jens C

2014-01-01

Abstract The inferior olivary nucleus (IO) in in vitro slices from postnatal mice (P5.5–P15.5) spontaneously generates clusters of neurons with synchronous calcium transients, and intracellular recordings from IO neurons suggest that electrical coupling between neighbouring IO neurons may serve as a synchronizing mechanism. Here, we studied the cluster-forming mechanism and find that clusters overlap extensively with an overlap distribution that resembles the distribution for a random overlap model. The average somatodendritic field size of single curly IO neurons was ∼6400 μm2, which is slightly smaller than the average IO cluster size. Eighty-seven neurons with overlapping dendrites were estimated to be contained in the principal olive mean cluster size, and about six non-overlapping curly IO neurons could be contained within the largest clusters. Clusters could also be induced by iontophoresis with glutamate. Induced clusters were inhibited by tetrodotoxin, carbenoxelone and 18β-glycyrrhetinic acid, suggesting that sodium action potentials and electrical coupling are involved in glutamate-induced cluster formation, which could also be induced by activation of N-methyl-d-aspartate and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors. Spikelets and a small transient depolarizing response were observed during glutamate-induced cluster formation. Calcium transients spread with decreasing velocity during cluster formation, and somatic action potentials and cluster formation are accompanied by large dendritic calcium transients. In conclusion, cluster formation depends on gap junctions, sodium action potentials and spontaneous clusters occur randomly throughout the IO. The relative slow signal spread during cluster formation, combined with a strong dendritic influx of calcium, may signify that active dendritic properties contribute to cluster formation. PMID:24042500

Symmetries and stability of chimera states in small, globally-coupled networks

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Bansal, Kanika; Murphy, Thomas E.; Roy, Rajarshi

It has recently been demonstrated that symmetries in a network's topology can help predict the patterns of synchronized clusters that can emerge in a network of coupled oscillators. This and related discoveries have led to increased interest in both network symmetries and cluster synchronization. In parallel with these discoveries, interest in chimera states-dynamical patterns in which a network separates into coherent and incoherent portions-has grown, and chimeras have now been observed in a variety of experimental systems. We present an opto-electronic experiment in which both chimera states and synchronized clusters are observed in a small, globally-coupled network. We show that the symmetries and sub-symmetries of the network permit the formation of the chimera and cluster states. A recently developed group theoretical approach enables us to predict the stability of the observed chimera and cluster states, and highlights the close relationship between chimera and cluster states as belonging to the broader phenomenon of partial synchronization.

Protonation and Proton-Coupled Electron Transfer at S-Ligated [4Fe-4S] Clusters

PubMed Central

Morris, Wesley D.; Darcy, Julia W.; Mayer, James M.

2015-01-01

Biological [Fe-S] clusters are increasingly recognized to undergo proton-coupled electron transfer (PCET), but the site of protonation, mechanism, and role for PCET remains largely unknown. Here we explore this reactivity with synthetic model clusters. Protonation of the arylthiolate-ligated [4Fe-4S] cluster [Fe4S4(SAr)4]2- (1, SAr = S-2,4-6-(iPr)3C6H2) leads to thiol dissociation, reversibly forming [Fe4S4(SAr)3L]1- (2) + ArSH (L = solvent, and/or conjugate base). Solutions of 2 + ArSH react with the nitroxyl radical TEMPO to give [Fe4S4(SAr)4]1- (1ox) and TEMPOH. This reaction involves PCET coupled to thiolate association and may proceed via the unobserved protonated cluster [Fe4S4(SAr)3(HSAr)]1-(1-H). Similar reactions with this and related clusters proceed comparably. An understanding of the PCET thermochemistry of this cluster system has been developed, encompassing three different redox levels and two protonation states. PMID:25965413

First principles studies of electron tunneling in proteins

PubMed Central

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A.

2014-01-01

A first principles study of electronic tunneling along the chain of seven Fe/S clusters in respiratory complex I, a key enzyme in the respiratory electron transport chain, is described. The broken-symmetry states of the Fe/S metal clusters calculated at both DFT and semi-empirical ZINDO levels were utilized to examine both the extremely weak electronic couplings between Fe/S clusters and the tunneling pathways, which provide a detailed atomistic-level description of the charge transfer process in the protein. One-electron tunneling approximation was found to hold within a reasonable accuracy, with only a moderate induced polarization of the core electrons. The method is demonstrated to be able to calculate accurately the coupling matrix elements as small as 10−4 cm−1. A distinct signature of the wave properties of electrons is observed as quantum interferences of multiple tunneling pathways. PMID:25383312

Efficient electronic structure theory via hierarchical scale-adaptive coupled-cluster formalism: I. Theory and computational complexity analysis

NASA Astrophysics Data System (ADS)

Lyakh, Dmitry I.

2018-03-01

A novel reduced-scaling, general-order coupled-cluster approach is formulated by exploiting hierarchical representations of many-body tensors, combined with the recently suggested formalism of scale-adaptive tensor algebra. Inspired by the hierarchical techniques from the renormalisation group approach, H/H2-matrix algebra and fast multipole method, the computational scaling reduction in our formalism is achieved via coarsening of quantum many-body interactions at larger interaction scales, thus imposing a hierarchical structure on many-body tensors of coupled-cluster theory. In our approach, the interaction scale can be defined on any appropriate Euclidean domain (spatial domain, momentum-space domain, energy domain, etc.). We show that the hierarchically resolved many-body tensors can reduce the storage requirements to O(N), where N is the number of simulated quantum particles. Subsequently, we prove that any connected many-body diagram consisting of a finite number of arbitrary-order tensors, e.g. an arbitrary coupled-cluster diagram, can be evaluated in O(NlogN) floating-point operations. On top of that, we suggest an additional approximation to further reduce the computational complexity of higher order coupled-cluster equations, i.e. equations involving higher than double excitations, which otherwise would introduce a large prefactor into formal O(NlogN) scaling.

Robustness of cluster synchronous patterns in small-world networks with inter-cluster co-competition balance

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

Zhang, Jianbao; Ma, Zhongjun, E-mail: mzj1234402@163.com; Chen, Guanrong

All edges in the classical Watts and Strogatz's small-world network model are unweighted and cooperative (positive). By introducing competitive (negative) inter-cluster edges and assigning edge weights to mimic more realistic networks, this paper develops a modified model which possesses co-competitive weighted couplings and cluster structures while maintaining the common small-world network properties of small average shortest path lengths and large clustering coefficients. Based on theoretical analysis, it is proved that the new model with inter-cluster co-competition balance has an important dynamical property of robust cluster synchronous pattern formation. More precisely, clusters will neither merge nor split regardless of adding ormore » deleting nodes and edges, under the condition of inter-cluster co-competition balance. Numerical simulations demonstrate the robustness of the model against the increase of the coupling strength and several topological variations.« less

Robustness of cluster synchronous patterns in small-world networks with inter-cluster co-competition balance

NASA Astrophysics Data System (ADS)

Zhang, Jianbao; Ma, Zhongjun; Chen, Guanrong

2014-06-01

All edges in the classical Watts and Strogatz's small-world network model are unweighted and cooperative (positive). By introducing competitive (negative) inter-cluster edges and assigning edge weights to mimic more realistic networks, this paper develops a modified model which possesses co-competitive weighted couplings and cluster structures while maintaining the common small-world network properties of small average shortest path lengths and large clustering coefficients. Based on theoretical analysis, it is proved that the new model with inter-cluster co-competition balance has an important dynamical property of robust cluster synchronous pattern formation. More precisely, clusters will neither merge nor split regardless of adding or deleting nodes and edges, under the condition of inter-cluster co-competition balance. Numerical simulations demonstrate the robustness of the model against the increase of the coupling strength and several topological variations.

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.

``Dressing'' lines and vertices in calculations of matrix elements with the coupled-cluster method and determination of Cs atomic properties

NASA Astrophysics Data System (ADS)

Derevianko, Andrei; Porsev, Sergey G.

2005-03-01

We consider evaluation of matrix elements with the coupled-cluster method. Such calculations formally involve infinite number of terms and we devise a method of partial summation (dressing) of the resulting series. Our formalism is built upon an expansion of the product C†C of cluster amplitudes C into a sum of n -body insertions. We consider two types of insertions: particle (hole) line insertion and two-particle (two-hole) random-phase-approximation-like insertion. We demonstrate how to “dress” these insertions and formulate iterative equations. We illustrate the dressing equations in the case when the cluster operator is truncated at single and double excitations. Using univalent systems as an example, we upgrade coupled-cluster diagrams for matrix elements with the dressed insertions and highlight a relation to pertinent fourth-order diagrams. We illustrate our formalism with relativistic calculations of the hyperfine constant A(6s) and the 6s1/2-6p1/2 electric-dipole transition amplitude for the Cs atom. Finally, we augment the truncated coupled-cluster calculations with otherwise omitted fourth order diagrams. The resulting analysis for Cs is complete through the fourth order of many-body perturbation theory and reveals an important role of triple and disconnected quadruple excitations.

Structure of Low-Lying Excited States of Guanine in DNA and Solution: Combined Molecular Mechanics and High-Level Coupled Cluster Studies

DOE PAGES

Kowalski, Karol; Valiev, Marat

2007-01-01

High-level ab-initio equation-of-motion coupled-cluster methods with singles, doubles, and noniterative triples are used, in conjunction with the combined quantum mechanical molecular mechanics approach, to investigate the structure of low-lying excited states of the guanine base in DNA and solvated environments. Our results indicate that while the excitation energy of the first excited state is barely changed compared to its gas-phase counterpart, the excitation energy of the second excited state is blue-shifted by 0.24 eV.

A coupled cluster theory with iterative inclusion of triple excitations and associated equation of motion formulation for excitation energy and ionization potential

NASA Astrophysics Data System (ADS)

Maitra, Rahul; Akinaga, Yoshinobu; Nakajima, Takahito

2017-08-01

A single reference coupled cluster theory that is capable of including the effect of connected triple excitations has been developed and implemented. This is achieved by regrouping the terms appearing in perturbation theory and parametrizing through two different sets of exponential operators: while one of the exponentials, involving general substitution operators, annihilates the ground state but has a non-vanishing effect when it acts on the excited determinant, the other is the regular single and double excitation operator in the sense of conventional coupled cluster theory, which acts on the Hartree-Fock ground state. The two sets of operators are solved as coupled non-linear equations in an iterative manner without significant increase in computational cost than the conventional coupled cluster theory with singles and doubles excitations. A number of physically motivated and computationally advantageous sufficiency conditions are invoked to arrive at the working equations and have been applied to determine the ground state energies of a number of small prototypical systems having weak multi-reference character. With the knowledge of the correlated ground state, we have reconstructed the triple excitation operator and have performed equation of motion with coupled cluster singles, doubles, and triples to obtain the ionization potential and excitation energies of these molecules as well. Our results suggest that this is quite a reasonable scheme to capture the effect of connected triple excitations as long as the ground state remains weakly multi-reference.

Typology of Couples Entering Alcohol Behavioral Couple Therapy: An Empirical Approach and Test of Predictive Validity on Treatment Response.

PubMed

Ladd, Benjamin O; McCrady, Barbara S

2016-01-01

This study aimed to examine whether classification of couples in which one partner has an alcohol problem is similar to that reported in the general couples literature. Typologies of couples seeking alcohol behavioral couple therapy (ABCT) were developed via hierarchical cluster analysis using behavioral codes of couple interactions during their first ABCT session. Four couples types based on in-session behavior were established reliably, labeled avoider, validator, hostile, and ambivalent-detached. These couple types resembled couples types found in previous research. Couple type was associated with baseline relationship satisfaction, but not alcohol use. Results suggest heterogeneity in couples with alcohol problems presenting to treatment; further study is needed to investigate the function of alcohol within these different types. © 2015 American Association for Marriage and Family Therapy.

Transition properties from the Hermitian formulation of the coupled cluster polarization propagator

NASA Astrophysics Data System (ADS)

Tucholska, Aleksandra M.; Modrzejewski, Marcin; Moszynski, Robert

2014-09-01

Theory of one-electron transition density matrices has been formulated within the time-independent coupled cluster method for the polarization propagator [R. Moszynski, P. S. Żuchowski, and B. Jeziorski, Coll. Czech. Chem. Commun. 70, 1109 (2005)]. Working expressions have been obtained and implemented with the coupled cluster method limited to single, double, and linear triple excitations (CC3). Selected dipole and quadrupole transition probabilities of the alkali earth atoms, computed with the new transition density matrices are compared to the experimental data. Good agreement between theory and experiment is found. The results obtained with the new approach are of the same quality as the results obtained with the linear response coupled cluster theory. The one-electron density matrices for the ground state in the CC3 approximation have also been implemented. The dipole moments for a few representative diatomic molecules have been computed with several variants of the new approach, and the results are discussed to choose the approximation with the best balance between the accuracy and computational efficiency.

Clonality and distribution of clinical Ureaplasma isolates recovered from male patients and infertile couples in China

PubMed Central

Ruan, Zhi; Yang, Ting; Shi, Xinyan; Kong, Yingying; Xie, Xinyou

2017-01-01

Ureaplasma spp. have gained increasing recognition as pathogens in both adult and neonatal patients with multiple clinical presentations. However, the clonality of this organism in the male population and infertile couples in China is largely unknown. In this study, 96 (53 U. parvum and 43 U. urealyticum) of 103 Ureaplasma spp. strains recovered from genital specimens from male patients and 15 pairs of infertile couples were analyzed using multilocus sequence typing (MLST)/expanded multilocus sequence typing (eMLST) schemes. A total of 39 sequence types (STs) and 53 expanded sequence types (eSTs) were identified, with three predominant STs (ST1, ST9 and ST22) and eSTs (eST16, eST41 and eST82). Moreover, phylogenetic analysis revealed two distinct clusters that were highly congruent with the taxonomic differences between the two Ureaplasma species. We found significant differences in the distributions of both clusters and sub-groups between the male and female patients (P < 0.001). Moreover, 66.7% and 40.0% of the male and female partners of the infertile couples tested positive for Ureaplasma spp. The present study also attained excellent agreement of the identification of both Ureaplasma species between paired urine and semen specimens from the male partners (k > 0.80). However, this concordance was observed only for the detection of U. urealyticum within the infertile couples. In conclusion, the distributions of the clusters and sub-groups significantly differed between the male and female patients. U. urealyticum is more likely to transmit between infertile couples and be associated with clinical manifestations by the specific epidemic clonal lineages. PMID:28859153

Clonality and distribution of clinical Ureaplasma isolates recovered from male patients and infertile couples in China.

PubMed

Ruan, Zhi; Yang, Ting; Shi, Xinyan; Kong, Yingying; Xie, Xinyou; Zhang, Jun

2017-01-01

Ureaplasma spp. have gained increasing recognition as pathogens in both adult and neonatal patients with multiple clinical presentations. However, the clonality of this organism in the male population and infertile couples in China is largely unknown. In this study, 96 (53 U. parvum and 43 U. urealyticum) of 103 Ureaplasma spp. strains recovered from genital specimens from male patients and 15 pairs of infertile couples were analyzed using multilocus sequence typing (MLST)/expanded multilocus sequence typing (eMLST) schemes. A total of 39 sequence types (STs) and 53 expanded sequence types (eSTs) were identified, with three predominant STs (ST1, ST9 and ST22) and eSTs (eST16, eST41 and eST82). Moreover, phylogenetic analysis revealed two distinct clusters that were highly congruent with the taxonomic differences between the two Ureaplasma species. We found significant differences in the distributions of both clusters and sub-groups between the male and female patients (P < 0.001). Moreover, 66.7% and 40.0% of the male and female partners of the infertile couples tested positive for Ureaplasma spp. The present study also attained excellent agreement of the identification of both Ureaplasma species between paired urine and semen specimens from the male partners (k > 0.80). However, this concordance was observed only for the detection of U. urealyticum within the infertile couples. In conclusion, the distributions of the clusters and sub-groups significantly differed between the male and female patients. U. urealyticum is more likely to transmit between infertile couples and be associated with clinical manifestations by the specific epidemic clonal lineages.

Effect of Coulomb Correlation on the Magnetic Properties of Mn Clusters.

PubMed

Huang, Chengxi; Zhou, Jian; Deng, Kaiming; Kan, Erjun; Jena, Puru

2018-05-03

In spite of decades of research, a fundamental understanding of the unusual magnetic behavior of small Mn clusters remains a challenge. Experiments show that Mn 2 is antiferromagnetic while small clusters containing up to five Mn atoms are ferromagnetic with magnetic moments of 5 μ B /atom and become ferrimagnetic as they grow further. Theoretical studies based on density functional theory (DFT), however, find Mn 2 to be ferromagnetic, with ferrimagnetic order setting in at different sizes that depend upon the computational methods used. While quantum chemical techniques correctly account for the antiferromagnetic ground state of Mn 2 , they are computationally too demanding to treat larger clusters, making it difficult to understand the evolution of magnetism. These studies clearly point to the importance of correlation and the need to find ways to treat it effectively for larger clusters and nanostructures. Here, we show that the DFT+ U method can be used to account for strong correlation. We determine the on-site Coulomb correlation, Hubbard U self-consistently by using the linear response theory and study its effect on the magnetic coupling of Mn clusters containing up to five atoms. With a calculated U value of 4.8 eV, we show that the ground state of Mn 2 is antiferromagnetic with a Mn-Mn distance of 3.34 Å, which agrees well with the electron spin resonance experiment. Equally important, we show that on-site Coulomb correlation also plays an important role in the evolution of magnetic coupling in larger clusters, as the results differ significantly from standard DFT calculations. We conclude that for a proper understanding of magnetism of Mn nanostructures (clusters, chains, and layers) one must take into account the effect of strong correlation.

Individual and couple-level risk factors for hepatitis C infection among heterosexual drug users: a multilevel dyadic analysis.

PubMed

McMahon, James M; Pouget, Enrique R; Tortu, Stephanie

2007-06-01

Hepatitis C virus (HCV) is the most common bloodborne pathogen in the United States and is a leading cause of liver-related morbidity and mortality. Although it is known that HCV is most commonly transmitted among injection drug users, the role of sexual transmission in the spread of HCV remains controversial because of inconsistent findings across studies involving heterosexual couples. A novel multilevel modeling technique designed to overcome the limitations of previous research was performed to assess multiple risk factors for HCV while partitioning the source of risk at the individual and couple level. The analysis was performed on risk exposure and HCV screening data obtained from 265 drug-using couples in East Harlem, New York City. In multivariable analysis, significant individual risk factors for HCV included a history of injection drug use, tattooing, and older age. At the couple level, HCV infection tended to cluster within couples, and this interdependence was accounted for by couples' drug-injection behavior. Individual and couple-level sexual behavior was not associated with HCV infection. Our results are consistent with prior research indicating that sexual contact plays little role in HCV transmission. Rather, couples' injection behavior appears to account for the clustering of HCV within heterosexual dyads.

Cluster-Glass Phase in Pyrochlore X Y Antiferromagnets with Quenched Disorder

NASA Astrophysics Data System (ADS)

Andrade, Eric C.; Hoyos, José A.; Rachel, Stephan; Vojta, Matthias

2018-03-01

We study the impact of quenched disorder (random exchange couplings or site dilution) on easy-plane pyrochlore antiferromagnets. In the clean system, order by disorder selects a magnetically ordered state from a classically degenerate manifold. In the presence of randomness, however, different orders can be chosen locally depending on details of the disorder configuration. Using a combination of analytical considerations and classical Monte Carlo simulations, we argue that any long-range-ordered magnetic state is destroyed beyond a critical level of randomness where the system breaks into magnetic domains due to random exchange anisotropies, becoming, therefore, a glass of spin clusters, in accordance with the available experimental data. These random anisotropies originate from off-diagonal exchange couplings in the microscopic Hamiltonian, establishing their relevance to other magnets with strong spin-orbit coupling.

Inclusion of orbital relaxation and correlation through the unitary group adapted open shell coupled cluster theory using non-relativistic and scalar relativistic Hamiltonians to study the core ionization potential of molecules containing light to medium-heavy elements

NASA Astrophysics Data System (ADS)

Sen, Sangita; Shee, Avijit; Mukherjee, Debashis

2018-02-01

The orbital relaxation attendant on ionization is particularly important for the core electron ionization potential (core IP) of molecules. The Unitary Group Adapted State Universal Coupled Cluster (UGA-SUMRCC) theory, recently formulated and implemented by Sen et al. [J. Chem. Phys. 137, 074104 (2012)], is very effective in capturing orbital relaxation accompanying ionization or excitation of both the core and the valence electrons [S. Sen et al., Mol. Phys. 111, 2625 (2013); A. Shee et al., J. Chem. Theory Comput. 9, 2573 (2013)] while preserving the spin-symmetry of the target states and using the neutral closed-shell spatial orbitals of the ground state. Our Ansatz invokes a normal-ordered exponential representation of spin-free cluster-operators. The orbital relaxation induced by a specific set of cluster operators in our Ansatz is good enough to eliminate the need for different sets of orbitals for the ground and the core-ionized states. We call the single configuration state function (CSF) limit of this theory the Unitary Group Adapted Open-Shell Coupled Cluster (UGA-OSCC) theory. The aim of this paper is to comprehensively explore the efficacy of our Ansatz to describe orbital relaxation, using both theoretical analysis and numerical performance. Whenever warranted, we also make appropriate comparisons with other coupled-cluster theories. A physically motivated truncation of the chains of spin-free T-operators is also made possible by the normal-ordering, and the operational resemblance to single reference coupled-cluster theory allows easy implementation. Our test case is the prediction of the 1s core IP of molecules containing a single light- to medium-heavy nucleus and thus, in addition to demonstrating the orbital relaxation, we have addressed the scalar relativistic effects on the accuracy of the IPs by using a hierarchy of spin-free Hamiltonians in conjunction with our theory. Additionally, the contribution of the spin-free component of the two-electron Gaunt term, not usually taken into consideration, has been estimated at the Self-Consistent Field (ΔSCF) level and is found to become increasingly important and eventually quite prominent for molecules with third period atoms and below. The accuracies of the IPs computed using UGA-OSCC are found to be of the same order as the Coupled Cluster Singles Doubles (ΔCCSD) values while being free from spin contamination. Since the UGA-OSCC uses a common set of orbitals for the ground state and the ion, it obviates the need of two N5 AO to MO transformation in contrast to the ΔCCSD method.

Inclusion of orbital relaxation and correlation through the unitary group adapted open shell coupled cluster theory using non-relativistic and scalar relativistic Hamiltonians to study the core ionization potential of molecules containing light to medium-heavy elements.

PubMed

Sen, Sangita; Shee, Avijit; Mukherjee, Debashis

2018-02-07

The orbital relaxation attendant on ionization is particularly important for the core electron ionization potential (core IP) of molecules. The Unitary Group Adapted State Universal Coupled Cluster (UGA-SUMRCC) theory, recently formulated and implemented by Sen et al. [J. Chem. Phys. 137, 074104 (2012)], is very effective in capturing orbital relaxation accompanying ionization or excitation of both the core and the valence electrons [S. Sen et al., Mol. Phys. 111, 2625 (2013); A. Shee et al., J. Chem. Theory Comput. 9, 2573 (2013)] while preserving the spin-symmetry of the target states and using the neutral closed-shell spatial orbitals of the ground state. Our Ansatz invokes a normal-ordered exponential representation of spin-free cluster-operators. The orbital relaxation induced by a specific set of cluster operators in our Ansatz is good enough to eliminate the need for different sets of orbitals for the ground and the core-ionized states. We call the single configuration state function (CSF) limit of this theory the Unitary Group Adapted Open-Shell Coupled Cluster (UGA-OSCC) theory. The aim of this paper is to comprehensively explore the efficacy of our Ansatz to describe orbital relaxation, using both theoretical analysis and numerical performance. Whenever warranted, we also make appropriate comparisons with other coupled-cluster theories. A physically motivated truncation of the chains of spin-free T-operators is also made possible by the normal-ordering, and the operational resemblance to single reference coupled-cluster theory allows easy implementation. Our test case is the prediction of the 1s core IP of molecules containing a single light- to medium-heavy nucleus and thus, in addition to demonstrating the orbital relaxation, we have addressed the scalar relativistic effects on the accuracy of the IPs by using a hierarchy of spin-free Hamiltonians in conjunction with our theory. Additionally, the contribution of the spin-free component of the two-electron Gaunt term, not usually taken into consideration, has been estimated at the Self-Consistent Field (ΔSCF) level and is found to become increasingly important and eventually quite prominent for molecules with third period atoms and below. The accuracies of the IPs computed using UGA-OSCC are found to be of the same order as the Coupled Cluster Singles Doubles (ΔCCSD) values while being free from spin contamination. Since the UGA-OSCC uses a common set of orbitals for the ground state and the ion, it obviates the need of two N 5 AO to MO transformation in contrast to the ΔCCSD method.

Communication: Finite size correction in periodic coupled cluster theory calculations of solids.

PubMed

Liao, Ke; Grüneis, Andreas

2016-10-14

We present a method to correct for finite size errors in coupled cluster theory calculations of solids. The outlined technique shares similarities with electronic structure factor interpolation methods used in quantum Monte Carlo calculations. However, our approach does not require the calculation of density matrices. Furthermore we show that the proposed finite size corrections achieve chemical accuracy in the convergence of second-order Møller-Plesset perturbation and coupled cluster singles and doubles correlation energies per atom for insulating solids with two atomic unit cells using 2 × 2 × 2 and 3 × 3 × 3 k-point meshes only.

A nonperturbative light-front coupled-cluster method

NASA Astrophysics Data System (ADS)

Hiller, J. R.

2012-10-01

The nonperturbative Hamiltonian eigenvalue problem for bound states of a quantum field theory is formulated in terms of Dirac's light-front coordinates and then approximated by the exponential-operator technique of the many-body coupled-cluster method. This approximation eliminates any need for the usual approximation of Fock-space truncation. Instead, the exponentiated operator is truncated, and the terms retained are determined by a set of nonlinear integral equations. These equations are solved simultaneously with an effective eigenvalue problem in the valence sector, where the number of constituents is small. Matrix elements can be calculated, with extensions of techniques from standard coupled-cluster theory, to obtain form factors and other observables.

Coulomb- and Antiferromagnetic-Induced Fission in Doubly Charged Cubelike Fe-S Clusters

NASA Astrophysics Data System (ADS)

Yang, Xin; Wang, Xue-Bin; Niu, Shuqiang; Pickett, Chris J.; Ichiye, Toshiko; Wang, Lai-Sheng

2002-09-01

We report the observation of symmetric fission in doubly charged Fe-S cluster anions, [Fe4S4X4]2- -->2[Fe2S2X2]- (X=Cl,Br), owing to both Coulomb repulsion and antiferromagnetic coupling. Photoelectron spectroscopy shows that both the parent and the fission fragments have similar electronic structures and confirms the inverted energy schemes due to the strong spin polarization of the Fe 3d levels. The current observation provides direct confirmation for the unusual spin couplings in the [Fe4S4X4]2- clusters, which contain two valent-delocalized and ferromagnetically coupled Fe2S2 subunits.

Solvatochromic shifts from coupled-cluster theory embedded in density functional theory

NASA Astrophysics Data System (ADS)

Höfener, Sebastian; Gomes, André Severo Pereira; Visscher, Lucas

2013-09-01

Building on the framework recently reported for determining general response properties for frozen-density embedding [S. Höfener, A. S. P. Gomes, and L. Visscher, J. Chem. Phys. 136, 044104 (2012)], 10.1063/1.3675845, in this work we report a first implementation of an embedded coupled-cluster in density-functional theory (CC-in-DFT) scheme for electronic excitations, where only the response of the active subsystem is taken into account. The formalism is applied to the calculation of coupled-cluster excitation energies of water and uracil in aqueous solution. We find that the CC-in-DFT results are in good agreement with reference calculations and experimental results. The accuracy of calculations is mainly sensitive to factors influencing the correlation treatment (basis set quality, truncation of the cluster operator) and to the embedding treatment of the ground-state (choice of density functionals). This allows for efficient approximations at the excited state calculation step without compromising the accuracy. This approximate scheme makes it possible to use a first principles approach to investigate environment effects with specific interactions at coupled-cluster level of theory at a cost comparable to that of calculations of the individual subsystems in vacuum.

Dynamic clustering of dynamin-amphiphysin helices regulates membrane constriction and fission coupled with GTP hydrolysis

PubMed Central

Kozai, Toshiya; Yang, Huiran; Ishikuro, Daiki; Seyama, Kaho; Kumagai, Yusuke; Abe, Tadashi; Yamada, Hiroshi; Uchihashi, Takayuki

2018-01-01

Dynamin is a mechanochemical GTPase essential for membrane fission during clathrin-mediated endocytosis. Dynamin forms helical complexes at the neck of clathrin-coated pits and their structural changes coupled with GTP hydrolysis drive membrane fission. Dynamin and its binding protein amphiphysin cooperatively regulate membrane remodeling during the fission, but its precise mechanism remains elusive. In this study, we analyzed structural changes of dynamin-amphiphysin complexes during the membrane fission using electron microscopy (EM) and high-speed atomic force microscopy (HS-AFM). Interestingly, HS-AFM analyses show that the dynamin-amphiphysin helices are rearranged to form clusters upon GTP hydrolysis and membrane constriction occurs at protein-uncoated regions flanking the clusters. We also show a novel function of amphiphysin in size control of the clusters to enhance biogenesis of endocytic vesicles. Our approaches using combination of EM and HS-AFM clearly demonstrate new mechanistic insights into the dynamics of dynamin-amphiphysin complexes during membrane fission. PMID:29357276

Dynamics of multi-frequency oscillator ensembles with resonant coupling

NASA Astrophysics Data System (ADS)

Lück, S.; Pikovsky, A.

2011-07-01

We study dynamics of populations of resonantly coupled oscillators having different frequencies. Starting from the coupled van der Pol equations we derive the Kuramoto-type phase model for the situation, where the natural frequencies of two interacting subpopulations are in relation 2:1. Depending on the parameter of coupling, ensembles can demonstrate fully synchronous clusters, partial synchrony (only one subpopulation synchronizes), or asynchrony in both subpopulations. Theoretical description of the dynamics based on the Watanabe-Strogatz approach is developed.

U.S. stock market interaction network as learned by the Boltzmann machine

DOE PAGES

Borysov, Stanislav S.; Roudi, Yasser; Balatsky, Alexander V.

2015-12-07

Here, we study historical dynamics of joint equilibrium distribution of stock returns in the U.S. stock market using the Boltzmann distribution model being parametrized by external fields and pairwise couplings. Within Boltzmann learning framework for statistical inference, we analyze historical behavior of the parameters inferred using exact and approximate learning algorithms. Since the model and inference methods require use of binary variables, effect of this mapping of continuous returns to the discrete domain is studied. The presented results show that binarization preserves the correlation structure of the market. Properties of distributions of external fields and couplings as well as themore » market interaction network and industry sector clustering structure are studied for different historical dates and moving window sizes. We demonstrate that the observed positive heavy tail in distribution of couplings is related to the sparse clustering structure of the market. We also show that discrepancies between the model’s parameters might be used as a precursor of financial instabilities.« less

Continuum Level Density of a Coupled-Channel System in the Complex Scaling Method

NASA Astrophysics Data System (ADS)

Suzuki, R.; Kruppa, A. T.; Giraud, B. G.; Katō, K.

2008-06-01

We study the continuum level density (CLD) in the formalism of the complex scaling method (CSM) for coupled-channel systems. We apply the formalism to the ^{4}He = [^{3}H + p] + [^3{He} + n] coupled-channel cluster model where there are resonances at low energy. Numerical calculations of the CLD in the CSM with a finite number of L^{2} basis functions are consistent with the exact result calculated from the S-matrix by solving coupled-channel equations. We also study channel densities. In this framework, the extended completeness relation (ECR) plays an important role.

Computational Chemistry Modeling of the Atmospheric Fate of Toxic Industrial Compounds (TICs)

DTIC Science & Technology

2007-06-01

1+G(3df,2p) number of atoms and number of basis functions) of the (LRG) compounds under study precludes the use of coupled 0 Zero Point Energy ( ZPE ...overlap (NDDO) The extrapolated energy = E(QCI) + E(LRG) - Hamiltonian that is reparameterized to accurately E(SML) + ZPE reproduce coupled cluster

Experimental synchronization of chaos in a large ring of mutually coupled single-transistor oscillators: phase, amplitude, and clustering effects.

PubMed

Minati, Ludovico

2014-12-01

In this paper, experimental evidence of multiple synchronization phenomena in a large (n = 30) ring of chaotic oscillators is presented. Each node consists of an elementary circuit, generating spikes of irregular amplitude and comprising one bipolar junction transistor, one capacitor, two inductors, and one biasing resistor. The nodes are mutually coupled to their neighbours via additional variable resistors. As coupling resistance is decreased, phase synchronization followed by complete synchronization is observed, and onset of synchronization is associated with partial synchronization, i.e., emergence of communities (clusters). While component tolerances affect community structure, the general synchronization properties are maintained across three prototypes and in numerical simulations. The clusters are destroyed by adding long distance connections with distant notes, but are otherwise relatively stable with respect to structural connectivity changes. The study provides evidence that several fundamental synchronization phenomena can be reliably observed in a network of elementary single-transistor oscillators, demonstrating their generative potential and opening way to potential applications of this undemanding setup in experimental modelling of the relationship between network structure, synchronization, and dynamical properties.

A theoretical study of the reaction of Ti+ with ethane

NASA Astrophysics Data System (ADS)

Moc, Jerzy; Fedorov, Dmitri G.; Gordon, Mark S.

2000-06-01

The doublet and quartet potential energy surfaces for the Ti++C2H6→TiC2H4++H2 and Ti++C2H6→TiCH2++CH4 reactions are studied using density functional theory (DFT) with the B3LYP functional and ab initio coupled cluster CCSD(T) methods with high quality basis sets. Structures have been optimized at the DFT level and the minima connected to each transition state (TS) by following the intrinsic reaction coordinate (IRC). Relative energies are calculated both at the DFT and coupled-cluster levels of theory. The relevant parts of the potential energy surface, especially key transition states, are also studied using multireference wave functions with the final energetics obtained with multireference second-order perturbation theory.

The protonation of N2O reexamined - A case study on the reliability of various electron correlation methods for minima and transition states

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1993-01-01

The protonation of N2O and the intramolecular proton transfer in N2OH(+) are studied using various basis sets and a variety of methods, including second-order many-body perturbation theory (MP2), singles and doubles coupled cluster (CCSD), the augmented coupled cluster (CCSD/T/), and complete active space self-consistent field (CASSCF) methods. For geometries, MP2 leads to serious errors even for HNNO(+); for the transition state, only CCSD/T/ produces a reliable geometry due to serious nondynamical correlation effects. The proton affinity at 298.15 K is estimated at 137.6 kcal/mol, in close agreement with recent experimental determinations of 137.3 +/- 1 kcal/mol.

Perturbative universal state-selective correction for state-specific multi-reference coupled cluster methods

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

Brabec, Jiri; Banik, Subrata; Kowalski, Karol

2016-10-28

The implementation details of the universal state-selective (USS) multi-reference coupled cluster (MRCC) formalism with singles and doubles (USS(2)) are discussed on the example of several benchmark systems. We demonstrate that the USS(2) formalism is capable of improving accuracies of state specific multi-reference coupled-cluster (MRCC) methods based on the Brillouin-Wigner and Mukherjee’s sufficiency conditions. Additionally, it is shown that the USS(2) approach significantly alleviates problems associated with the lack of invariance of MRCC theories upon the rotation of active orbitals. We also discuss the perturbative USS(2) formulations that significantly reduce numerical overhead of the full USS(2) method.

Communication: Time-dependent optimized coupled-cluster method for multielectron dynamics

NASA Astrophysics Data System (ADS)

Sato, Takeshi; Pathak, Himadri; Orimo, Yuki; Ishikawa, Kenichi L.

2018-02-01

Time-dependent coupled-cluster method with time-varying orbital functions, called time-dependent optimized coupled-cluster (TD-OCC) method, is formulated for multielectron dynamics in an intense laser field. We have successfully derived the equations of motion for CC amplitudes and orthonormal orbital functions based on the real action functional, and implemented the method including double excitations (TD-OCCD) and double and triple excitations (TD-OCCDT) within the optimized active orbitals. The present method is size extensive and gauge invariant, a polynomial cost-scaling alternative to the time-dependent multiconfiguration self-consistent-field method. The first application of the TD-OCC method of intense-laser driven correlated electron dynamics in Ar atom is reported.

Communication: Time-dependent optimized coupled-cluster method for multielectron dynamics.

PubMed

Sato, Takeshi; Pathak, Himadri; Orimo, Yuki; Ishikawa, Kenichi L

2018-02-07

Time-dependent coupled-cluster method with time-varying orbital functions, called time-dependent optimized coupled-cluster (TD-OCC) method, is formulated for multielectron dynamics in an intense laser field. We have successfully derived the equations of motion for CC amplitudes and orthonormal orbital functions based on the real action functional, and implemented the method including double excitations (TD-OCCD) and double and triple excitations (TD-OCCDT) within the optimized active orbitals. The present method is size extensive and gauge invariant, a polynomial cost-scaling alternative to the time-dependent multiconfiguration self-consistent-field method. The first application of the TD-OCC method of intense-laser driven correlated electron dynamics in Ar atom is reported.

Chimeras with multiple coherent regions

NASA Astrophysics Data System (ADS)

Ujjwal, Sangeeta Rani; Ramaswamy, Ramakrishna

2013-09-01

We study chimeric states in a coupled phase oscillator system with piecewise linear nonlocal coupling. By modifying the details of the coupling, it is possible to obtain multiple chimeric states with a specified number of coherent regions and with specified phase relationships. The case of a two-component chimera is illustrated and the generalization to arbitrary chimeric configurations is discussed. The phase relations between the two clusters of phase oscillators is described in some detail.

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.

Perturbative treatment of spin-orbit-coupling within spin-free exact two-component theory using equation-of-motion coupled-cluster methods

NASA Astrophysics Data System (ADS)

Cheng, Lan; Wang, Fan; Stanton, John F.; Gauss, Jürgen

2018-01-01

A scheme is reported for the perturbative calculation of spin-orbit coupling (SOC) within the spin-free exact two-component theory in its one-electron variant (SFX2C-1e) in combination with the equation-of-motion coupled-cluster singles and doubles method. Benchmark calculations of the spin-orbit splittings in 2Π and 2P radicals show that the accurate inclusion of scalar-relativistic effects using the SFX2C-1e scheme extends the applicability of the perturbative treatment of SOC to molecules that contain heavy elements. The contributions from relaxation of the coupled-cluster amplitudes are shown to be relatively small; significant contributions from correlating the inner-core orbitals are observed in calculations involving third-row and heavier elements. The calculation of term energies for the low-lying electronic states of the PtH radical, which serves to exemplify heavy transition-metal containing systems, further demonstrates the quality that can be achieved with the pragmatic approach presented here.

Chimeras and clusters in networks of hyperbolic chaotic oscillators

NASA Astrophysics Data System (ADS)

Cano, A. V.; Cosenza, M. G.

2017-03-01

We show that chimera states, where differentiated subsets of synchronized and desynchronized dynamical elements coexist, can emerge in networks of hyperbolic chaotic oscillators subject to global interactions. As local dynamics we employ Lozi maps, which possess hyperbolic chaotic attractors. We consider a globally coupled system of these maps and use two statistical quantities to describe its collective behavior: the average fraction of elements belonging to clusters and the average standard deviation of state variables. Chimera states, clusters, complete synchronization, and incoherence are thus characterized on the space of parameters of the system. We find that chimera states are related to the formation of clusters in the system. In addition, we show that chimera states arise for a sufficiently long range of interactions in nonlocally coupled networks of these maps. Our results reveal that, under some circumstances, hyperbolicity does not impede the formation of chimera states in networks of coupled chaotic systems, as it had been previously hypothesized.

Electron interactions, spin-orbit coupling, intersite correlations in pyrochlore iridates: a comparison of single-site and cluster calculations

NASA Astrophysics Data System (ADS)

Wang, Runzhi; Go, Ara; Millis, Andrew

Pyrochlore iridates (R2 Ir2O7) are studied using density functional theory plus single-site and cluster dynamical mean-field theory (DFT+DMFT). The calculations include spin-orbit coupling. Significant differences between the single-site and cluster calculations are found. The single-site approximation fails to account for the properties of the paramagnetic insulator phase, in particular predicting a larger gap than found in experiments, while cluster calculations yield gaps consistent with transport data. A ground-state phase diagram is computed. Paramagnetic metal, metallic all-in/all-out (AIAO) and insulating AIAO phases are found. Tilted Weyl cones are observed in the AIAO metallic phase for a relatively wide range of interaction strength. Our paramagnetic calculations predict almost identical behaviors for the Y and Eu compound, conflicting with the strong material dependence reported in experiments. Inclusion of magnetic order restores the material difference. The physical origin of the difference is discussed. The results indicate that intersite effects, most likely of antiferromagnetic origin, play an important role in studying the physics of pyrochlore iridates. This work is supported by DOE-ER046169.

Highly anisotropic exchange interactions in a trigonal bipyramidal cyanide-bridged Ni(II)3Os(III)2 cluster.

PubMed

Palii, Andrei V; Reu, Oleg S; Ostrovsky, Sergei M; Klokishner, Sophia I; Tsukerblat, Boris S; Hilfiger, Matthew; Shatruk, Michael; Prosvirin, Andrey; Dunbar, Kim R

2009-06-25

This article is a part of our efforts to control the magnetic anisotropy in cyanide-based exchange-coupled systems with the eventual goal to obtain single-molecule magnets with higher blocking temperatures. We give the theoretical interpretation of the magnetic properties of the new pentanuclear complex {[Ni(II)(tmphen)(2)](3)[Os(III)(CN)(6)](2)} x 6 CH(3)CN (Ni(II)(3)Os(III)(2) cluster). Because the system contains the heavy Os(III) ions, spin-orbit coupling considerably exceeds the contributions from the low-symmetry crystal field and exchange coupling. The magnetic properties of the Ni(II)(3)Os(III)(2) cluster are described in the framework of a highly anisotropic pseudo-spin Hamiltonian that corresponds to the limit of strong spin-orbital coupling and takes into account the complex molecular structure. The model provides a good fit to the experimental data and allows the conclusion that the trigonal axis of the bipyramidal Ni(II)(3)Os(III)(2) cluster is a hard axis of magnetization. This explains the fact that in contrast with the isostructural trigonal bipyramidal Mn(III)(2)Mn(II)(3) cluster, the Ni(II)(3)Os(III)(2) system does not exhibit the single-molecule magnetic behavior.

Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states.

PubMed

Ku, Wai Lim; Girvan, Michelle; Ott, Edward

2015-12-01

In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field is chaotic. We argue that this second type of behavior is "extensive" in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.

Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states

NASA Astrophysics Data System (ADS)

Ku, Wai Lim; Girvan, Michelle; Ott, Edward

2015-12-01

In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field is chaotic. We argue that this second type of behavior is "extensive" in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.

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.

Exchange coupling transformations in Cu (II) heterospin complexes of “breathing crystals” under structural phase transitions

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

Morozov, Vitaly A.; Petrova, Marina V.; Lukzen, Nikita N., E-mail: luk@tomo.nsc.ru

2015-08-15

Family of “breathing crystals” is the polymer-chain complexes of Cu(hfac){sub 2} with nitroxides. The polymer chains consist of one-, two- or three-spin clusters. The “breathing crystals” experience simultaneous magnetic and Jahn-Teller type structural phase transitions with change of total cluster spin and drastic change of bond lengths (ca. 10-12%). For the first time the intra-cluster magnetic couplings in ”breathing crystals” have been calculated both by band structure methods GGA + U and hybrid DFT (B3LYP and PBE0) for the isolated exchange clusters. The temperature dependence of the magnetic coupling constant was calculated for two polymer-chain compounds of the “breathing crystal”more » family - C{sub 21}H{sub 19}CuF{sub 12}N{sub 4}O{sub 6} with the chains containing two-spin clusters and C{sub 22}H{sub 21}CuF{sub 12}N{sub 4}O{sub 6} with the chains of alternating three-spin clusters and one-spin sites. It was found that adding a Hubbard-like parameter not only to the copper 3d electrons but also to the oxygen 2p electrons (GGA + U{sub d} + U{sub p} approach) results in an improved description of exchange coupling in the “breathing crystal” compounds. At the same time treatment of the isolated clusters by a large basis hybrid DFT with high computational cost provides a similar quality fit of the experimental magneto-chemical data as that for the GGA + U{sub d} + U{sub p} band structure calculation scheme. Our calculations also showed that in spite of the abrupt transformation of the magnetic coupling constant under the phase transition, the band gap in the “breathing crystals” remains about the same value with temperature decrease.« less

Ferromagnetic spin coupling in the chromium dimer cation: Measurements by photodissociation spectroscopy combined with coupled-cluster calculations

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

Egashira, Kazuhiro, E-mail: egashira@clusterlab.jp; Yamada, Yurika; Kita, Yukiumi

2015-02-07

The magnetic coupling of the chromium dimer cation, Cr{sub 2}{sup +}, has been an outstanding problem for decades. An optical absorption spectrum of Cr{sub 2}{sup +} has been obtained by photodissociation spectroscopy in the photon-energy range from 2.0 to 5.0 eV. Besides, calculations have been performed by the equation-of-motion coupled-cluster singles and doubles method for vertical excitation of the species. Their coincidence supports our assignment that the ground electronic state exhibits a ferromagnetic spin coupling, which is contrary to those of neutral and negatively charged dimers, Cr{sub 2} and Cr{sub 2}{sup −}, in their lowest spin states.

Time delay in the Kuramoto model of coupled-phase oscillators

NASA Astrophysics Data System (ADS)

Yeung, Man Kit Stephen

1999-10-01

The Kuramoto model is a mean-field model of coupled phase oscillators with distributed natural frequencies. It was proposed to study collective synchronization in large systems of nonlinear oscillators. Here we generalize this model to allow time-delayed interactions. Despite the delay, synchronization is still possible. We derive exact stability conditions for the incoherent state, and for synchronized states and clustering states in the special case of noiseless identical oscillators. We also study the bifurcations of these states. We find that the incoherent state loses stability in a Hopf bifurcation. In the absence of noise, this leads to partial synchrony, where some oscillators are entrained to a common frequency. New phenomena caused by the delay include multistability among synchronization, incoherence, and clustering; and unsteady solutions with time-dependent order parameters. The experimental implications of the model are discussed for populations of chirping crickets, where the finite speed of sound causes communication delays, and for physical systems such as coupled phase- locked loops, lasers, and communication satellites.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Efficient One-Step Generation of Cluster State with Charge Qubits in Circuit QED

NASA Astrophysics Data System (ADS)

Wang, Yi-Min; Li, Cheng-Zu

2010-01-01

We propose theoretical schemes to generate highly entangled cluster state with superconducting qubits in a circuit QED architecture. Charge qubits are located inside a superconducting transmission line, which serves as a quantum data bus. We show that large clusters state can be efficiently generated in just one step with the long-range Ising-like unitary operators. The quantum operations which are generally realized by two coupling mechanisms: either voltage coupling or current coupling, depend only on global geometric features and are insensitive not only to the thermal state of the transmission line but also to certain random operation errors. Thus high-fidelity one-way quantum computation can be achieved.

Electrical coupled Morris-Lecar neurons: From design to pattern analysis

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

Binczak, S.; Behdad, R.; Rossé, M.

2016-06-08

In this study, an experimental electronic neuron based on Morris-Lecar model is presented, able to become an experimental unit tool to study collective association of robust coupled neurons. The circuit design is given according to the ionic currents of this model. A weak coupling of such neurons under Multisim Software can generate clusters based on the boundary conditions of the neurons and their initial conditions. For this study, we work in the region close to the fold bifurcation of limit cycles. In this region two limit cycles exist, one of the cycles is stable and another one is unstable.

Photoelectron Angular Distributions of Transition Metal Dioxide Anions - a joint experimental and theoretical study

NASA Astrophysics Data System (ADS)

Iordanov, Ivan; Gunaratne, Dasitha; Harmon, Christopher; Sofo, Jorge; Castleman, A. W., Jr.

2012-02-01

Angular-resolved photoelectron spectroscopy (PES) studies of the MO2- (M=Ti, Zr, Hf, Co, Rh) clusters are presented for the first time along with theoretical calculations of their properties. We confirm previously reported non-angular PES results for the vertical detachment energies (VDE), vibrational energies and geometric structures of these clusters and further explore the effect of the 'lanthanide contraction' on the MO2- clusters by comparing the electronic spectra of 4d and 5d transition metal dioxides. Angular-resolved PES provides the angular momentum contributions to the HOMO of these clusters and we use theoretical calculations to examine the HOMO and compare to our experimental results. First-principles calculations are done using both density functional theory (DFT) and the coupled-cluster, singles, doubles and triples (CCSD(T)) methods.

Graph partitions and cluster synchronization in networks of oscillators

PubMed Central

Schaub, Michael T.; O’Clery, Neave; Billeh, Yazan N.; Delvenne, Jean-Charles; Lambiotte, Renaud; Barahona, Mauricio

2017-01-01

Synchronization over networks depends strongly on the structure of the coupling between the oscillators. When the coupling presents certain regularities, the dynamics can be coarse-grained into clusters by means of External Equitable Partitions of the network graph and their associated quotient graphs. We exploit this graph-theoretical concept to study the phenomenon of cluster synchronization, in which different groups of nodes converge to distinct behaviors. We derive conditions and properties of networks in which such clustered behavior emerges, and show that the ensuing dynamics is the result of the localization of the eigenvectors of the associated graph Laplacians linked to the existence of invariant subspaces. The framework is applied to both linear and non-linear models, first for the standard case of networks with positive edges, before being generalized to the case of signed networks with both positive and negative interactions. We illustrate our results with examples of both signed and unsigned graphs for consensus dynamics and for partial synchronization of oscillator networks under the master stability function as well as Kuramoto oscillators. PMID:27781454

Robustness and structure of complex networks

NASA Astrophysics Data System (ADS)

Shao, Shuai

This dissertation covers the two major parts of my PhD research on statistical physics and complex networks: i) modeling a new type of attack -- localized attack, and investigating robustness of complex networks under this type of attack; ii) discovering the clustering structure in complex networks and its influence on the robustness of coupled networks. Complex networks appear in every aspect of our daily life and are widely studied in Physics, Mathematics, Biology, and Computer Science. One important property of complex networks is their robustness under attacks, which depends crucially on the nature of attacks and the structure of the networks themselves. Previous studies have focused on two types of attack: random attack and targeted attack, which, however, are insufficient to describe many real-world damages. Here we propose a new type of attack -- localized attack, and study the robustness of complex networks under this type of attack, both analytically and via simulation. On the other hand, we also study the clustering structure in the network, and its influence on the robustness of a complex network system. In the first part, we propose a theoretical framework to study the robustness of complex networks under localized attack based on percolation theory and generating function method. We investigate the percolation properties, including the critical threshold of the phase transition pc and the size of the giant component Pinfinity. We compare localized attack with random attack and find that while random regular (RR) networks are more robust against localized attack, Erdoḧs-Renyi (ER) networks are equally robust under both types of attacks. As for scale-free (SF) networks, their robustness depends crucially on the degree exponent lambda. The simulation results show perfect agreement with theoretical predictions. We also test our model on two real-world networks: a peer-to-peer computer network and an airline network, and find that the real-world networks are much more vulnerable to localized attack compared with random attack. In the second part, we extend the tree-like generating function method to incorporating clustering structure in complex networks. We study the robustness of a complex network system, especially a network of networks (NON) with clustering structure in each network. We find that the system becomes less robust as we increase the clustering coefficient of each network. For a partially dependent network system, we also find that the influence of the clustering coefficient on network robustness decreases as we decrease the coupling strength, and the critical coupling strength qc, at which the first-order phase transition changes to second-order, increases as we increase the clustering coefficient.

Experimental synchronization of chaos in a large ring of mutually coupled single-transistor oscillators: Phase, amplitude, and clustering effects

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

Minati, Ludovico, E-mail: lminati@ieee.org, E-mail: ludovico.minati@unitn.it

In this paper, experimental evidence of multiple synchronization phenomena in a large (n = 30) ring of chaotic oscillators is presented. Each node consists of an elementary circuit, generating spikes of irregular amplitude and comprising one bipolar junction transistor, one capacitor, two inductors, and one biasing resistor. The nodes are mutually coupled to their neighbours via additional variable resistors. As coupling resistance is decreased, phase synchronization followed by complete synchronization is observed, and onset of synchronization is associated with partial synchronization, i.e., emergence of communities (clusters). While component tolerances affect community structure, the general synchronization properties are maintained across three prototypes andmore » in numerical simulations. The clusters are destroyed by adding long distance connections with distant notes, but are otherwise relatively stable with respect to structural connectivity changes. The study provides evidence that several fundamental synchronization phenomena can be reliably observed in a network of elementary single-transistor oscillators, demonstrating their generative potential and opening way to potential applications of this undemanding setup in experimental modelling of the relationship between network structure, synchronization, and dynamical properties.« less

Clusters in nonsmooth oscillator networks

NASA Astrophysics Data System (ADS)

Nicks, Rachel; Chambon, Lucie; Coombes, Stephen

2018-03-01

For coupled oscillator networks with Laplacian coupling, the master stability function (MSF) has proven a particularly powerful tool for assessing the stability of the synchronous state. Using tools from group theory, this approach has recently been extended to treat more general cluster states. However, the MSF and its generalizations require the determination of a set of Floquet multipliers from variational equations obtained by linearization around a periodic orbit. Since closed form solutions for periodic orbits are invariably hard to come by, the framework is often explored using numerical techniques. Here, we show that further insight into network dynamics can be obtained by focusing on piecewise linear (PWL) oscillator models. Not only do these allow for the explicit construction of periodic orbits, their variational analysis can also be explicitly performed. The price for adopting such nonsmooth systems is that many of the notions from smooth dynamical systems, and in particular linear stability, need to be modified to take into account possible jumps in the components of Jacobians. This is naturally accommodated with the use of saltation matrices. By augmenting the variational approach for studying smooth dynamical systems with such matrices we show that, for a wide variety of networks that have been used as models of biological systems, cluster states can be explicitly investigated. By way of illustration, we analyze an integrate-and-fire network model with event-driven synaptic coupling as well as a diffusively coupled network built from planar PWL nodes, including a reduction of the popular Morris-Lecar neuron model. We use these examples to emphasize that the stability of network cluster states can depend as much on the choice of single node dynamics as it does on the form of network structural connectivity. Importantly, the procedure that we present here, for understanding cluster synchronization in networks, is valid for a wide variety of systems in biology, physics, and engineering that can be described by PWL oscillators.

Polynomial Similarity Transformation Theory: A smooth interpolation between coupled cluster doubles and projected BCS applied to the reduced BCS Hamiltonian

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

Degroote, M.; Henderson, T. M.; Zhao, J.

We present a similarity transformation theory based on a polynomial form of a particle-hole pair excitation operator. In the weakly correlated limit, this polynomial becomes an exponential, leading to coupled cluster doubles. In the opposite strongly correlated limit, the polynomial becomes an extended Bessel expansion and yields the projected BCS wavefunction. In between, we interpolate using a single parameter. The e ective Hamiltonian is non-hermitian and this Polynomial Similarity Transformation Theory follows the philosophy of traditional coupled cluster, left projecting the transformed Hamiltonian onto subspaces of the Hilbert space in which the wave function variance is forced to be zero.more » Similarly, the interpolation parameter is obtained through minimizing the next residual in the projective hierarchy. We rationalize and demonstrate how and why coupled cluster doubles is ill suited to the strongly correlated limit whereas the Bessel expansion remains well behaved. The model provides accurate wave functions with energy errors that in its best variant are smaller than 1% across all interaction stengths. The numerical cost is polynomial in system size and the theory can be straightforwardly applied to any realistic Hamiltonian.« less

Radiative Feedback of Forming Star Clusters on Their GMC Environments: Theory and Simulation

NASA Astrophysics Data System (ADS)

Howard, C. S.; Pudritz, R. E.; Harris, W. E.

2013-07-01

Star clusters form from dense clumps within a molecular cloud. Radiation from these newly formed clusters feeds back on their natal molecular cloud through heating and ionization which ultimately stops gas accretion into the cluster. Recent studies suggest that radiative feedback effects from a single cluster may be sufficient to disrupt an entire cloud over a short timescale. Simulating cluster formation on a large scale, however, is computationally demanding due to the high number of stars involved. For this reason, we present a model for representing the radiative output of an entire cluster which involves randomly sampling an initial mass function (IMF) as the cluster accretes mass. We show that this model is able to reproduce the star formation histories of observed clusters. To examine the degree to which radiative feedback shapes the evolution of a molecular cloud, we use the FLASH adaptive-mesh refinement hydrodynamics code to simulate cluster formation in a turbulent cloud. Unlike previous studies, sink particles are used to represent a forming cluster rather than individual stars. Our cluster model is then coupled with a raytracing scheme to treat radiative transfer as the clusters grow in mass. This poster will outline the details of our model and present preliminary results from our 3D hydrodynamical simulations.

Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states

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

Ku, Wai Lim; Girvan, Michelle; Ott, Edward

In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field ismore » chaotic. We argue that this second type of behavior is “extensive” in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.« less

Discontinuities-free complete-active-space state–specific multi–reference coupled cluster theory for describing bond stretching and dissociation

DOE PAGES

Zaporozhets, Irina A.; Ivanov, Vladimir V.; Lyakh, Dmitry I.; ...

2015-07-13

The earlier proposed multi-reference state-specific coupled-cluster theory with the complete active space reference suffered from a problem of energy discontinuities when the formal reference state was changing in the calculation of the potential energy curve (PEC). A simple remedy to the discontinuity problem is found and is presented in this work. It involves using natural complete active space self-consistent field active orbitals in the complete active space coupled-cluster calculations. As a result, the approach gives smooth PECs for different types of dissociation problems, as illustrated in the calculations of the dissociation of the single bond in the hydrogen fluorine moleculemore » and of the symmetric double-bond dissociation in the water molecule.« less

Cluster synchronization in networks of identical oscillators with α-function pulse coupling.

PubMed

Chen, Bolun; Engelbrecht, Jan R; Mirollo, Renato

2017-02-01

We study a network of N identical leaky integrate-and-fire model neurons coupled by α-function pulses, weighted by a coupling parameter K. Studies of the dynamics of this system have mostly focused on the stability of the fully synchronized and the fully asynchronous splay states, which naturally depends on the sign of K, i.e., excitation vs inhibition. We find that there is also a rich set of attractors consisting of clusters of fully synchronized oscillators, such as fixed (N-1,1) states, which have synchronized clusters of sizes N-1 and 1, as well as splay states of clusters with equal sizes greater than 1. Additionally, we find limit cycles that clarify the stability of previously observed quasiperiodic behavior. Our framework exploits the neutrality of the dynamics for K=0 which allows us to implement a dimensional reduction strategy that simplifies the dynamics to a continuous flow on a codimension 3 subspace with the sign of K determining the flow direction. This reduction framework naturally incorporates a hierarchy of partially synchronized subspaces in which the new attracting states lie. Using high-precision numerical simulations, we describe completely the sequence of bifurcations and the stability of all fixed points and limit cycles for N=2-4. The set of possible attracting states can be used to distinguish different classes of neuron models. For instance from our previous work [Chaos 24, 013114 (2014)CHAOEH1054-150010.1063/1.4858458] we know that of the types of partially synchronized states discussed here, only the (N-1,1) states can be stable in systems of identical coupled sinusoidal (i.e., Kuramoto type) oscillators, such as θ-neuron models. Upon introducing a small variation in individual neuron parameters, the attracting fixed points we discuss here generalize to equivalent fixed points in which neurons need not fire coincidently.

Cluster synchronization in networks of identical oscillators with α -function pulse coupling

NASA Astrophysics Data System (ADS)

Chen, Bolun; Engelbrecht, Jan R.; Mirollo, Renato

2017-02-01

We study a network of N identical leaky integrate-and-fire model neurons coupled by α -function pulses, weighted by a coupling parameter K . Studies of the dynamics of this system have mostly focused on the stability of the fully synchronized and the fully asynchronous splay states, which naturally depends on the sign of K , i.e., excitation vs inhibition. We find that there is also a rich set of attractors consisting of clusters of fully synchronized oscillators, such as fixed (N -1 ,1 ) states, which have synchronized clusters of sizes N -1 and 1, as well as splay states of clusters with equal sizes greater than 1. Additionally, we find limit cycles that clarify the stability of previously observed quasiperiodic behavior. Our framework exploits the neutrality of the dynamics for K =0 which allows us to implement a dimensional reduction strategy that simplifies the dynamics to a continuous flow on a codimension 3 subspace with the sign of K determining the flow direction. This reduction framework naturally incorporates a hierarchy of partially synchronized subspaces in which the new attracting states lie. Using high-precision numerical simulations, we describe completely the sequence of bifurcations and the stability of all fixed points and limit cycles for N =2 -4 . The set of possible attracting states can be used to distinguish different classes of neuron models. For instance from our previous work [Chaos 24, 013114 (2014), 10.1063/1.4858458] we know that of the types of partially synchronized states discussed here, only the (N -1 ,1 ) states can be stable in systems of identical coupled sinusoidal (i.e., Kuramoto type) oscillators, such as θ -neuron models. Upon introducing a small variation in individual neuron parameters, the attracting fixed points we discuss here generalize to equivalent fixed points in which neurons need not fire coincidently.

Effect of a chameleon scalar field on the cosmic microwave background

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

Davis, Anne-Christine; Schelpe, Camilla A. O.; Shaw, Douglas J.

2009-09-15

We show that a direct coupling between a chameleonlike scalar field and photons can give rise to a modified Sunyaev-Zel'dovich (SZ) effect in the cosmic microwave background (CMB). The coupling induces a mixing between chameleon particles and the CMB photons when they pass through the magnetic field of a galaxy cluster. Both the intensity and the polarization of the radiation are modified. The degree of modification depends strongly on the properties of the galaxy cluster such as magnetic field strength and electron number density. Existing SZ measurements of the Coma cluster enable us to place constraints on the photon-chameleon coupling.more » The constrained conversion probability in the cluster is P{sub Coma}(204 GHz)<6.2x10{sup -5} at 95% confidence, corresponding to an upper bound on the coupling strength of g{sub eff}{sup (cell)}<2.2x10{sup -8} GeV{sup -1} or g{sub eff}{sup (Kolmo)}<(7.2-32.5)x10{sup -10} GeV{sup -1}, depending on the model that is assumed for the cluster magnetic field structure. We predict the radial profile of the chameleonic CMB intensity decrement. We find that the chameleon effect extends farther toward the edges of the cluster than the thermal SZ effect. Thus we might see a discrepancy between the x-ray emission data and the observed SZ intensity decrement. We further predict the expected change to the CMB polarization arising from the existence of a chameleonlike scalar field. These predictions could be verified or constrained by future CMB experiments.« less

Recognition and Matching of Clustered Mature Litchi Fruits Using Binocular Charge-Coupled Device (CCD) Color Cameras

PubMed Central

Wang, Chenglin; Tang, Yunchao; Zou, Xiangjun; Luo, Lufeng; Chen, Xiong

2017-01-01

Recognition and matching of litchi fruits are critical steps for litchi harvesting robots to successfully grasp litchi. However, due to the randomness of litchi growth, such as clustered growth with uncertain number of fruits and random occlusion by leaves, branches and other fruits, the recognition and matching of the fruit become a challenge. Therefore, this study firstly defined mature litchi fruit as three clustered categories. Then an approach for recognition and matching of clustered mature litchi fruit was developed based on litchi color images acquired by binocular charge-coupled device (CCD) color cameras. The approach mainly included three steps: (1) calibration of binocular color cameras and litchi image acquisition; (2) segmentation of litchi fruits using four kinds of supervised classifiers, and recognition of the pre-defined categories of clustered litchi fruit using a pixel threshold method; and (3) matching the recognized clustered fruit using a geometric center-based matching method. The experimental results showed that the proposed recognition method could be robust against the influences of varying illumination and occlusion conditions, and precisely recognize clustered litchi fruit. In the tested 432 clustered litchi fruits, the highest and lowest average recognition rates were 94.17% and 92.00% under sunny back-lighting and partial occlusion, and sunny front-lighting and non-occlusion conditions, respectively. From 50 pairs of tested images, the highest and lowest matching success rates were 97.37% and 91.96% under sunny back-lighting and non-occlusion, and sunny front-lighting and partial occlusion conditions, respectively. PMID:29112177

Clustering impact regime with shocks in freely evolving granular gas

NASA Astrophysics Data System (ADS)

Isobe, Masaharu

2017-06-01

A freely cooling granular gas without any external force evolves from the initial homogeneous state to the inhomogeneous clustering state, at which the energy decay deviates from the Haff's law. The asymptotic behavior of energy in the inelastic hard sphere model have been predicted by several theories, which are based on the mode coupling theory or extension of inelastic hard rods gas. In this study, we revisited the clustering regime of freely evolving granular gas via large-scale molecular dynamics simulation with up to 16.7 million inelastic hard disks. We found novel regime regarding on collisions between "clusters" spontaneously appearing after clustering regime, which can only be identified more than a few million particles system. The volumetric dilatation pattern of semicircular shape originated from density shock propagation are well characterized on the appearing of "cluster impact" during the aggregation process of clusters.

Partial synchronization of relaxation oscillators with repulsive coupling in autocatalytic integrate-and-fire model and electrochemical experiments

NASA Astrophysics Data System (ADS)

Kori, Hiroshi; Kiss, István Z.; Jain, Swati; Hudson, John L.

2018-04-01

Experiments and supporting theoretical analysis are presented to describe the synchronization patterns that can be observed with a population of globally coupled electrochemical oscillators close to a homoclinic, saddle-loop bifurcation, where the coupling is repulsive in the electrode potential. While attractive coupling generates phase clusters and desynchronized states, repulsive coupling results in synchronized oscillations. The experiments are interpreted with a phenomenological model that captures the waveform of the oscillations (exponential increase) followed by a refractory period. The globally coupled autocatalytic integrate-and-fire model predicts the development of partially synchronized states that occur through attracting heteroclinic cycles between out-of-phase two-cluster states. Similar behavior can be expected in many other systems where the oscillations occur close to a saddle-loop bifurcation, e.g., with Morris-Lecar neurons.

Chimera and phase-cluster states in populations of coupled chemical oscillators

NASA Astrophysics Data System (ADS)

Tinsley, Mark R.; Nkomo, Simbarashe; Showalter, Kenneth

2012-09-01

Populations of coupled oscillators may exhibit two coexisting subpopulations, one with synchronized oscillations and the other with unsynchronized oscillations, even though all of the oscillators are coupled to each other in an equivalent manner. This phenomenon, discovered about ten years ago in theoretical studies, was then further characterized and named the chimera state after the Greek mythological creature made up of different animals. The highly counterintuitive coexistence of coherent and incoherent oscillations in populations of identical oscillators, each with an equivalent coupling structure, inspired great interest and a flurry of theoretical activity. Here we report on experimental studies of chimera states and their relation to other synchronization states in populations of coupled chemical oscillators. Our experiments with coupled Belousov-Zhabotinsky oscillators and corresponding simulations reveal chimera behaviour that differs significantly from the behaviour found in theoretical studies of phase-oscillator models.

Standing waves, clustering, and phase waves in 1D simulations of kinetic relaxation oscillations in NO+NH 3 on Pt(1 0 0) coupled by diffusion

NASA Astrophysics Data System (ADS)

Uecker, Hannes

2004-04-01

The Lombardo-Imbihl-Fink (LFI) ODE model of the NO+NH 3 reaction on a Pt(1 0 0) surface shows stable relaxation oscillations with very sharp transitions for temperatures T between 404 and 433 K. Here we study numerically the effect of linear diffusive coupling of these oscillators in one spatial dimension. Depending on the parameters and initial conditions we find a rich variety of spatio-temporal patterns which we group into four main regimes: bulk oscillations (BOs), standing waves (SW), phase clusters (PC), and phase waves (PW). Two key ingredients for SW and PC are identified, namely the relaxation type of the ODE oscillations and a nonlocal (and nonglobal) coupling due to relatively fast diffusion of the kinetically slaved variables NH 3 and H. In particular, the latter replaces the global coupling through the gas phase used to obtain SW and PC in models of related surface reactions. The PW exist only under the assumption of (relatively) slow diffusion of NH 3 and H.

Rational synthesis of high nuclearity Mo/Fe/S clusters: the reductive coupling approach in the convenient synthesis of (Cl(4)-cat)(2)Mo(2)Fe(6)S(8)(PR(3))(6) [R = Et, (n)Pr, (n)Bu] and the new [(Cl(4)-cat)(2)Mo(2)Fe(2)S(3)O(PEt(3))(3)Cl]-1/2(Fe(PEt(3))(2)(MeCN)(4)) and (Cl(4)-cat)(2)Mo(2)Fe(3)S(5)(PEt(3))(5) clusters.

PubMed

Han, J; Koutmos, M; Ahmad, S A; Coucouvanis, D

2001-11-05

A general method for the synthesis of high nuclearity Mo/Fe/S clusters is presented and involves the reductive coupling of the (Et(4)N)(2)[(Cl(4)-cat)MoOFeS(2)Cl(2)] (I) and (Et(4)N)(2)[Fe(2)S(2)Cl(4)] (II) clusters. The reaction of I and II with Fe(PR(3))(2)Cl(2) or sodium salts of noncoordinating anions such as NaPF(6) or NaBPh(4) in the presence of PR(3) (R = Et, (n)Pr, or (n)Bu) affords (Cl(4)-cat)(2)Mo(2)Fe(6)S(8)(PR(3))(6) [R = Et (IIIa), (n)Pr (IIIb), (n)Bu (IIIc)], Fe(6)S(6)(PEt(3))(4)Cl(2) (IV) and (PF(6))[Fe(6)S(8)(P(n)Pr(3))(6)] (V) as byproducts. The isolation of (Et(4)N)[Fe(PEt(3))Cl(3)] (VI), NaCl, and SPEt(3) supports a reductive coupling mechanism. Cluster IV and V also have been synthesized by the reductive self-coupling of compound II. The reductive coupling reaction between I and II by PEt(3) and NaPF(6) in a 1:1 ratio produces the (Et(4)N)(2)[(Cl(4)-cat)Mo(L)Fe(3)S(4)Cl(3)] clusters [L = MeCN (VIIa), THF (VIIb)]. The hitherto unknown [(Cl(4)-cat)(2)Mo(2)Fe(2)S(3)O(PEt(3))(3)Cl](+) cluster (VIII) has been isolated as the 2:1 salt of the (Fe(PEt(3))(2)(MeCN)(4))(2+) cation after the reductive self-coupling reaction of I in the presence of Fe(PEt(3))(2)Cl(2). Cluster VIII crystallizes in the monoclinic space group P2(1)/c with a = 11.098(3) A, b = 22.827(6) A, c = 25.855(6) A, beta = 91.680(4) degrees, and Z = 4. The formal oxidation states of metal atoms in VIII have been assigned as Mo(III), Mo(IV), Fe(II), and Fe(III) on the basis of zero-field Mössbauer spectra. The Fe(PEt(3))(2)(MeCN)(4) cation of VIII is also synthesized independently, isolated as the BPh(4)(-) salt (IX), and has been structurally characterized. The reductive coupling of compound I also affords in low yield the new (Cl(4)-cat)(2)Mo(2)Fe(3)S(5)(PEt(3))(5) cluster (X) as a byproduct. Cluster X crystallizes in the monoclinic space group P2(1)/n with a = 14.811(3) A, b = 22.188(4) A, c = 21.864(4) A, beta = 100.124(3) degrees, and Z = 4 and the structure shows very short Mo-Fe, Fe-Fe, Mo-S, Fe-S bonds. The oxidation states of the metal atoms in this neutral cluster (X) have been assigned as Mo(IV)Mo(III)Fe(II)Fe(II)Fe(III) based on zero-field Mössbauer and magnetic measurement. All Fe atoms are high spin and two of the three Fe-Fe distances are found at 2.4683(9) A and 2.4721(9) A.

Solution of the sign problem in the Potts model at fixed fermion number

NASA Astrophysics Data System (ADS)

Alexandru, Andrei; Bergner, Georg; Schaich, David; Wenger, Urs

2018-06-01

We consider the heavy-dense limit of QCD at finite fermion density in the canonical formulation and approximate it by a three-state Potts model. In the strong-coupling limit, the model is free of the sign problem. Away from the strong coupling, the sign problem is solved by employing a cluster algorithm which allows to average each cluster over the Z (3 ) sectors. Improved estimators for physical quantities can be constructed by taking into account the triality of the clusters, that is, their transformation properties with respect to Z (3 ) transformations.

Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.; Sousa Alencar, Ana G.; Scuseria, Gustavo E.

2015-12-01

Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f0 actinyl series (UO22+, NpO23+, PuO24+), the isoelectronic NUN, and thorium (ThO, ThO2+) and nobelium (NoO, NoO2) oxides are studied.

Application of Hermitian time-dependent coupled-cluster response Ansätze of second order to excitation energies and frequency-dependent dipole polarizabilities

NASA Astrophysics Data System (ADS)

Wälz, Gero; Kats, Daniel; Usvyat, Denis; Korona, Tatiana; Schütz, Martin

2012-11-01

Linear-response methods, based on the time-dependent variational coupled-cluster or the unitary coupled-cluster model, and truncated at the second order according to the Møller-Plesset partitioning, i.e., the TD-VCC[2] and TD-UCC[2] linear-response methods, are presented and compared. For both of these methods a Hermitian eigenvalue problem has to be solved to obtain excitation energies and state eigenvectors. The excitation energies thus are guaranteed always to be real valued, and the eigenvectors are mutually orthogonal, in contrast to response theories based on “traditional” coupled-cluster models. It turned out that the TD-UCC[2] working equations for excitation energies and polarizabilities are equivalent to those of the second-order algebraic diagrammatic construction scheme ADC(2). Numerical tests are carried out by calculating TD-VCC[2] and TD-UCC[2] excitation energies and frequency-dependent dipole polarizabilities for several test systems and by comparing them to the corresponding values obtained from other second- and higher-order methods. It turns out that the TD-VCC[2] polarizabilities in the frequency regions away from the poles are of a similar accuracy as for other second-order methods, as expected from the perturbative analysis of the TD-VCC[2] polarizability expression. On the other hand, the TD-VCC[2] excitation energies are systematically too low relative to other second-order methods (including TD-UCC[2]). On the basis of these results and an analysis presented in this work, we conjecture that the perturbative expansion of the Jacobian converges more slowly for the TD-VCC formalism than for TD-UCC or for response theories based on traditional coupled-cluster models.

An AB Initio Study of SbH_2 and BiH_2: the Renner Effect, Spin-Orbit Coupling, Local Mode Vibrations and Rovibronic Energy Level Clustering in SbH_2

NASA Astrophysics Data System (ADS)

Ostojic, Bojana; Schwerdtfeger, Peter; Bunker, Phil; Jensen, Per

2016-06-01

We present the results of ab initio calculations for the lower electronic states of the Group 15 (pnictogen) dihydrides, SbH_2 and BiH_2. For each of these molecules the two lowest electronic states become degenerate at linearity and are therefore subject to the Renner effect. Spin-orbit coupling is also strong in these two heavy-element containing molecules. For the lowest two electronic states of SbH_2, we construct the three dimensional potential energy surfaces and corresponding dipole moment and transition moment surfaces by multi-reference configuration interaction techniques. Including both the Renner effect and spin-orbit coupling, we calculate term values and simulate the rovibrational and rovibronic spectra of SbH_2. Excellent agreement is obtained with the results of matrix isolation infrared spectroscopic studies and with gas phase electronic spectroscopic studies in absorption [1,2]. For the heavier dihydride BiH_2 we calculate bending potential curves and the spin-orbit coupling constant for comparison. For SbH_2 we further study the local mode vibrational behavior and the formation of rovibronic energy level clusters in high angular momentum states. [1] X. Wang, P. F. Souter and L. Andrews, J. Phys. Chem. A 107, 4244-4249 (2003) [2] N. Basco and K. K. Lee, Spectroscopy Letters 1, 13-15 (1968)

Wiggler magnetic field assisted third harmonic generation in expanding clusters

NASA Astrophysics Data System (ADS)

Vij, Shivani

2018-04-01

A simple theoretical model is constructed to study the wiggler magnetic field assisted third harmonic generation of intense short pulse laser in a cluster in its expanding phase. The ponderomotive force of laser causes density perturbations in cluster electron density which couples with wiggler magnetic field to produce a nonlinear current that generates transverse third harmonic. An intense short pulse laser propagating through a gas embedded with atomic clusters, converts it into hot plasma balls via tunnel ionization. Initially, the electron plasma frequency inside the clusters ω pe > \\sqrt{3}{ω }1 (with ω 1 being the frequency of the laser). As the cluster expands under Coulomb force and hydrodynamic pressure, ω pe decreases to \\sqrt{3}{ω }1. At this time, there is resonant enhancement in the efficiency of the third harmonic generation. The efficiency of third harmonic generation is enhanced due to cluster plasmon resonance and by phase matching due to wiggler magnetic field. The effect of cluster size on the expansion rate is studied to observe that the clusters of different radii would expand differently. The impact of laser intensity and wiggler magnetic field on the efficiency of third harmonic generation is also explored.

First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects

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

Varghese, Jithin J.; Mushrif, Samir H., E-mail: shmushrif@ntu.edu.sg

Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cu{sub n} where n = 2–12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barriermore » for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C–H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH{sub 3} and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CH{sub x} (x = 1–3) species and recombination of H with CH{sub x} have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.« less

Maritime Continent seasonal climate biases in AMIP experiments of the CMIP5 multimodel ensemble

NASA Astrophysics Data System (ADS)

Toh, Ying Ying; Turner, Andrew G.; Johnson, Stephanie J.; Holloway, Christopher E.

2018-02-01

The fidelity of 28 Coupled Model Intercomparison Project phase 5 (CMIP5) models in simulating mean climate over the Maritime Continent in the Atmospheric Model Intercomparison Project (AMIP) experiment is evaluated in this study. The performance of AMIP models varies greatly in reproducing seasonal mean climate and the seasonal cycle. The multi-model mean has better skill at reproducing the observed mean climate than the individual models. The spatial pattern of 850 hPa wind is better simulated than the precipitation in all four seasons. We found that model horizontal resolution is not a good indicator of model performance. Instead, a model's local Maritime Continent biases are somewhat related to its biases in the local Hadley circulation and global monsoon. The comparison with coupled models in CMIP5 shows that AMIP models generally performed better than coupled models in the simulation of the global monsoon and local Hadley circulation but less well at simulating the Maritime Continent annual cycle of precipitation. To characterize model systematic biases in the AMIP runs, we performed cluster analysis on Maritime Continent annual cycle precipitation. Our analysis resulted in two distinct clusters. Cluster I models are able to capture both the winter monsoon and summer monsoon shift, but they overestimate the precipitation; especially during the JJA and SON seasons. Cluster II models simulate weaker seasonal migration than observed, and the maximum rainfall position stays closer to the equator throughout the year. The tropics-wide properties of these clusters suggest a connection between the skill of simulating global properties of the monsoon circulation and the skill of simulating the regional scale of Maritime Continent precipitation.

Cluster assembly in nitrogenase.

PubMed

Sickerman, Nathaniel S; Rettberg, Lee A; Lee, Chi Chung; Hu, Yilin; Ribbe, Markus W

2017-05-09

The versatile enzyme system nitrogenase accomplishes the challenging reduction of N 2 and other substrates through the use of two main metalloclusters. For molybdenum nitrogenase, the catalytic component NifDK contains the [Fe 8 S 7 ]-core P-cluster and a [MoFe 7 S 9 C-homocitrate] cofactor called the M-cluster. These chemically unprecedented metalloclusters play a critical role in the reduction of N 2 , and both originate from [Fe 4 S 4 ] clusters produced by the actions of NifS and NifU. Maturation of P-cluster begins with a pair of these [Fe 4 S 4 ] clusters on NifDK called the P*-cluster. An accessory protein NifZ aids in P-cluster fusion, and reductive coupling is facilitated by NifH in a stepwise manner to form P-cluster on each half of NifDK. For M-cluster biosynthesis, two [Fe 4 S 4 ] clusters on NifB are coupled with a carbon atom in a radical-SAM dependent process, and concomitant addition of a 'ninth' sulfur atom generates the [Fe 8 S 9 C]-core L-cluster. On the scaffold protein NifEN, L-cluster is matured to M-cluster by the addition of Mo and homocitrate provided by NifH. Finally, matured M-cluster in NifEN is directly transferred to NifDK, where a conformational change locks the cofactor in place. Mechanistic insights into these fascinating biosynthetic processes are detailed in this chapter. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

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).

Pulse-coupled mixed-mode oscillators: Cluster states and extreme noise sensitivity

NASA Astrophysics Data System (ADS)

Karamchandani, Avinash J.; Graham, James N.; Riecke, Hermann

2018-04-01

Motivated by rhythms in the olfactory system of the brain, we investigate the synchronization of all-to-all pulse-coupled neuronal oscillators exhibiting various types of mixed-mode oscillations (MMOs) composed of sub-threshold oscillations (STOs) and action potentials ("spikes"). We focus particularly on the impact of the delay in the interaction. In the weak-coupling regime, we reduce the system to a Kuramoto-type equation with non-sinusoidal phase coupling and the associated Fokker-Planck equation. Its linear stability analysis identifies the appearance of various cluster states. Their type depends sensitively on the delay and the width of the pulses. Interestingly, long delays do not imply slow population rhythms, and the number of emerging clusters only loosely depends on the number of STOs. Direct simulations of the oscillator equations reveal that for quantitative agreement of the weak-coupling theory the coupling strength and the noise have to be extremely small. Even moderate noise leads to significant skipping of STO cycles, which can enhance the diffusion coefficient in the Fokker-Planck equation by two orders of magnitude. Introducing an effective diffusion coefficient extends the range of agreement significantly. Numerical simulations of the Fokker-Planck equation reveal bistability and solutions with oscillatory order parameters that result from nonlinear mode interactions. These are confirmed in simulations of the full spiking model.

Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the 199Hg Atom

NASA Astrophysics Data System (ADS)

Sahoo, B. K.; Das, B. P.

2018-05-01

Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P ,T -odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P ,T -odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to 199Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the ^{199}Hg Atom.

PubMed

Sahoo, B K; Das, B P

2018-05-18

Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P,T-odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P,T-odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to ^{199}Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

Globular clusters and environmental effects in galaxy clusters

NASA Astrophysics Data System (ADS)

Sales, Laura

2016-10-01

Globular clusters are old compact stellar systems orbiting around galaxies of all types. Tens of thousands of them can also be found populating the intra-cluster regions of nearby galaxy clusters like Virgo and Coma. Thanks to the HST Frontier Fields program, GCs are starting now to be detected also in intermediate redshift clusters. Yet, despite their ubiquity, a theoretical model for the formation and evolution of GCs is still missing, especially within the cosmological context.Here we propose to use cosmological hydrodynamical simulations of 18 galaxy clusters coupled to a post-processing GC formation model to explore the assembly of galaxies in clusters together with their expected GC population. The method, which has already been implemented and tested, will allow us to characterize for the first time the number, radial distribution and kinematics of GCs in clusters, with products directly comparable to observational maps. We will explore cluster-to-cluster variations and also characterize the build up of the intra-cluster component of GCs with time.As the method relies on a detailed study of the star-formation history of galaxies, we will jointly constrain the predicted quenching time-scales for satellites and the occurrence of starburst events associated to infall and orbital pericenters of galaxies in massive clusters. This will inform further studies on the distribution, velocity and properties of post-starburst galaxies in past, ongoing and future HST programs.

Combination of Wavefunction and Density Functional Approximations for Describing Electronic Correlation

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.

Perhaps the most important approximations to the electronic structure problem in quantum chemistry are those based on coupled cluster and density functional theories. Coupled cluster theory has been called the ``gold standard'' of quantum chemistry due to the high accuracy that it achieves for weakly correlated systems. Kohn-Sham density functionals based on semilocal approximations are, without a doubt, the most widely used methods in chemistry and material science because of their high accuracy/cost ratio. The root of the success of coupled cluster and density functionals is their ability to efficiently describe the dynamic part of the electron correlation. However, both traditional coupled cluster and density functional approximations may fail catastrophically when substantial static correlation is present. This severely limits the applicability of these methods to a plethora of important chemical and physical problems such as, e.g., the description of bond breaking, transition states, transition metal-, lanthanide- and actinide-containing compounds, and superconductivity. In an attempt to tackle this problem, nonstandard (single-reference) coupled cluster-based techniques that aim to describe static correlation have been recently developed: pair coupled cluster doubles (pCCD) and singlet-paired coupled cluster doubles (CCD0). The ability to describe static correlation in pCCD and CCD0 comes, however, at the expense of important amounts of dynamic correlation so that the high accuracy of standard coupled cluster becomes unattainable. Thus, the reliable and efficient description of static and dynamic correlation in a simultaneous manner remains an open problem for quantum chemistry and many-body theory in general. In this thesis, different ways to combine pCCD and CCD0 with density functionals in order to describe static and dynamic correlation simultaneously (and efficiently) are explored. The combination of wavefunction and density functional methods has a long history in quantum chemistry (practical implementations have appeared in the literature since the 1970s). However, this kind of techniques have not achieved widespread use due to problems such as double counting of correlation and the symmetry dilemma--the fact that wavefunction methods respect the symmetries of Hamiltonian, while modern functionals are designed to work with broken symmetry densities. Here, particular mathematical features of pCCD and CCD0 are exploited to avoid these problems in an efficient manner. The two resulting families of approximations, denoted as pCCD+DFT and CCD0+DFT, are shown to be able to describe static and dynamic correlation in standard benchmark calculations. Furthermore, it is also shown that CCD0+DFT lends itself to combination with correlation from the direct random phase approximation (dRPA). Inclusion of dRPA in the long-range via the technique of range-separation allows for the description of dispersion correlation, the remaining part of the correlation. Thus, when combined with the dRPA, CCD0+DFT can account for all three-types of electron correlation that are necessary to accurately describe molecular systems. Lastly, applications of CCD0+DFT to actinide chemistry are considered in this work. The accuracy of CCD0+DFT for predicting equilibrium geometries and vibrational frequencies of actinide molecules and ions is assessed and compared to that of well-established quantum chemical methods. For this purpose, the f0 actinyl series (UO2 2+, NpO 23+, PuO24+, the isoelectronic NUN, and Thorium (ThO, ThO2+) and Nobelium (NoO, NoO2) oxides are studied. It is shown that the CCD0+DFT description of these species agrees with available experimental data and is comparable with the results given by the highest-level calculations that are possible for such heavy compounds while being, at least, an order of magnitude lower in computational cost.

Generation of strongly coupled Xe cluster nanoplasmas by low intensive soft x-ray laser irradiation

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

Namba, S.; Hasegawa, N.; Kishimoto, M.

A seeding gas jet including Xe clusters was irradiated with a laser-driven plasma soft x-ray laser pulse ({lambda}=13.9 nm, {approx}7 ps, {<=}5 Multiplication-Sign 10{sup 9} W/cm{sup 2}), where the laser photon energy is high enough to ionize 4d core electrons. In order to clarify how the innershell ionization followed by the Auger electron emission is affected under the intense laser irradiation, the electron energy distribution was measured. Photoelectron spectra showed that the peak position attributed to 4d hole shifted to lower energy and the spectral width was broadened with increasing cluster size. Moreover, the energy distribution exhibited that a stronglymore » coupled cluster nanoplasma with several eV was generated.« less

Cluster Randomized Controlled Trial Evaluation of a Gender Equity and Family Planning Intervention for Married Men and Couples in Rural India

PubMed Central

Raj, Anita; Ghule, Mohan; Ritter, Julie; Battala, Madhusudana; Gajanan, Velhal; Nair, Saritha; Dasgupta, Anindita; Silverman, Jay G.; Balaiah, Donta; Saggurti, Niranjan

2016-01-01

Background Despite ongoing recommendations to increase male engagement and gender-equity (GE) counseling in family planning (FP) services, few such programs have been implemented and rigorously evaluated. This study evaluates the impact of CHARM, a three-session GE+FP counseling intervention delivered by male health care providers to married men, alone (sessions 1&2) and with their wives (session 3) in India. Methods and Findings A two-armed cluster randomized controlled trial was conducted with young married couples (N = 1081 couples) recruited from 50 geographic clusters (25 clusters randomized to CHARM and a control condition, respectively) in rural Maharashtra, India. Couples were surveyed on demographics, contraceptive behaviors, and intimate partner violence (IPV) attitudes and behaviors at baseline and 9 &18-month follow-ups, with pregnancy testing at baseline and 18-month follow-up. Outcome effects on contraceptive use and incident pregnancy, and secondarily, on contraceptive communication and men’s IPV attitudes and behaviors, were assessed using logistic generalized linear mixed models. Most men recruited from CHARM communities (91.3%) received at least one CHARM intervention session; 52.5% received the couple’s session with their wife. Findings document that women from the CHARM condition, relative to controls, were more likely to report contraceptive communication at 9-month follow-up (AOR = 1.77, p = 0.04) and modern contraceptive use at 9 and 18-month follow-ups (AORs = 1.57–1.58, p = 0.05), and they were less likely to report sexual IPV at 18-month follow-up (AOR = 0.48, p = 0.01). Men in the CHARM condition were less likely than those in the control clusters to report attitudes accepting of sexual IPV at 9-month (AOR = 0.64, p = 0.03) and 18-month (AOR = 0.51, p = 0.004) follow-up, and attitudes accepting of physical IPV at 18-month follow-up (AOR = 0.64, p = 0.02). No significant effect on pregnancy was seen. Conclusions Findings demonstrate that men can be engaged in FP programming in rural India, and that such an approach inclusive of GE counseling can improve contraceptive practices and reduce sexual IPV in married couples. Trial Registration ClinicalTrials.gov NCT01593943 PMID:27167981

Synchronization states and multistability in a ring of periodic oscillators: Experimentally variable coupling delays

NASA Astrophysics Data System (ADS)

Williams, Caitlin R. S.; Sorrentino, Francesco; Murphy, Thomas E.; Roy, Rajarshi

2013-12-01

We experimentally study the complex dynamics of a unidirectionally coupled ring of four identical optoelectronic oscillators. The coupling between these systems is time-delayed in the experiment and can be varied over a wide range of delays. We observe that as the coupling delay is varied, the system may show different synchronization states, including complete isochronal synchrony, cluster synchrony, and two splay-phase states. We analyze the stability of these solutions through a master stability function approach, which we show can be effectively applied to all the different states observed in the experiment. Our analysis supports the experimentally observed multistability in the system.

Computational study on the molecular structures and photoelectron spectra of bimetallic oxide clusters MW2O9(-/0) (M=V, Nb, Ta).

PubMed

Chen, Wen-Jie; Zhang, Chang-Fu; Zhang, Xian-Hui; Zhang, Yong-Fan; Huang, Xin

2013-05-15

Density functional theory (DFT) and coupled cluster theory (CCSD(T)) calculations are carried out to investigate the electronic and structural properties of a series of bimetallic oxide clusters MW2O9(-/0) (M=V, Nb, Ta). Generalized Koopmans' theorem is applied to predict the vertical detachment energies (VDEs) and simulate the photoelectron spectra (PES). Theoretical calculations at the B3LYP level yield singlet and doublet ground states for the bimetallic anionic and neutral clusters, respectively. All the clusters present the six-membered ring structures with different symmetries, except that the TaW2O9(-) cluster shows a chained style with a penta-coordinated tantalum atom. Spin density analyses reveal oxygen radical species in all neutral clusters, consistent with their structural characteristics. Moreover, additional calculations are performed to study the oxidation reaction of CO molecule with the W3O9(+) cation and the isoelectronic VW2O9 cluster, and results indicate that the introduction of vanadium at tungsten site can efficiently improve the oxidation reactivity. Copyright © 2013 Elsevier B.V. All rights reserved.

Impact of symmetry breaking in networks of globally coupled oscillators

NASA Astrophysics Data System (ADS)

Premalatha, K.; Chandrasekar, V. K.; Senthilvelan, M.; Lakshmanan, M.

2015-05-01

We analyze the consequences of symmetry breaking in the coupling in a network of globally coupled identical Stuart-Landau oscillators. We observe that symmetry breaking leads to increased disorderliness in the dynamical behavior of oscillatory states and consequently results in a rich variety of dynamical states. Depending on the strength of the nonisochronicity parameter, we find various dynamical states such as amplitude chimera, amplitude cluster, frequency chimera, and frequency cluster states. In addition we also find disparate transition routes to recently observed chimera death states in the presence of symmetry breaking even with global coupling. We also analytically verify the chimera death region, which corroborates the numerical results. These results are compared with that of the symmetry-preserving case as well.

Characteristics of airflow and particle deposition in COPD current smokers

NASA Astrophysics Data System (ADS)

Zou, Chunrui; Choi, Jiwoong; Haghighi, Babak; Choi, Sanghun; Hoffman, Eric A.; Lin, Ching-Long

2017-11-01

A recent imaging-based cluster analysis of computed tomography (CT) lung images in a chronic obstructive pulmonary disease (COPD) cohort identified four clusters, viz. disease sub-populations. Cluster 1 had relatively normal airway structures; Cluster 2 had wall thickening; Cluster 3 exhibited decreased wall thickness and luminal narrowing; Cluster 4 had a significant decrease of luminal diameter and a significant reduction of lung deformation, thus having relatively low pulmonary functions. To better understand the characteristics of airflow and particle deposition in these clusters, we performed computational fluid and particle dynamics analyses on representative cluster patients and healthy controls using CT-based airway models and subject-specific 3D-1D coupled boundary conditions. The results show that particle deposition in central airways of cluster 4 patients was noticeably increased especially with increasing particle size despite reduced vital capacity as compared to other clusters and healthy controls. This may be attributable in part to significant airway constriction in cluster 4. This study demonstrates the potential application of cluster-guided CFD analysis in disease populations. NIH Grants U01HL114494 and S10-RR022421, and FDA Grant U01FD005837.

Dataset of Fourier transform-infrared coupled with chemometric analysis used to distinguish accessions of Garcinia mangostana L. in Peninsular Malaysia.

PubMed

Samsir, Sri A'jilah; Bunawan, Hamidun; Yen, Choong Chee; Noor, Normah Mohd

2016-09-01

In this dataset, we distinguish 15 accessions of Garcinia mangostana from Peninsular Malaysia using Fourier transform-infrared spectroscopy coupled with chemometric analysis. We found that the position and intensity of characteristic peaks at 3600-3100 cm(-) (1) in IR spectra allowed discrimination of G. mangostana from different locations. Further principal component analysis (PCA) of all the accessions suggests the two main clusters were formed: samples from Johor, Melaka, and Negeri Sembilan (South) were clustered together in one group while samples from Perak, Kedah, Penang, Selangor, Kelantan, and Terengganu (North and East Coast) were in another clustered group.

Coupled and extended quintessence: Theoretical differences and structure formation

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

Pettorino, Valeria; Baccigalupi, Carlo

2008-05-15

The case of a coupling between dark energy and matter [coupled quintessence (CQ)] or gravity [extended quintessence (EQ)] has recently attracted a deep interest and has been widely investigated both in the Einstein and in the Jordan frames (EF, JF), within scalar-tensor theories. Focusing on the simplest models proposed so far, in this paper we study the relation existing between the two scenarios, isolating the Weyl scaling which allows one to express them in the EF and JF. Moreover, we perform a comparative study of the behavior of linear perturbations in both scenarios, which turn out to behave in amore » markedly different way. In particular, while the clustering is enhanced in the considered CQ models with respect to the corresponding quintessence ones where the coupling is absent and to the ordinary cosmologies with a cosmological constant and cold dark matter ({lambda}CDM), structures in EQ models may grow slower. This is likely to have direct consequences on the inner properties of nonlinear structures, like cluster concentration, as well as on the weak lensing shear on large scales. Finally, we specialize our study for interfacing linear dynamics and N-body simulations in these cosmologies, giving a recipe for the corrections to be included in N-body codes in order to take into account the modifications to the expansion rate, growth of structures, and strength of gravity.« less

Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

NASA Astrophysics Data System (ADS)

Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

2018-05-01

We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

The electronic structure of vanadium monochloride cation (VCl+): Tackling the complexities of transition metal species

NASA Astrophysics Data System (ADS)

DeYonker, Nathan J.; Halfen, DeWayne T.; Allen, Wesley D.; Ziurys, Lucy M.

2014-11-01

Six electronic states (X 4Σ-, A 4Π, B 4Δ, 2Φ, 2Δ, 2Σ+) of the vanadium monochloride cation (VCl+) are described using large basis set coupled cluster theory. For the two lowest quartet states (X 4Σ- and A 4Π), a focal point analysis (FPA) approach was used that conjoined a correlation-consistent family of basis sets up to aug-cc-pwCV5Z-DK with high-order coupled cluster theory through pentuple (CCSDTQP) excitations. FPA adiabatic excitation energies (T0) and spectroscopic constants (re, r0, Be, B0, bar De, He, ωe, v0, αe, ωexe) were extrapolated to the valence complete basis set Douglas-Kroll (DK) aug-cc-pV∞Z-DK CCSDT level of theory, and additional treatments accounted for higher-order valence electron correlation, core correlation, and spin-orbit coupling. Due to the delicate interplay between dynamical and static electronic correlation, single reference coupled cluster theory is able to provide the correct ground electronic state (X 4Σ-), while multireference configuration interaction theory cannot. Perturbations from the first- and second-order spin orbit coupling of low-lying states with quartet spin multiplicity reveal an immensely complex rotational spectrum relative to the isovalent species VO, VS, and TiCl. Computational data on the doublet manifold suggest that the lowest-lying doublet state (2Γ) has a Te of ˜11 200 cm-1. Overall, this study shows that laboratory and theoretical rotational spectroscopists must work more closely in tandem to better understand the bonding and structure of molecules containing transition metals.

Low rank factorization of the Coulomb integrals for periodic coupled cluster theory.

PubMed

Hummel, Felix; Tsatsoulis, Theodoros; Grüneis, Andreas

2017-03-28

We study a tensor hypercontraction decomposition of the Coulomb integrals of periodic systems where the integrals are factorized into a contraction of six matrices of which only two are distinct. We find that the Coulomb integrals can be well approximated in this form already with small matrices compared to the number of real space grid points. The cost of computing the matrices scales as O(N 4 ) using a regularized form of the alternating least squares algorithm. The studied factorization of the Coulomb integrals can be exploited to reduce the scaling of the computational cost of expensive tensor contractions appearing in the amplitude equations of coupled cluster methods with respect to system size. We apply the developed methodologies to calculate the adsorption energy of a single water molecule on a hexagonal boron nitride monolayer in a plane wave basis set and periodic boundary conditions.

Optical properties of hybrid spherical nanoclusters containing quantum emitters and metallic nanoparticles

NASA Astrophysics Data System (ADS)

Yannopapas, V.; Paspalakis, E.

2018-05-01

We study theoretically the optical response of a hybrid spherical cluster containing quantum emitters and metallic nanoparticles. The quantum emitters are modeled as two-level quantum systems whose dielectric function is obtained via a density matrix approach wherein the modified spontaneous emission decay rate at the position of each quantum emitter is calculated via the electromagnetic Green's tensor. The problem of light scattering off the hybrid cluster is solved by employing the coupled-dipole method. We find, in particular, that the presence of the quantum emitters in the cluster, even in small fractions, can significantly alter the absorption and extinction spectra of the sole cluster of the metallic nanoparticles, where the corresponding electromagnetic modes can have a weak plexcitonic character under suitable conditions.

Using experimental data to test an n -body dynamical model coupled with an energy-based clusterization algorithm at low incident energies

NASA Astrophysics Data System (ADS)

Kumar, Rohit; Puri, Rajeev K.

2018-03-01

Employing the quantum molecular dynamics (QMD) approach for nucleus-nucleus collisions, we test the predictive power of the energy-based clusterization algorithm, i.e., the simulating annealing clusterization algorithm (SACA), to describe the experimental data of charge distribution and various event-by-event correlations among fragments. The calculations are constrained into the Fermi-energy domain and/or mildly excited nuclear matter. Our detailed study spans over different system masses, and system-mass asymmetries of colliding partners show the importance of the energy-based clusterization algorithm for understanding multifragmentation. The present calculations are also compared with the other available calculations, which use one-body models, statistical models, and/or hybrid models.

Metastable Autoionizing States of Molecules and Radicals in Highly Energetic Environment

DTIC Science & Technology

2016-03-22

electronic states. The specific aims are to develop and calibrate complex-scaled equation-of-motion coupled cluster (cs-EOM- CC ) and CAP (complex...absorbing potential) augmented EOM- CC methods. We have implemented and benchmarked cs-EOM-CCSD and CAP- augmented EOM-CCSD methods for excitation energies...motion coupled cluster (cs-EOM- CC ) and CAP (complex absorbing potential) augmented EOM- CC methods. We have implemented and benchmarked cs-EOM-CCSD and

Attenuated coupled cluster: a heuristic polynomial similarity transformation incorporating spin symmetry projection into traditional coupled cluster theory

NASA Astrophysics Data System (ADS)

Gomez, John A.; Henderson, Thomas M.; Scuseria, Gustavo E.

2017-11-01

In electronic structure theory, restricted single-reference coupled cluster (CC) captures weak correlation but fails catastrophically under strong correlation. Spin-projected unrestricted Hartree-Fock (SUHF), on the other hand, misses weak correlation but captures a large portion of strong correlation. The theoretical description of many important processes, e.g. molecular dissociation, requires a method capable of accurately capturing both weak and strong correlation simultaneously, and would likely benefit from a combined CC-SUHF approach. Based on what we have recently learned about SUHF written as particle-hole excitations out of a symmetry-adapted reference determinant, we here propose a heuristic CC doubles model to attenuate the dominant spin collective channel of the quadratic terms in the CC equations. Proof of principle results presented here are encouraging and point to several paths forward for improving the method further.

Partially linearized external models to active-space coupled-cluster through connected hextuple excitations.

PubMed

Xu, Enhua; Ten-No, Seiichiro L

2018-06-05

Partially linearized external models to active-space coupled-cluster through hextuple excitations, for example, CC{SDtqph} L , CCSD{tqph} L , and CCSD{tqph} hyb, are implemented and compared with the full active-space CCSDtqph. The computational scaling of CCSDtqph coincides with that for the standard coupled-cluster singles and doubles (CCSD), yet with a much large prefactor. The approximate schemes to linearize the external excitations higher than doubles are significantly cheaper than the full CCSDtqph model. These models are applied to investigate the bond dissociation energies of diatomic molecules (HF, F 2 , CuH, and CuF), and the potential energy surfaces of the bond dissociation processes of HF, CuH, H 2 O, and C 2 H 4 . Among the approximate models, CCSD{tqph} hyb provides very accurate descriptions compared with CCSDtqph for all of the tested systems. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

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.

Substructures in DAFT/FADA survey clusters based on XMM and optical data

NASA Astrophysics Data System (ADS)

Durret, F.; DAFT/FADA Team

2014-07-01

The DAFT/FADA survey was initiated to perform weak lensing tomography on a sample of 90 massive clusters in the redshift range [0.4,0.9] with HST imaging available. The complementary deep multiband imaging constitutes a high quality imaging data base for these clusters. In X-rays, we have analysed the XMM-Newton and/or Chandra data available for 32 clusters, and for 23 clusters we fit the X-ray emissivity with a beta-model and subtract it to search for substructures in the X-ray gas. This study was coupled with a dynamical analysis for the 18 clusters with at least 15 spectroscopic galaxy redshifts in the cluster range, based on a Serna & Gerbal (SG) analysis. We detected ten substructures in eight clusters by both methods (X-rays and SG). The percentage of mass included in substructures is found to be roughly constant with redshift, with values of 5-15%. Most of the substructures detected both in X-rays and with the SG method are found to be relatively recent infalls, probably at their first cluster pericenter approach.

Superexchange coupling and slow magnetic relaxation in a transuranium polymetallic complex.

PubMed

Magnani, N; Colineau, E; Eloirdi, R; Griveau, J-C; Caciuffo, R; Cornet, S M; May, I; Sharrad, C A; Collison, D; Winpenny, R E P

2010-05-14

{Np(VI)O2Cl2}{Np(V)O2Cl(thf)3}2 is the first studied example of a polymetallic transuranic complex displaying both slow relaxation of the magnetization and effective superexchange interactions between 5f centers. The coupling constant for Np(V)-Np(VI) pairs is 10.8 K, more than 1 order of magnitude larger than the common values found for rare-earth ions in similar environments. The dynamic magnetic behavior displays slow relaxation of magnetization of molecular origin with an energy barrier of 140 K, which is nearly twice the size of the highest barrier found in polymetallic clusters of the d block. Our observations also suggest that future actinide-based molecular magnets will have very different behavior to lanthanide-based clusters.

Theoretical study of the magnetic behavior of hexanuclear Cu(II) and Ni(II) polysiloxanolato complexes.

PubMed

Ruiz, Eliseo; Cano, Joan; Alvarez, Santiago; Caneschi, Andrea; Gatteschi, Dante

2003-06-04

A theoretical density functional study of the exchange coupling in hexanuclear polysiloxanolato-bridged complexes of Cu(II) and Ni(II) is presented. By calculating the energies of three different spin configurations, we can obtain estimates of the first-, second-, and third-neighbor exchange coupling constants. The study has been carried out for the complete structures of the Cu pristine cluster and of the chloroenclathrated Ni complex as well as for the hypotethical pristine Ni compound and for magnetically dinuclear analogues M(2)Zn(4) (M = Cu, Ni).

Emergent patterns in interacting neuronal sub-populations

NASA Astrophysics Data System (ADS)

Kamal, Neeraj Kumar; Sinha, Sudeshna

2015-05-01

We investigate an ensemble of coupled model neurons, consisting of groups of varying sizes and intrinsic dynamics, ranging from periodic to chaotic, where the inter-group coupling interaction is effectively like a dynamic signal from a different sub-population. We observe that the minority group can significantly influence the majority group. For instance, when a small chaotic group is coupled to a large periodic group, the chaotic group de-synchronizes. However, counter-intuitively, when a small periodic group couples strongly to a large chaotic group, it leads to complete synchronization in the majority chaotic population, which also spikes at the frequency of the small periodic group. It then appears that the small group of periodic neurons can act like a pacemaker for the whole network. Further, we report the existence of varied clustering patterns, ranging from sets of synchronized clusters to anti-phase clusters, governed by the interplay of the relative sizes and dynamics of the sub-populations. So these results have relevance in understanding how a group can influence the synchrony of another group of dynamically different elements, reminiscent of event-related synchronization/de-synchronization in complex networks.

The Structure and Stability of Bn(+) Clusters

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The geometries of B+n clusters for n less than 14 have been optimized using density functional theory with the B3LYP functional. The most stable structure for each cluster is planar or quasi-planar. The B3LYP fragmentation energies are calibrated using coupled cluster theory. Overall, our corrected fragmentation energies are in reasonable agreement with experiment. Our results are compared with previous theoretical results.

Mesenchymal stem cells and their conditioned medium improve integration of purified induced pluripotent stem cell-derived cardiomyocyte clusters into myocardial tissue.

PubMed

Rubach, Martin; Adelmann, Roland; Haustein, Moritz; Drey, Florian; Pfannkuche, Kurt; Xiao, Bing; Koester, Annette; Udink ten Cate, Floris E A; Choi, Yeong-Hoon; Neef, Klaus; Fatima, Azra; Hannes, Tobias; Pillekamp, Frank; Hescheler, Juergen; Šarić, Tomo; Brockmeier, Konrad; Khalil, Markus

2014-03-15

Induced pluripotent stem cell-derived cardiomyocytes (iPS-CMs) might become therapeutically relevant to regenerate myocardial damage. Purified iPS-CMs exhibit poor functional integration into myocardial tissue. The aim of this study was to investigate whether murine mesenchymal stem cells (MSCs) or their conditioned medium (MScond) improves the integration of murine iPS-CMs into myocardial tissue. Vital or nonvital embryonic murine ventricular tissue slices were cocultured with purified clusters of iPS-CMs in combination with murine embryonic fibroblasts (MEFs), MSCs, or MScond. Morphological integration was assessed by visual scoring and functional integration by isometric force and field potential measurements. We observed a moderate morphological integration of iPS-CM clusters into vital, but a poor integration into nonvital, slices. MEFs and MSCs but not MScond improved morphological integration of CMs into nonvital slices and enabled purified iPS-CMs to confer force. Coculture of vital slices with iPS-CMs and MEFs or MSCs resulted in an improved electrical integration. A comparable improvement of electrical coupling was achieved with the cell-free MScond, indicating that soluble factors secreted by MSCs were involved in electrical coupling. We conclude that cells such as MSCs support the engraftment and adhesion of CMs, and confer force to noncontractile tissue. Furthermore, soluble factors secreted by MSCs mediate electrical coupling of purified iPS-CM clusters to myocardial tissue. These data suggest that MSCs may increase the functional engraftment and therapeutic efficacy of transplanted iPS-CMs into infarcted myocardium.

Mesenchymal Stem Cells and Their Conditioned Medium Improve Integration of Purified Induced Pluripotent Stem Cell–Derived Cardiomyocyte Clusters into Myocardial Tissue

PubMed Central

Rubach, Martin; Adelmann, Roland; Haustein, Moritz; Drey, Florian; Pfannkuche, Kurt; Xiao, Bing; Koester, Annette; Udink ten Cate, Floris E.A.; Choi, Yeong-Hoon; Neef, Klaus; Fatima, Azra; Hannes, Tobias; Pillekamp, Frank; Hescheler, Juergen; Šarić, Tomo; Brockmeier, Konrad

2014-01-01

Induced pluripotent stem cell–derived cardiomyocytes (iPS-CMs) might become therapeutically relevant to regenerate myocardial damage. Purified iPS-CMs exhibit poor functional integration into myocardial tissue. The aim of this study was to investigate whether murine mesenchymal stem cells (MSCs) or their conditioned medium (MScond) improves the integration of murine iPS-CMs into myocardial tissue. Vital or nonvital embryonic murine ventricular tissue slices were cocultured with purified clusters of iPS-CMs in combination with murine embryonic fibroblasts (MEFs), MSCs, or MScond. Morphological integration was assessed by visual scoring and functional integration by isometric force and field potential measurements. We observed a moderate morphological integration of iPS-CM clusters into vital, but a poor integration into nonvital, slices. MEFs and MSCs but not MScond improved morphological integration of CMs into nonvital slices and enabled purified iPS-CMs to confer force. Coculture of vital slices with iPS-CMs and MEFs or MSCs resulted in an improved electrical integration. A comparable improvement of electrical coupling was achieved with the cell-free MScond, indicating that soluble factors secreted by MSCs were involved in electrical coupling. We conclude that cells such as MSCs support the engraftment and adhesion of CMs, and confer force to noncontractile tissue. Furthermore, soluble factors secreted by MSCs mediate electrical coupling of purified iPS-CM clusters to myocardial tissue. These data suggest that MSCs may increase the functional engraftment and therapeutic efficacy of transplanted iPS-CMs into infarcted myocardium. PMID:24219308

Weak Lensing Peaks in Simulated Light-Cones: Investigating the Coupling between Dark Matter and Dark Energy

NASA Astrophysics Data System (ADS)

Giocoli, Carlo; Moscardini, Lauro; Baldi, Marco; Meneghetti, Massimo; Metcalf, Robert B.

2018-05-01

In this paper, we study the statistical properties of weak lensing peaks in light-cones generated from cosmological simulations. In order to assess the prospects of such observable as a cosmological probe, we consider simulations that include interacting Dark Energy (hereafter DE) models with coupling term between DE and Dark Matter. Cosmological models that produce a larger population of massive clusters have more numerous high signal-to-noise peaks; among models with comparable numbers of clusters those with more concentrated haloes produce more peaks. The most extreme model under investigation shows a difference in peak counts of about 20% with respect to the reference ΛCDM model. We find that peak statistics can be used to distinguish a coupling DE model from a reference one with the same power spectrum normalisation. The differences in the expansion history and the growth rate of structure formation are reflected in their halo counts, non-linear scale features and, through them, in the properties of the lensing peaks. For a source redshift distribution consistent with the expectations of future space-based wide field surveys, we find that typically seventy percent of the cluster population contributes to weak-lensing peaks with signal-to-noise ratios larger than two, and that the fraction of clusters in peaks approaches one-hundred percent for haloes with redshift z ≤ 0.5. Our analysis demonstrates that peak statistics are an important tool for disentangling DE models by accurately tracing the structure formation processes as a function of the cosmic time.

Consensus of satellite cluster flight using an energy-matching optimal control method

NASA Astrophysics Data System (ADS)

Luo, Jianjun; Zhou, Liang; Zhang, Bo

2017-11-01

This paper presents an optimal control method for consensus of satellite cluster flight under a kind of energy matching condition. Firstly, the relation between energy matching and satellite periodically bounded relative motion is analyzed, and the satellite energy matching principle is applied to configure the initial conditions. Then, period-delayed errors are adopted as state variables to establish the period-delayed errors dynamics models of a single satellite and the cluster. Next a novel satellite cluster feedback control protocol with coupling gain is designed, so that the satellite cluster periodically bounded relative motion consensus problem (period-delayed errors state consensus problem) is transformed to the stability of a set of matrices with the same low dimension. Based on the consensus region theory in the research of multi-agent system consensus issues, the coupling gain can be obtained to satisfy the requirement of consensus region and decouple the satellite cluster information topology and the feedback control gain matrix, which can be determined by Linear quadratic regulator (LQR) optimal method. This method can realize the consensus of satellite cluster period-delayed errors, leading to the consistency of semi-major axes (SMA) and the energy-matching of satellite cluster. Then satellites can emerge the global coordinative cluster behavior. Finally the feasibility and effectiveness of the present energy-matching optimal consensus for satellite cluster flight is verified through numerical simulations.

Ground-state phase diagram in the Kugel-Khomskii model with finite spin-orbit interactions

NASA Astrophysics Data System (ADS)

Koga, Akihisa; Nakauchi, Shiryu; Nasu, Joji

2018-05-01

We study ground-state properties in the Kugel-Khomskii model on the two-dimensional honeycomb lattice. Using the cluster mean-field approximations, we deal with the exchange and spin-orbit couplings on an equal footing. We then discuss the stability of the ferromagnetically ordered states against the nonmagnetic state, which is adiabatically connected to the quantum spin liquid state realized in a strong spin-orbit coupling limit.

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

Wykes, M., E-mail: mikewykes@gmail.com; Parambil, R.; Gierschner, J.

Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescencemore » spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.« less

A quasiparticle-based multi-reference coupled-cluster method.

PubMed

Rolik, Zoltán; Kállay, Mihály

2014-10-07

The purpose of this paper is to introduce a quasiparticle-based multi-reference coupled-cluster (MRCC) approach. The quasiparticles are introduced via a unitary transformation which allows us to represent a complete active space reference function and other elements of an orthonormal multi-reference (MR) basis in a determinant-like form. The quasiparticle creation and annihilation operators satisfy the fermion anti-commutation relations. On the basis of these quasiparticles, a generalization of the normal-ordered operator products for the MR case can be introduced as an alternative to the approach of Mukherjee and Kutzelnigg [Recent Prog. Many-Body Theor. 4, 127 (1995); Mukherjee and Kutzelnigg, J. Chem. Phys. 107, 432 (1997)]. Based on the new normal ordering any quasiparticle-based theory can be formulated using the well-known diagram techniques. Beyond the general quasiparticle framework we also present a possible realization of the unitary transformation. The suggested transformation has an exponential form where the parameters, holding exclusively active indices, are defined in a form similar to the wave operator of the unitary coupled-cluster approach. The definition of our quasiparticle-based MRCC approach strictly follows the form of the single-reference coupled-cluster method and retains several of its beneficial properties. Test results for small systems are presented using a pilot implementation of the new approach and compared to those obtained by other MR methods.

Molecules based on M(v) (M=Mo, W) and Ni(II) ions: a new class of trigonal bipyramidal cluster and confirmation of SMM behavior for the pentadecanuclear molecule {NiII[NiII(tmphen)(MeOH)]6[Ni(H2O)3]2[micro-CN]30[WV(CN)3]6}.

PubMed

Hilfiger, Matthew G; Zhao, Hanhua; Prosvirin, Andrey; Wernsdorfer, Wolfgang; Dunbar, Kim R

2009-07-14

The preparation, single crystal X-ray crystallography, and magnetic properties are reported for four new clusters based on [M'V(CN)8]3- octacyanometallates (M'=Mo, W). Reactions of [M'V(CN)8]3- with mononuclear NiII ions in the presence of the tmphen blocking ligand (tmphen=3,4,7,8-tetramethyl-1,10-phenanthroline) in a 2:3:6 ratio, respectively, lead to the formation of the trigonal bipyramidal clusters [NiII(tmphen)2]3[M'V(CN)8]2. Analogous reactions with the same starting materials performed in a 2:3:2 ratio, respectively, produce pentadecanuclear clusters of the type {NiII[NiII(tmphen)(MeOH)]6[Ni(H2O)3]2[micro-CN]30[WV(CN)3]6}. The W2Ni3 (1) and Mo2Ni3(2) pentanuclear clusters and the W6Ni9 (3) and Mo6Ni9 (4) pentadecanuclear molecules are isostructural to each other and crystallize in the space groups P2(1)/c and R3 respectively. Magnetic measurements indicate that the ground states for the trigonal bipyamidal clusters are S=4 as a consequence of ferromagnetic coupling with JW-Ni=9.5 cm(-1), JMo-Ni=10 cm(-1). The pentadecanuclear clusters exhibit ferromagnetic coupling as well, which leads to S=12 ground states (JW-Ni=12 cm(-1), JMo-Ni=12.2 cm(-1)). Reduced magnetization studies on the W-Ni analogues support the conclusion that they exhibit a negative axial anisotropy term; the fits give D values of -0.24 cm(-1) for the W2Ni3 cluster and D=-0.04 cm(-1)for the W6Ni9 cluster. AC susceptibility measurements indicate the beginning of an out-of-phase signal for the W2Ni3 and the W6Ni9 compounds, but detailed low temperature studies on small crystals by the microSQUID technique indicate that only the pentadecanuclear cluster exhibits hysteresis in accord with SMM behavior. Neither Mo cluster reveals any evidence for slow paramagnetic relaxation at low temperatures.

A comparison of the coupled cluster and internally contracted averaged coupled-pair functional levels of theory for the calculation of the MCH2(+) binding energies for M = Sc to Cu

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Scuseria, Gustavo E.

1992-01-01

The correlation contribution to the M-C binding energy for the MCH2(+) systems can exceed 100 kcal/mol. At the self-consistent field (SCF) level, these systems can be more than 50 kcal/mol above the fragment energies. In spite of the poor zeroth-order reference, the coupled cluster single and double excitation method with a perturbational estimate of triple excitations, CCSD(T), method is shown to provide an accurate description of these systems. The maximum difference between the CCSD(T) and internally contracted averaged coupled-pair functional binding energies is 1.5 kcal/mol for CrCH2(+), with the remaining systems agreeing to within 1.0 kcal/mol.

Spatially explicit population estimates for black bears based on cluster sampling

USGS Publications Warehouse

Humm, J.; McCown, J. Walter; Scheick, B.K.; Clark, Joseph D.

2017-01-01

We estimated abundance and density of the 5 major black bear (Ursus americanus) subpopulations (i.e., Eglin, Apalachicola, Osceola, Ocala-St. Johns, Big Cypress) in Florida, USA with spatially explicit capture-mark-recapture (SCR) by extracting DNA from hair samples collected at barbed-wire hair sampling sites. We employed a clustered sampling configuration with sampling sites arranged in 3 × 3 clusters spaced 2 km apart within each cluster and cluster centers spaced 16 km apart (center to center). We surveyed all 5 subpopulations encompassing 38,960 km2 during 2014 and 2015. Several landscape variables, most associated with forest cover, helped refine density estimates for the 5 subpopulations we sampled. Detection probabilities were affected by site-specific behavioral responses coupled with individual capture heterogeneity associated with sex. Model-averaged bear population estimates ranged from 120 (95% CI = 59–276) bears or a mean 0.025 bears/km2 (95% CI = 0.011–0.44) for the Eglin subpopulation to 1,198 bears (95% CI = 949–1,537) or 0.127 bears/km2 (95% CI = 0.101–0.163) for the Ocala-St. Johns subpopulation. The total population estimate for our 5 study areas was 3,916 bears (95% CI = 2,914–5,451). The clustered sampling method coupled with information on land cover was efficient and allowed us to estimate abundance across extensive areas that would not have been possible otherwise. Clustered sampling combined with spatially explicit capture-recapture methods has the potential to provide rigorous population estimates for a wide array of species that are extensive and heterogeneous in their distribution.

Copper Efflux Is Induced during Anaerobic Amino Acid Limitation in Escherichia coli To Protect Iron-Sulfur Cluster Enzymes and Biogenesis

PubMed Central

Fung, Danny Ka Chun; Lau, Wai Yin; Chan, Wing Tat

2013-01-01

Adaptation to changing environments is essential to bacterial physiology. Here we report a unique role of the copper homeostasis system in adapting Escherichia coli to its host-relevant environment of anaerobiosis coupled with amino acid limitation. We found that expression of the copper/silver efflux pump CusCFBA was significantly upregulated during anaerobic amino acid limitation in E. coli without the supplement of exogenous copper. Inductively coupled plasma mass spectrometry analysis of the total intracellular copper content combined with transcriptional assay of the PcusC-lacZ reporter in the presence of specific Cu(I) chelators indicated that anaerobic amino acid limitation led to the accumulation of free Cu(I) in the periplasmic space of E. coli, resulting in Cu(I) toxicity. Cells lacking cusCFBA and another copper transporter, copA, under this condition displayed growth defects and reduced ATP production during fumarate respiration. Ectopic expression of the Fe-S cluster enzyme fumarate reductase (Frd), or supplementation with amino acids whose biosynthesis involves Fe-S cluster enzymes, rescued the poor growth of ΔcusC cells. Yet, Cu(I) treatment did not impair the Frd activity in vitro. Further studies revealed that the alternative Fe-S cluster biogenesis system Suf was induced during the anaerobic amino acid limitation, and ΔcusC enhanced this upregulation, indicating the impairment of the Fe-S cluster assembly machinery and the increased Fe-S cluster demands under this condition. Taken together, we conclude that the copper efflux system CusCFBA is induced during anaerobic amino acid limitation to protect Fe-S cluster enzymes and biogenesis from the endogenously originated Cu(I) toxicity, thus facilitating the physiological adaptation of E. coli. PMID:23893112

Effect of non-monetary incentives on uptake of couples' counselling and testing among clients attending mobile HIV services in rural Zimbabwe: a cluster-randomised trial.

PubMed

Sibanda, Euphemia L; Tumushime, Mary; Mufuka, Juliet; Mavedzenge, Sue Napierala; Gudukeya, Stephano; Bautista-Arredondo, Sergio; Hatzold, Karin; Thirumurthy, Harsha; McCoy, Sandra I; Padian, Nancy; Copas, Andrew; Cowan, Frances M

2017-09-01

Couples' HIV testing and counselling (CHTC) is associated with greater engagement with HIV prevention and care than individual testing and is cost-effective, but uptake remains suboptimal. Initiating discussion of CHTC might result in distrust between partners. Offering incentives for CHTC could change the focus of the pre-test discussion. We aimed to determine the impact of incentives for CHTC on uptake of couples testing and HIV case diagnosis in rural Zimbabwe. In this cluster-randomised trial, 68 rural communities (the clusters) in four districts receiving mobile HIV testing services were randomly assigned (1:1) to incentives for CHTC or not. Allocation was not masked to participants and researchers. Randomisation was stratified by district and proximity to a health facility. Within each stratum random permutation was done to allocate clusters to the study groups. In intervention communities, residents were informed that couples who tested together could select one of three grocery items worth US$1·50. Standard mobilisation for testing was done in comparison communities. The primary outcome was the proportion of individuals testing with a partner. Analysis was by intention to treat. 3 months after CHTC, couple-testers from four communities per group individually completed a telephone survey to evaluate any social harms resulting from incentives or CHTC. The effect of incentives on CHTC was estimated using logistic regression with random effects adjusting for clustering. The trial was registered with the Pan African Clinical Trial Registry, number PACTR201606001630356. From May 26, 2015, to Jan 29, 2016, of 24 679 participants counselled with data recorded, 14 099 (57·1%) were in the intervention group and 10 580 (42·9%) in the comparison group. 7852 (55·7%) testers in the intervention group versus 1062 (10·0%) in the comparison group tested with a partner (adjusted odds ratio 13·5 [95% CI 10·5-17·4]). Among 427 (83·7%) of 510 eligible participants who completed the telephone survey, 11 (2·6%) reported that they were pressured or themselves pressured their partner to test together; none regretted couples' testing. Relationship unrest was reported by eight individuals (1·9%), although none attributed this to incentives. Small non-monetary incentives, which are potentially scalable, were associated with significantly increased CHTC and HIV case diagnosis. Incentives did not increase social harms beyond the few typically encountered with CHTC without incentives. The intervention could help achieve UNAIDS 90-90-90 targets. The study was funded by the UK Department for International Development, Irish AID, and Swedish SIDA, through Population Services International Zimbabwe under the Integrated Support Program. Copyright © 2017 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 license. Published by Elsevier Ltd.. All rights reserved.

Analysis of Fiber Clustering in Composite Materials Using High-Fidelity Multiscale Micromechanics

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Aboudi, Jacob; Arnold, Steven M.

2015-01-01

A new multiscale micromechanical approach is developed for the prediction of the behavior of fiber reinforced composites in presence of fiber clustering. The developed method is based on a coupled two-scale implementation of the High-Fidelity Generalized Method of Cells theory, wherein both the local and global scales are represented using this micromechanical method. Concentration tensors and effective constitutive equations are established on both scales and linked to establish the required coupling, thus providing the local fields throughout the composite as well as the global properties and effective nonlinear response. Two nondimensional parameters, in conjunction with actual composite micrographs, are used to characterize the clustering of fibers in the composite. Based on the predicted local fields, initial yield and damage envelopes are generated for various clustering parameters for a polymer matrix composite with both carbon and glass fibers. Nonlinear epoxy matrix behavior is also considered, with results in the form of effective nonlinear response curves, with varying fiber clustering and for two sets of nonlinear matrix parameters.

Exploring personality clusters among parents of ED subjects. Relationship with parents' psychopathology, attachment, and family dynamics.

PubMed

Amianto, Federico; Daga, Giovanni Abbate; Bertorello, Antonella; Fassino, Secondo

2013-10-01

Eating disorders are some of the most difficult mental disorders to treat and manage. Family interacts with genetic dispositions and other pathogenic factors, and may influence the outburst, development and outcome of EDs. The present study explores with a cluster analysis the personality traits of parents of ED subjects. One-hundred-eight mothers and 104 fathers were tested with Temperament Character Inventory (TCI), Eating Disorder Inventory-2 (EDI-2), State-Trait Anger Expression Inventory (STAX), Family Assessment Device (FAD), Attachment Style Questionnaire (ASQ), Symptom Questionnaire (SQ), Psychological Well-Being scales (PWB). The cluster distribution of parents based on personality traits was explored. Parents' clusters TCI scores were compared as regards personality, psychopathology, attachment and family features. Cross distribution of temperament and character clusters in mothers and fathers, among couples and ED diagnoses of the daughters was explored. Two clusters of mothers and fathers were identified with temperament clustering. Character traits led to two mothers and three fathers clusters. Mothers temperament cluster 1 (MTC1) correspond to a explosive/adventurous profile, MTC2 to a cautious/passive-dependent profile. Fathers temperament cluster 1 (FTC1) was explosive/methodic, FTC2 was independent/methodic. Character clustering distinguished very immature mothers (MCC1) and majority (65%) of character mature mothers with low self-transcendence (MCC2). A third of fathers was severely immature (FCC1), a third impaired as regards relationships (poor cooperativeness and self-transcendence; FCC2), and one third character mature fathers with low self-transcendence (FCC3). Each cluster evidences specific psychopathology and attachment characteristics. FTC1 was more frequently associated with character immaturity. No significant clusters' cross correlation was found in parental couples. Parents' clusters analyze in depth the univocal picture of prototypical mothers and fathers of EDs. Parents not disturbed as regards personality traits are not exceptions. Since EDs are multifactor disorders family dynamics related to parents' personality may be very relevant or even marginal in their pathogenesis. Conversely, parenting may be negatively influenced by relatively marginal personality malfunctions of parents. The clustering approach to the complexity of personality-related dynamics of ED families improves the picture of ED parents. Psychoeducational, counseling and psychotherapeutic family interventions should consider the specific underlying personality of parents. Copyright © 2013 Elsevier Inc. All rights reserved.

Development of a Typology of Dual-Earner Couples Caring for Children and Aging Parents

ERIC Educational Resources Information Center

Cullen, Jennifer C.; Hammer, Leslie B.; Neal, Margaret B.; Sinclair, Robert R.

2009-01-01

Using a national sample of 267 couples, the authors identify distinct profiles of dual-earner couples in the sandwiched generation (i.e., those caring for children and aging parents) using cluster analysis and then assess the relationship between these profiles and work-family conflict. The profiles are defined by characteristics of couples' child…

Complex and unexpected dynamics in simple genetic regulatory networks

NASA Astrophysics Data System (ADS)

Borg, Yanika; Ullner, Ekkehard; Alagha, Afnan; Alsaedi, Ahmed; Nesbeth, Darren; Zaikin, Alexey

2014-03-01

One aim of synthetic biology is to construct increasingly complex genetic networks from interconnected simpler ones to address challenges in medicine and biotechnology. However, as systems increase in size and complexity, emergent properties lead to unexpected and complex dynamics due to nonlinear and nonequilibrium properties from component interactions. We focus on four different studies of biological systems which exhibit complex and unexpected dynamics. Using simple synthetic genetic networks, small and large populations of phase-coupled quorum sensing repressilators, Goodwin oscillators, and bistable switches, we review how coupled and stochastic components can result in clustering, chaos, noise-induced coherence and speed-dependent decision making. A system of repressilators exhibits oscillations, limit cycles, steady states or chaos depending on the nature and strength of the coupling mechanism. In large repressilator networks, rich dynamics can also be exhibited, such as clustering and chaos. In populations of Goodwin oscillators, noise can induce coherent oscillations. In bistable systems, the speed with which incoming external signals reach steady state can bias the network towards particular attractors. These studies showcase the range of dynamical behavior that simple synthetic genetic networks can exhibit. In addition, they demonstrate the ability of mathematical modeling to analyze nonlinearity and inhomogeneity within these systems.

[Application of Kohonen Self-Organizing Feature Maps in QSAR of human ADMET and kinase data sets].

PubMed

Hegymegi-Barakonyi, Bálint; Orfi, László; Kéri, György; Kövesdi, István

2013-01-01

QSAR predictions have been proven very useful in a large number of studies for drug design, such as kinase inhibitor design as targets for cancer therapy, however the overall predictability often remains unsatisfactory. To improve predictability of ADMET features and kinase inhibitory data, we present a new method using Kohonen's Self-Organizing Feature Map (SOFM) to cluster molecules based on explanatory variables (X) and separate dissimilar ones. We calculated SOFM clusters for a large number of molecules with human ADMET and kinase inhibitory data, and we showed that chemically similar molecules were in the same SOFM cluster, and within such clusters the QSAR models had significantly better predictability. We used also target variables (Y, e.g. ADMET) jointly with X variables to create a novel type of clustering. With our method, cells of loosely coupled XY data could be identified and separated into different model building sets.

Nature of phase transitions in Axelrod-like coupled Potts models in two dimensions

NASA Astrophysics Data System (ADS)

Gandica, Yerali; Chiacchiera, Silvia

2016-03-01

We study F coupled q -state Potts models in a two-dimensional square lattice. The interaction between the different layers is attractive to favor a simultaneous alignment in all of them, and its strength is fixed. The nature of the phase transition for zero field is numerically determined for F =2 ,3 . Using the Lee-Kosterlitz method, we find that it is continuous for F =2 and q =2 , whereas it is abrupt for higher values of q and/or F . When a continuous or a weakly first-order phase transition takes place, we also analyze the properties of the geometrical clusters. This allows us to determine the fractal dimension D of the incipient infinite cluster and to examine the finite-size scaling of the cluster number density via data collapse. A mean-field approximation of the model, from which some general trends can be determined, is presented too. Finally, since this lattice model has been recently considered as a thermodynamic counterpart of the Axelrod model of social dynamics, we discuss our results in connection with this one.

Nature of phase transitions in Axelrod-like coupled Potts models in two dimensions.

PubMed

Gandica, Yerali; Chiacchiera, Silvia

2016-03-01

We study F coupled q-state Potts models in a two-dimensional square lattice. The interaction between the different layers is attractive to favor a simultaneous alignment in all of them, and its strength is fixed. The nature of the phase transition for zero field is numerically determined for F = 2,3. Using the Lee-Kosterlitz method, we find that it is continuous for F = 2 and q = 2, whereas it is abrupt for higher values of q and/or F. When a continuous or a weakly first-order phase transition takes place, we also analyze the properties of the geometrical clusters. This allows us to determine the fractal dimension D of the incipient infinite cluster and to examine the finite-size scaling of the cluster number density via data collapse. A mean-field approximation of the model, from which some general trends can be determined, is presented too. Finally, since this lattice model has been recently considered as a thermodynamic counterpart of the Axelrod model of social dynamics, we discuss our results in connection with this one.

Large resistance change on magnetic tunnel junction based molecular spintronics devices

NASA Astrophysics Data System (ADS)

Tyagi, Pawan; Friebe, Edward

2018-05-01

Molecular bridges covalently bonded to two ferromagnetic electrodes can transform ferromagnetic materials and produce intriguing spin transport characteristics. This paper discusses the impact of molecule induced strong coupling on the spin transport. To study molecular coupling effect the octametallic molecular cluster (OMC) was bridged between two ferromagnetic electrodes of a magnetic tunnel junction (Ta/Co/NiFe/AlOx/NiFe/Ta) along the exposed side edges. OMCs induced strong inter-ferromagnetic electrode coupling to yield drastic changes in transport properties of the magnetic tunnel junction testbed at the room temperature. These OMCs also transformed the magnetic properties of magnetic tunnel junctions. SQUID and ferromagnetic resonance studies provided insightful data to explain transport studies on the magnetic tunnel junction based molecular spintronics devices.

Solar Wind/Magnetosphere/Ionosphere Coupling and the Temporal and Spatial Evolution of Boundary Layers using Cluster, Polar and other ISTP Satellites

NASA Technical Reports Server (NTRS)

Maynard, Nelson C.

2004-01-01

Our analysis concerns macro and meso-scale aspects of coupling between the IMF and the magnetosphere-ionosphere system, as opposed to the microphysics of determining how electron gyrotropy is broken and merging actually occurs. We correlate observed behaviors at Cluster and at Polar with temporal variations in other regions, such as in the ionosphere as measured by SuperDARN. Addressing problems with simultaneous observations from diverse locations properly constrains our interpretations.

Systematic design of active spaces for multi-reference calculations of singlet-triplet gaps of organic diradicals, with benchmarks against doubly electron-attached coupled-cluster data

NASA Astrophysics Data System (ADS)

Stoneburner, Samuel J.; Shen, Jun; Ajala, Adeayo O.; Piecuch, Piotr; Truhlar, Donald G.; Gagliardi, Laura

2017-10-01

Singlet-triplet gaps in diradical organic π-systems are of interest in many applications. In this study, we calculate them in a series of molecules, including cyclobutadiene and its derivatives and cyclopentadienyl cation, by using correlated participating orbitals within the complete active space (CAS) and restricted active space (RAS) self-consistent field frameworks, followed by second-order perturbation theory (CASPT2 and RASPT2). These calculations are evaluated by comparison with the results of doubly electron-attached (DEA) equation-of-motion (EOM) coupled-cluster (CC) calculations with up to 4-particle-2-hole (4p-2h) excitations. We find active spaces that can accurately reproduce the DEA-EOMCC(4p-2h) data while being small enough to be applicable to larger organic diradicals.

Dispersion correction derived from first principles for density functional theory and Hartree-Fock theory.

PubMed

Guidez, Emilie B; Gordon, Mark S

2015-03-12

The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost.

Classical plasma dynamics of Mie-oscillations in atomic clusters

NASA Astrophysics Data System (ADS)

Kull, H.-J.; El-Khawaldeh, A.

2018-04-01

Mie plasmons are of basic importance for the absorption of laser light by atomic clusters. In this work we first review the classical Rayleigh-theory of a dielectric sphere in an external electric field and Thomson’s plum-pudding model applied to atomic clusters. Both approaches allow for elementary discussions of Mie oscillations, however, they also indicate deficiencies in describing the damping mechanisms by electrons crossing the cluster surface. Nonlinear oscillator models have been widely studied to gain an understanding of damping and absorption by outer ionization of the cluster. In the present work, we attempt to address the issue of plasmon relaxation in atomic clusters in more detail based on classical particle simulations. In particular, we wish to study the role of thermal motion on plasmon relaxation, thereby extending nonlinear models of collective single-electron motion. Our simulations are particularly adopted to the regime of classical kinetics in weakly coupled plasmas and to cluster sizes extending the Debye-screening length. It will be illustrated how surface scattering leads to the relaxation of Mie oscillations in the presence of thermal motion and of electron spill-out at the cluster surface. This work is intended to give, from a classical perspective, further insight into recent work on plasmon relaxation in quantum plasmas [1].

Reactivity of Cubane-Type [(OC)(3)MFe(3)S(4)(SR)(3)](3-) Clusters (M = Mo, W): Interconversion with Cuboidal [Fe(3)S(4)](0) Clusters and Electron Transfer.

PubMed

Raebiger, James W.; Crawford, Charles A.; Zhou, Jian; Holm, R. H.

1997-03-12

The title clusters, several examples of which have been reported earlier, have been prepared by two different methods and subjected to structural and reactivity studies. The compounds (Et(4)N)(3)[(OC)(3)MFe(3)S(4)(Smes)(3)].MeCN (M = Mo/W) are isomorphous and crystallize in monoclinic space group P2(1)/n with a = 13.412(1)/13.297(1) Å, b = 19.0380(1)/18.9376(3) Å, c = 26.4210(1)/26.2949(1) Å, beta = 97.87(1)/97.549(1) degrees, and Z = 4. The clusters contain long M-S (2.62/2.59 Å) and M-Fe (3.22/3.19 Å) bonds, consistent with the reported structure of [(OC)(3)MoFe(3)S(4)(SEt)(3)](3-) (3). Reaction of [(OC)(3)MoFe(3)S(4)(LS(3))](3-) (7) with CO in the presence of NaPF(6) affords cuboidal [Fe(3)S(4)(LS(3))](3-) (9), also prepared in this laboratory by another route as a synthetic analogue of protein-bound [Fe(3)S(4)](0) clusters. The clusters [Fe(3)S(4)(SR)(3)](3-) (R = mes, Et), of limited stability, were generated by the same reaction. Treatment of 9 with [M(CO)(3)(MeCN)(3)] affords 7 and its M = W analogue. The clusters [(OC)(3)MFe(3)S(4)(SR)(3)](3-) form a four-member electron transfer series in which the 3- cluster can be once reduced (4-) and twice oxidized (2-, 1-) to afford clusters of the indicated charges. The correct assignment of redox couple to potential in the redox series of six clusters is presented, correcting an earlier misassignment of the redox series of 3. Carbonyl stretching frequencies are shown to be sensitive to cluster oxidation state, showing that the M sites and Fe(3)S(4) fragments are electronically coupled despite the long bond distances. (LS(3) = 1,3,5-tris((4,6-dimethyl-3-mercaptophenyl)thio)-2,4,6-tris(p-tolylthio)benzenate(3-); mes = mesityl.)

Optical potential from first principles

DOE PAGES

Rotureau, J.; Danielewicz, P.; Hagen, G.; ...

2017-02-15

Here, we develop a method to construct a microscopic optical potential from chiral interactions for nucleon-nucleus scattering. The optical potential is constructed by combining the Green’s function approach with the coupled-cluster method. To deal with the poles of the Green’s function along the real energy axis we employ a Berggren basis in the complex energy plane combined with the Lanczos method. Using this approach, we perform a proof-of-principle calculation of the optical potential for the elastic neutron scattering on 16O. For the computation of the ground-state of 16O, we use the coupled-cluster method in the singles-and-doubles approximation, while for themore » A ±1 nuclei we use particle-attached/removed equation-of-motion method truncated at two-particle-one-hole and one-particle-two-hole excitations, respectively. We verify the convergence of the optical potential and scattering phase shifts with respect to the model-space size and the number of discretized complex continuum states. We also investigate the absorptive component of the optical potential (which reflects the opening of inelastic channels) by computing its imaginary volume integral and find an almost negligible absorptive component at low-energies. To shed light on this result, we computed excited states of 16O using equation-of-motion coupled-cluster method with singles-and- doubles excitations and we found no low-lying excited states below 10 MeV. Furthermore, most excited states have a dominant two-particle-two-hole component, making higher-order particle-hole excitations necessary to achieve a precise description of these core-excited states. We conclude that the reduced absorption at low-energies can be attributed to the lack of correlations coming from the low-order cluster truncation in the employed coupled-cluster method.« less

Cooperative Jahn-Teller phase transition of icosahedral molecular units

NASA Astrophysics Data System (ADS)

Nasrollahi, Seyed H.; Vvedensky, Dimitri D.

2017-02-01

Non-linear molecules undergo distortions when the orbital degeneracy of the highest occupied level is lifted by the Jahn-Teller effect. If such molecules or clusters of atoms are coupled to one another, the system may experience a cooperative Jahn-Teller effect (CJTE). In this paper, we describe a model of how the CJTE leads to the crystallization of the disordered phase. The model Hamiltonian is based on a normal mode decomposition of the clusters in order to maintain the symmetry labels. We take account of the electron-strain and the electron-phonon couplings and, by displacing the coordinates of the oscillators, obtain a term that explicitly couples the Jahn-Teller centers, enabling us to perform a mean-field analysis. The calculation of the free energy then becomes straightforward, and obtaining phase diagrams in various regimes follows from the minimization of this free energy. The results show that the character of the phase transition may change from strong to weak first order and even to second-order, depending on the coupling to the vibrational modes. Taken together, these results may serve as a paradigm for crystallization near the transition temperature, where the atoms tend to form clusters of icosahedral symmetry.

A new scheme for perturbative triples correction to (0,1) sector of Fock space multi-reference coupled cluster method: theory, implementation, and examples.

PubMed

Dutta, Achintya Kumar; Vaval, Nayana; Pal, Sourav

2015-01-28

We propose a new elegant strategy to implement third order triples correction in the light of many-body perturbation theory to the Fock space multi-reference coupled cluster method for the ionization problem. The computational scaling as well as the storage requirement is of key concerns in any many-body calculations. Our proposed approach scales as N(6) does not require the storage of triples amplitudes and gives superior agreement over all the previous attempts made. This approach is capable of calculating multiple roots in a single calculation in contrast to the inclusion of perturbative triples in the equation of motion variant of the coupled cluster theory, where each root needs to be computed in a state-specific way and requires both the left and right state vectors together. The performance of the newly implemented scheme is tested by applying to methylene, boron nitride (B2N) anion, nitrogen, water, carbon monoxide, acetylene, formaldehyde, and thymine monomer, a DNA base.

Bridging single and multireference coupled cluster theories with universal state selective formalism

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

Bhaskaran-Nair, Kiran; Kowalski, Karol

2013-05-28

The universal state selective (USS) multireference approach is used to construct new energy functionals which offers a unique possibility of bridging single and multireference coupled cluster theories (SR/MRCC). These functionals, which can be used to develop iterative and non-iterative approaches, utilize a special form of the trial wavefunctions, which assure additive separability (or size-consistency) of the USS energies in the non-interacting subsystem limit. When the USS formalism is combined with approximate SRCC theories, the resulting formalism can be viewed as a size-consistent version of the method of moments of coupled cluster equations (MMCC) employing a MRCC trial wavefunction. Special casesmore » of the USS formulations, which utilize single reference state specific CC (V.V. Ivanov, D.I. Lyakh, L. Adamowicz, Phys. Chem. Chem. Phys. 11, 2355 (2009)) and tailored CC (T. Kinoshita, O. Hino, R.J. Bartlett, J. Chem. Phys. 123, 074106 (2005)) expansions are also discussed.« less

Modeling tensional homeostasis in multicellular clusters.

PubMed

Tam, Sze Nok; Smith, Michael L; Stamenović, Dimitrije

2017-03-01

Homeostasis of mechanical stress in cells, or tensional homeostasis, is essential for normal physiological function of tissues and organs and is protective against disease progression, including atherosclerosis and cancer. Recent experimental studies have shown that isolated cells are not capable of maintaining tensional homeostasis, whereas multicellular clusters are, with stability increasing with the size of the clusters. Here, we proposed simple mathematical models to interpret experimental results and to obtain insight into factors that determine homeostasis. Multicellular clusters were modeled as one-dimensional arrays of linearly elastic blocks that were either jointed or disjointed. Fluctuating forces that mimicked experimentally measured cell-substrate tractions were obtained from Monte Carlo simulations. These forces were applied to the cluster models, and the corresponding stress field in the cluster was calculated by solving the equilibrium equation. It was found that temporal fluctuations of the cluster stress field became attenuated with increasing cluster size, indicating that the cluster approached tensional homeostasis. These results were consistent with previously reported experimental data. Furthermore, the models revealed that key determinants of tensional homeostasis in multicellular clusters included the cluster size, the distribution of traction forces, and mechanical coupling between adjacent cells. Based on these findings, we concluded that tensional homeostasis was a multicellular phenomenon. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Desynchronization boost by non-uniform coordinated reset stimulation in ensembles of pulse-coupled neurons

PubMed Central

Lücken, Leonhard; Yanchuk, Serhiy; Popovych, Oleksandr V.; Tass, Peter A.

2013-01-01

Several brain diseases are characterized by abnormal neuronal synchronization. Desynchronization of abnormal neural synchrony is theoretically compelling because of the complex dynamical mechanisms involved. We here present a novel type of coordinated reset (CR) stimulation. CR means to deliver phase resetting stimuli at different neuronal sub-populations sequentially, i.e., at times equidistantly distributed in a stimulation cycle. This uniform timing pattern seems to be intuitive and actually applies to the neural network models used for the study of CR so far. CR resets the population to an unstable cluster state from where it passes through a desynchronized transient, eventually resynchronizing if left unperturbed. In contrast, we show that the optimal stimulation times are non-uniform. Using the model of weakly pulse-coupled neurons with phase response curves, we provide an approach that enables to determine optimal stimulation timing patterns that substantially maximize the desynchronized transient time following the application of CR stimulation. This approach includes an optimization search for clusters in a low-dimensional pulse coupled map. As a consequence, model-specific non-uniformly spaced cluster states cause considerably longer desynchronization transients. Intriguingly, such a desynchronization boost with non-uniform CR stimulation can already be achieved by only slight modifications of the uniform CR timing pattern. Our results suggest that the non-uniformness of the stimulation times can be a medically valuable parameter in the calibration procedure for CR stimulation, where the latter has successfully been used in clinical and pre-clinical studies for the treatment of Parkinson's disease and tinnitus. PMID:23750134

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.

Effect of H bond removal and changes in the position of the iron-sulphur head domain on the spin-lattice relaxation properties of the [2Fe-2S](2+) Rieske cluster in cytochrome bc(1).

PubMed

Sarewicz, Marcin; Dutka, Małgorzata; Pietras, Rafał; Borek, Arkadiusz; Osyczka, Artur

2015-10-14

Here, comparative electron spin-lattice relaxation studies of the 2Fe-2S iron-sulphur (Fe-S) cluster embedded in a large membrane protein complex - cytochrome bc1 - are reported. Structural modifications of the local environment alone (mutations S158A and Y160W removing specific H bonds between Fe-S and amino acid side chains) or in combination with changes in global protein conformation (mutations/inhibitors changing the position of the Fe-S binding domain within the protein complex) resulted in different redox potentials as well as g-, g-strain and the relaxation rates (T1(-1)) for the Fe-S cluster. The relaxation rates for T < 25 K were measured directly by inversion recovery, while for T > 60 K they were deduced from simulation of continuous wave EPR spectra of the cluster using a model that included anisotropy of Lorentzian broadening. In all cases, the relaxation rate involved contributions from direct, second-order Raman and Orbach processes, each dominating over different temperature ranges. The analysis of T1(-1) (T) over the range 5-120 K yielded the values of the Orbach energy (EOrb), Debye temperature θD and Raman process efficiency CRam for each variant of the protein. As the Orbach energy was generally higher for mutants S158A and Y160W, compared to wild-type protein (WT), it is suggested that H bond removal influences the geometry leading to increased strength of antiferromagnetic coupling between two Fe ions of the cluster. While θD was similar for all variants (∼107 K), the efficiency of the Raman process generally depends on the spin-orbit coupling that is lower for S158A and Y160W mutants, when compared to the WT. However, in several cases CRam did not only correlate with spin-orbit coupling but was also influenced by other factors - possibly the modification of protein rigidity and therefore the vibrational modes around the Fe-S cluster that change upon the movement of the iron-sulphur head domain.

Testing chameleon gravity with the Coma cluster

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

Terukina, Ayumu; Yamamoto, Kazuhiro; Lombriser, Lucas

2014-04-01

We propose a novel method to test the gravitational interactions in the outskirts of galaxy clusters. When gravity is modified, this is typically accompanied by the introduction of an additional scalar degree of freedom, which mediates an attractive fifth force. The presence of an extra gravitational coupling, however, is tightly constrained by local measurements. In chameleon modifications of gravity, local tests can be evaded by employing a screening mechanism that suppresses the fifth force in dense environments. While the chameleon field may be screened in the interior of the cluster, its outer region can still be affected by the extramore » force, introducing a deviation between the hydrostatic and lensing mass of the cluster. Thus, the chameleon modification can be tested by combining the gas and lensing measurements of the cluster. We demonstrate the operability of our method with the Coma cluster, for which both a lensing measurement and gas observations from the X-ray surface brightness, the X-ray temperature, and the Sunyaev-Zel'dovich effect are available. Using the joint observational data set, we perform a Markov chain Monte Carlo analysis of the parameter space describing the different profiles in both the Newtonian and chameleon scenarios. We report competitive constraints on the chameleon field amplitude and its coupling strength to matter. In the case of f(R) gravity, corresponding to a specific choice of the coupling, we find an upper bound on the background field amplitude of |f{sub R0}| < 6 × 10{sup −5}, which is currently the tightest constraint on cosmological scales.« less

Rotational spectroscopic study of carbonyl sulfide solvated with hydrogen molecules.

PubMed

Michaud, Julie M; Jäger, Wolfgang

2008-10-14

Rotational spectra of small-sized (H(2))(N)-OCS clusters with N = 2-7 were measured using a pulsed-jet Fourier transform microwave spectrometer. These include spectra of pure (para-H(2))(N)-OCS clusters, pure (ortho-H(2))(N)-OCS clusters, and mixed ortho-H(2) and para-H(2) containing clusters. The rotational lines of ortho-H(2) molecules containing clusters show proton spin-proton spin hyperfine structure, and the pattern evolves as the number of ortho-H(2) molecules in the cluster increases. Various isotopologues of the clusters were investigated, including those with O(13)CS, OC(33)S, OC(34)S, and O(13)C(34)S. Nuclear quadrupole hyperfine structures of rotational transitions were observed for (33)S (nuclear spin quantum number I = 3/2) containing isotopologues. The (33)S nuclear quadrupole coupling constants are compared to the corresponding constant of the OCS monomer and those of the He(N)-OCS clusters. The assignment of the number of solvating hydrogen molecules N is supported by the analyses of the proton spin-proton spin hyperfine structures of the mixed clusters, the dependence of line intensities on sample conditions (pressure and concentrations), and the agreement of the (para-H(2))(N)-OCS and (ortho-H(2))(N)-OCS rotational constants with those from a previous infrared study [J. Tang and A. R. W. McKellar, J. Chem. Phys. 121, 3087 (2004)].

Dynamical evolution of galaxies in dense cluster environment.

NASA Astrophysics Data System (ADS)

Gnedin, O. Y.

1997-12-01

I present the results of study of the dynamics of galaxies in clusters of galaxies. The effects of the galaxy environment could be quite dramatic. The time-varying gravitational potential of the cluster subjects the galaxies to strong tidal effects. The tidal density cutoff effectively strips the dark matter halos and leads to highly concentrated structures in the galactic centers. The fast gravitational tidal shocks raise the random motion of stars in the galaxies, transforming the thin disks into the kinematically hot thick configurations. The tidal shocks also cause relaxation of stellar energies that enhances the rate of accretion onto the galactic centers. These effects of the time-varying cluster potential have not been consistently taken into account before. I present numerical N-body simulations of galaxies using the Self-Consistent Field code with 10(7) - 10(8) particles. The code is coupled with the PM code that provides a fully dynamic simulation of the cluster potential. The tidal field of the cluster along the galaxy trajectories is imposed as an external perturbation on the galaxies in the SCF scheme. Recent HST observations show that the high-redshift (z > 0.4) clusters contain numerous bright blue spirals, often with distorted profiles, whereas the nearby clusters are mostly populated by featureless ellipticals. The goal of my study is to understand whether dynamics is responsible for the observed strong evolution of galaxies in clusters.

Solving Coupled Gross--Pitaevskii Equations on a Cluster of PlayStation 3 Computers

NASA Astrophysics Data System (ADS)

Edwards, Mark; Heward, Jeffrey; Clark, C. W.

2009-05-01

At Georgia Southern University we have constructed an 8+1--node cluster of Sony PlayStation 3 (PS3) computers with the intention of using this computing resource to solve problems related to the behavior of ultra--cold atoms in general with a particular emphasis on studying bose--bose and bose--fermi mixtures confined in optical lattices. As a first project that uses this computing resource, we have implemented a parallel solver of the coupled time--dependent, one--dimensional Gross--Pitaevskii (TDGP) equations. These equations govern the behavior of dual-- species bosonic mixtures. We chose the split--operator/FFT to solve the coupled 1D TDGP equations. The fast Fourier transform component of this solver can be readily parallelized on the PS3 cpu known as the Cell Broadband Engine (CellBE). Each CellBE chip contains a single 64--bit PowerPC Processor Element known as the PPE and eight ``Synergistic Processor Element'' identified as the SPE's. We report on this algorithm and compare its performance to a non--parallel solver as applied to modeling evaporative cooling in dual--species bosonic mixtures.

Wave failure at strong coupling in intracellular C a2 + signaling system with clustered channels

NASA Astrophysics Data System (ADS)

Li, Xiang; Wu, Yuning; Gao, Xuejuan; Cai, Meichun; Shuai, Jianwei

2018-01-01

As an important intracellular signal, C a2 + ions control diverse cellular functions. In this paper, we discuss the C a2 + signaling with a two-dimensional model in which the inositol 1,4,5-trisphosphate (I P3 ) receptor channels are distributed in clusters on the endoplasmic reticulum membrane. The wave failure at large C a2 + diffusion coupling is discussed in detail in the model. We show that with varying model parameters the wave failure is a robust behavior with either deterministic or stochastic channel dynamics. We suggest that the wave failure should be a general behavior in inhomogeneous diffusing systems with clustered excitable regions and may occur in biological C a2 + signaling systems.

Theoretical study on the spectroscopic properties of CO3(*-).nH2O clusters: extrapolation to bulk.

PubMed

Pathak, Arup K; Mukherjee, Tulsi; Maity, Dilip K

2008-10-24

Vertical detachment energies (VDE) and UV/Vis absorption spectra of hydrated carbonate radical anion clusters, CO(3)(*-).nH(2)O (n=1-8), are determined by means of ab initio electronic structure theory. The VDE values of the hydrated clusters are calculated with second-order Moller-Plesset perturbation (MP2) and coupled cluster theory using the 6-311++G(d,p) set of basis functions. The bulk VDE value of an aqueous carbonate radical anion solution is predicted to be 10.6 eV from the calculated weighted average VDE values of the CO(3)(*-).nH(2)O clusters. UV/Vis absorption spectra of the hydrated clusters are calculated by means of time-dependent density functional theory using the Becke three-parameter nonlocal exchange and the Lee-Yang-Parr nonlocal correlation functional (B3LYP). The simulated UV/Vis spectrum of the CO(3)(*-).8H(2)O cluster is in excellent agreement with the reported experimental spectrum for CO(3)(*-) (aq), obtained based on pulse radiolysis experiments.

Electric dipole (hyper)polarizabilities of selected X2Y2 and X3Y3 (X = Al, Ga, In and Y = P, As): III-V semiconductor clusters. An ab initio comparative study.

PubMed

Karamanis, Panaghiotis; Pouchan, Claude; Leszczynski, Jerzy

2008-12-25

A systematic ab initio comparative study of the (hyper)polarizabilities of selected III-V stoichiometric semiconductor clusters has been carried out. Our investigation focuses on the ground state structures of the dimers and on two dissimilar trimer configurations of aluminum, gallium, indium phosphide and arsenide. The basis set effect on both the polarizabilities and hyperpolarizabilities of the studied systems has been explicitly taken into account relying on the augmented correlation consistent aug-cc-pVnZ (n = D, T, Q, and 5) basis sets series. In addition, a rough estimation of the effects of the relativistic effects on the investigated properties is provided by extension of the study to include calculations performed with relativistic electron core potentials (or pseudopotentials). Electron correlation effects have been estimated utilizing methods of increasing predictive reliability, e.g., the Møller-Plesset many body perturbation theory and the couple cluster approach. Our results reveal that in the considered semiconductor species the Group III elements (Al, Ga, In) play a vital role on the values of their relative (hyper)polarizability. At all levels of theory employed the most hyperpolarizable clusters are the indium derivatives while the aluminum arsenide clusters also exhibit high, comparable hyperpolarizabilities. The less hyperpolarizable species are those composed of gallium and this is associated with the strong influence of the nuclear charge on the valence electrons of Ga due to the poor shielding that is provided by the semicore d electrons. In addition, the analysis of the electronic structure and the hyperpolarizability magnitudes reveals that clusters, in which their bonding is characterized by strong electron transfer from the electropositive to the electronegative atoms, are less hyperpolarizable than species in which the corresponding electron transfer is weaker. Lastly, from the methodological point of view our results point out that the hyperpolarizabilities of those species converge when an augmented triple-zeta quality basis set is used and, also, that the second order Møller-Plesset approximation (MP2) overestimates considerably their second hyperpolarizabilities with respect to the highest level of coupled cluster theory applied in this study (CCSD(T)).

Equation of motion coupled cluster methods for electron attachment and ionization potential in polyacenes

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

Bhaskaran-Nair, Kiran; Kowalski, Karol; Jarrell, Mark

2015-11-05

Polyacenes have attracted considerable attention due to their use in organic based optoelectronic materials. Polyacenes are polycyclic aromatic hydrocarbons composed of fused benzene rings. Key to understanding and design of new functional materials is an understanding of their excited state properties starting with their electron affinity (EA) and ionization potential (IP). We have developed a highly accurate and com- putationally e*fficient EA/IP equation of motion coupled cluster singles and doubles (EA/IP-EOMCCSD) method that is capable of treating large systems and large basis set. In this study we employ the EA/IP-EOMCCSD method to calculate the electron affinity and ionization potential ofmore » naphthalene, anthracene, tetracene, pentacene, hex- acene and heptacene. We have compared our results with other previous theoretical studies and experimental data. Our EA/IP results are in very good agreement with experiment and when compared with the other theoretical investigations our results represent the most accurate calculations as compared to experiment.« less

Numerical studies from quantum to macroscopic scales of carbon nanoparticules in hydrogen plasma

NASA Astrophysics Data System (ADS)

Lombardi, Guillaume; Ngandjong, Alain; Mezei, Zsolt; Mougenot, Jonathan; Michau, Armelle; Hassouni, Khaled; Seydou, Mahamadou; Maurel, François

2016-09-01

Dusty plasmas take part in large scientific domains from Universe Science to nanomaterial synthesis processes. They are often generated by growth from molecular precursor. This growth leads to the formation of larger clusters which induce solid germs nucleation. Particle formed are described by an aerosol dynamic taking into account coagulation, molecular deposition and transport processes. These processes are controlled by the elementary particle. So there is a strong coupling between particle dynamics and plasma discharge equilibrium. This study is focused on the development of a multiscale physic and numeric model of hydrogen plasmas and carbon particles around three essential coupled axes to describe the various physical phenomena: (i) Macro/mesoscopic fluid modeling describing in an auto-coherent way, characteristics of the plasma, molecular clusters and aerosol behavior; (ii) the classic molecular dynamics offering a description to the scale molecular of the chains of chemical reactions and the phenomena of aggregation; (iii) the quantum chemistry to establish the activation barriers of the different processes driving the nanopoarticule formation.

Finite-Time and Fixed-Time Cluster Synchronization With or Without Pinning Control.

PubMed

Liu, Xiwei; Chen, Tianping

2018-01-01

In this paper, the finite-time and fixed-time cluster synchronization problem for complex networks with or without pinning control are discussed. Finite-time (or fixed-time) synchronization has been a hot topic in recent years, which means that the network can achieve synchronization in finite-time, and the settling time depends on the initial values for finite-time synchronization (or the settling time is bounded by a constant for any initial values for fixed-time synchronization). To realize the finite-time and fixed-time cluster synchronization, some simple distributed protocols with or without pinning control are designed and the effectiveness is rigorously proved. Several sufficient criteria are also obtained to clarify the effects of coupling terms for finite-time and fixed-time cluster synchronization. Especially, when the cluster number is one, the cluster synchronization becomes the complete synchronization problem; when the network has only one node, the coupling term between nodes will disappear, and the synchronization problem becomes the simplest master-slave case, which also includes the stability problem for nonlinear systems like neural networks. All these cases are also discussed. Finally, numerical simulations are presented to demonstrate the correctness of obtained theoretical results.

An Ab Initio Study of CuCO

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1994-01-01

Modified coupled-pair functional (MCPF) calculations and coupled cluster singles and doubles calculations, which include a perturbational estimate of the connected triples [CCSD(T)], yield a bent structure for CuCO, thus, supporting the prediction of a nonlinear structure based on density functional (DF) calculations. Our best estimate for the binding energy is 4.9 +/- 1.4 kcal/mol; this is in better agreement with experiment (6.0 +/- 1.2 kcal/mol) than the DF approach which yields a value (19.6 kcal/mol) significantly larger than experiment.

One-sided and mutually aggressive couples: Differences in attachment, conflict prevalence, and coping.

PubMed

Burk, William J; Seiffge-Krenke, Inge

2015-12-01

This study investigated concurrent links between adolescent romantic couples' reports of aggression (relational and physical) and relationship functioning (e.g., attachment security, conflict prevalence, coping strategies, jealousy, and affiliative and romantic relationship quality) using a pattern-oriented approach. The sample included 194 romantic partner dyads (Mage=16.99 years for females and Mage=18.41 years for males). A hierarchical cluster analysis identified five distinct subgroups of dyads based on male and female reports of relational and physical aggression, ranging from nonaggressive couples (42%), to those characterized by aggressive females (18%), aggressive males (14%), physically aggressive females (20%), and mutually aggressive females and males (6%). Clusters in which one partner was perceived as either relationally or physically aggressive were characterized by higher rates of conflict, less adaptive coping, and more jealousy (particularly in males). The mutually aggressive couples showed the least adaptive relationship functioning, with high rates of conflict, a deficit in reflection and emotion regulation in conflict situations, and a lack of affiliative relationship qualities. The discussion focuses on the formative character of aggression in these early romantic relations, the aggravating impact of mutual aggression on relationship functioning, and the gender-specific functions of aggression in relationships characterized by unilateral aggression. Copyright © 2015 Elsevier Ltd. All rights reserved.

Relativistic coupled-cluster and density-functional studies of argon at high pressure

NASA Astrophysics Data System (ADS)

Schwerdtfeger, Peter; Steenbergen, Krista G.; Pahl, Elke

2017-06-01

The equation of state P (V ,T ) for solid argon is determined by the calculation of accurate static and vibrational terms in the free energy. The static component comes from a quantum theoretical many-body expansion summing over all energetic contributions from two-, three-, and four-body fragments treated with relativistic coupled cluster theory, while the lattice vibrations are described at an anharmonic level including two- and three-body forces as well as temperature effects. The dynamic part is calculated within the Debye and Einstein approximation, as well as by a more accurate phonon treatment where the vibrational motions in the lattice are coupled. Our results are in good agreement with room-temperature high-pressure experimental data up to ˜20 GPa. In the 20-100 GPa pressure range, however, we see considerable deviations between experiment and theory, perhaps indicating missing four-body contributions (beyond the quadruple dipole terms included here), missing five and higher-body effects, and the need to go beyond the coupled cluster singles-doubles with perturbative triples treatment in such higher-body forces. This contrasts with the results for solid neon, where excellent agreement has been achieved taking only two- and three-body forces into account [P. Schwerdtfeger and A. Hermann, Phys. Rev. B 80, 064106 (2009), 10.1103/PhysRevB.80.064106]. We demonstrate that the phase transition from fcc to hcp cannot account for the large discrepancies observed. Density functional calculations give very mixed results in the high-pressure region, but some functionals such as optB88-vdW (proposed by Lundqvist and co-workers) describe the many-body forces in argon reasonably well over the range of pressures investigated. Theoretical investigations of the heavier rare gas solids reaching experimental accuracy in the high-pressure regime therefore remain a significant challenge.

Large resistance change on magnetic tunnel junction based molecular spintronics devices

DOE PAGES

Tyagi, Pawan; Friebe, Edward

2018-01-12

Here, molecular bridges covalently bonded to two ferromagnetic electrodes can transform ferromagnetic materials and produce intriguing spin transport characteristics. This paper discusses the impact of molecule induced strong coupling on the spin transport. To study molecular coupling effect the octametallic molecular cluster (OMC) was bridged between two ferromagnetic electrodes of a magnetic tunnel junction (Ta/Co/NiFe/AlOx/NiFe/Ta) along the exposed side edges. OMCs induced strong inter-ferromagnetic electrode coupling to yield drastic changes in transport properties of the magnetic tunnel junction testbed at the room temperature. These OMCs also transformed the magnetic properties of magnetic tunnel junctions. SQUID and ferromagnetic resonance studies providedmore » insightful data to explain transport studies on the magnetic tunnel junction based molecular spintronics devices.« less

Large resistance change on magnetic tunnel junction based molecular spintronics devices

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

Tyagi, Pawan; Friebe, Edward

Here, molecular bridges covalently bonded to two ferromagnetic electrodes can transform ferromagnetic materials and produce intriguing spin transport characteristics. This paper discusses the impact of molecule induced strong coupling on the spin transport. To study molecular coupling effect the octametallic molecular cluster (OMC) was bridged between two ferromagnetic electrodes of a magnetic tunnel junction (Ta/Co/NiFe/AlOx/NiFe/Ta) along the exposed side edges. OMCs induced strong inter-ferromagnetic electrode coupling to yield drastic changes in transport properties of the magnetic tunnel junction testbed at the room temperature. These OMCs also transformed the magnetic properties of magnetic tunnel junctions. SQUID and ferromagnetic resonance studies providedmore » insightful data to explain transport studies on the magnetic tunnel junction based molecular spintronics devices.« less

Experiments with arbitrary networks in time-multiplexed delay systems

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Schmadel, Don C.; Murphy, Thomas E.; Roy, Rajarshi

2017-12-01

We report a new experimental approach using an optoelectronic feedback loop to investigate the dynamics of oscillators coupled on large complex networks with arbitrary topology. Our implementation is based on a single optoelectronic feedback loop with time delays. We use the space-time interpretation of systems with time delay to create large networks of coupled maps. Others have performed similar experiments using high-pass filters to implement the coupling; this restricts the network topology to the coupling of only a few nearest neighbors. In our experiment, the time delays and coupling are implemented on a field-programmable gate array, allowing the creation of networks with arbitrary coupling topology. This system has many advantages: the network nodes are truly identical, the network is easily reconfigurable, and the network dynamics occur at high speeds. We use this system to study cluster synchronization and chimera states in both small and large networks of different topologies.

Magnetic and transport signatures of Rashba spin-orbit coupling on the Kondo lattice model in two dimensional clusters

NASA Astrophysics Data System (ADS)

Riera, Jose

2014-03-01

Motivated by emergent phenomena at oxide surfaces and heterostructures, particularly those involving transition metal oxides with perovskite crystal structure such as LaTiO3/SrTiO3, we examine the Kondo lattice model in the presence of a Rashba spin-orbit coupling (RSOC). Using an array of numerical techniques, under the assumption that the electrons on localized orbitals may be treated as classical continuum spins, we compute various charge, spin and transport properties on square clusters and on ladders at zero and finite temperatures. The main goal is to determine magnetic and transport signatures due to the RSOC. The same model can be used to study at an effective level the combined effect on magnetic and transport properties of Rashba and ferromagnetic moments, such as the ones present at LMnO3/SrMnO3 interfaces. Support from CONICET (ARGENTINA).

Quantum-chemical investigation of the structures and electronic spectra of the nucleic acid bases at the coupled cluster CC2 level.

PubMed

Fleig, Timo; Knecht, Stefan; Hättig, Christof

2007-06-28

We study the ground-state structures and singlet- and triplet-excited states of the nucleic acid bases by applying the coupled cluster model CC2 in combination with a resolution-of-the-identity approximation for electron interaction integrals. Both basis set effects and the influence of dynamic electron correlation on the molecular structures are elucidated; the latter by comparing CC2 with Hartree-Fock and Møller-Plesset perturbation theory to second order. Furthermore, we investigate basis set and electron correlation effects on the vertical excitation energies and compare our highest-level results with experiment and other theoretical approaches. It is shown that small basis sets are insufficient for obtaining accurate results for excited states of these molecules and that the CC2 approach to dynamic electron correlation is a reliable and efficient tool for electronic structure calculations on medium-sized molecules.

Novel strategy to implement active-space coupled-cluster methods

NASA Astrophysics Data System (ADS)

Rolik, Zoltán; Kállay, Mihály

2018-03-01

A new approach is presented for the efficient implementation of coupled-cluster (CC) methods including higher excitations based on a molecular orbital space partitioned into active and inactive orbitals. In the new framework, the string representation of amplitudes and intermediates is used as long as it is beneficial, but the contractions are evaluated as matrix products. Using a new diagrammatic technique, the CC equations are represented in a compact form due to the string notations we introduced. As an application of these ideas, a new automated implementation of the single-reference-based multi-reference CC equations is presented for arbitrary excitation levels. The new program can be considered as an improvement over the previous implementations in many respects; e.g., diagram contributions are evaluated by efficient vectorized subroutines. Timings for test calculations for various complete active-space problems are presented. As an application of the new code, the weak interactions in the Be dimer were studied.

Proteins as templates for complex synthetic metalloclusters: towards biologically programmed heterogeneous catalysis

PubMed Central

Fehl, Charlie

2016-01-01

Despite nature’s prevalent use of metals as prosthetics to adapt or enhance the behaviour of proteins, our ability to programme such architectural organization remains underdeveloped. Multi-metal clusters buried in proteins underpin the most remarkable chemical transformations in nature, but we are not yet in a position to fully mimic or exploit such systems. With the advent of copious, relevant structural information, judicious mechanistic studies and the use of accessible computational methods in protein design coupled with new synthetic methods for building biomacromolecules, we can envisage a ‘new dawn’ that will allow us to build de novo metalloenzymes that move beyond mono-metal centres. In particular, we highlight the need for systems that approach the multi-centred clusters that have evolved to couple electron shuttling with catalysis. Such hybrids may be viewed as exciting mid-points between homogeneous and heterogeneous catalysts which also exploit the primary benefits of biocatalysis. PMID:27279776

Plasma flow around and charge distribution of a dust cluster in a rf discharge

NASA Astrophysics Data System (ADS)

Schleede, J.; Lewerentz, L.; Bronold, F. X.; Schneider, R.; Fehske, H.

2018-04-01

We employ a particle-in-cell Monte Carlo collision/particle-particle particle-mesh simulation to study the plasma flow around and the charge distribution of a three-dimensional dust cluster in the sheath of a low-pressure rf argon discharge. The geometry of the cluster and its position in the sheath are fixed to the experimental values, prohibiting a mechanical response of the cluster. Electrically, however, the cluster and the plasma environment, mimicking also the experimental situation, are coupled self-consistently. We find a broad distribution of the charges collected by the grains. The ion flux shows on the scale of the Debye length strong focusing and shadowing inside and outside the cluster due to the attraction of the ions to the negatively charged grains, whereas the electron flux is characterized on this scale only by a weak spatial modulation of its magnitude depending on the rf phase. On the scale of the individual dust potentials, however, the electron flux deviates in the vicinity of the cluster strongly from the laminar flow associated with the plasma sheath. It develops convection patterns to compensate for the depletion of electrons inside the dust cluster.

The electronic structure of vanadium monochloride cation (VCl{sup +}): Tackling the complexities of transition metal species

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

DeYonker, Nathan J., E-mail: ndyonker@memphis.edu; Halfen, DeWayne T.; Ziurys, Lucy M.

Six electronic states (X {sup 4}Σ{sup −}, A {sup 4}Π, B {sup 4}Δ, {sup 2}Φ, {sup 2}Δ, {sup 2}Σ{sup +}) of the vanadium monochloride cation (VCl{sup +}) are described using large basis set coupled cluster theory. For the two lowest quartet states (X {sup 4}Σ{sup −} and A {sup 4}Π), a focal point analysis (FPA) approach was used that conjoined a correlation-consistent family of basis sets up to aug-cc-pwCV5Z-DK with high-order coupled cluster theory through pentuple (CCSDTQP) excitations. FPA adiabatic excitation energies (T{sub 0}) and spectroscopic constants (r{sub e}, r{sub 0}, B{sub e}, B{sub 0}, D{sup ¯}{sub e}, H{sub e},more » ω{sub e}, v{sub 0}, α{sub e}, ω{sub e}x{sub e}) were extrapolated to the valence complete basis set Douglas-Kroll (DK) aug-cc-pV∞Z-DK CCSDT level of theory, and additional treatments accounted for higher-order valence electron correlation, core correlation, and spin-orbit coupling. Due to the delicate interplay between dynamical and static electronic correlation, single reference coupled cluster theory is able to provide the correct ground electronic state (X {sup 4}Σ{sup −}), while multireference configuration interaction theory cannot. Perturbations from the first- and second-order spin orbit coupling of low-lying states with quartet spin multiplicity reveal an immensely complex rotational spectrum relative to the isovalent species VO, VS, and TiCl. Computational data on the doublet manifold suggest that the lowest-lying doublet state ({sup 2}Γ) has a T{sub e} of ∼11 200 cm{sup −1}. Overall, this study shows that laboratory and theoretical rotational spectroscopists must work more closely in tandem to better understand the bonding and structure of molecules containing transition metals.« less

Formation and Assembly of Massive Star Clusters

NASA Astrophysics Data System (ADS)

McMillan, Stephen

The formation of stars and star clusters is a major unresolved problem in astrophysics. It is central to modeling stellar populations and understanding galaxy luminosity distributions in cosmological models. Young massive clusters are major components of starburst galaxies, while globular clusters are cornerstones of the cosmic distance scale and represent vital laboratories for studies of stellar dynamics and stellar evolution. Yet how these clusters form and how rapidly and efficiently they expel their natal gas remain unclear, as do the consequences of this gas expulsion for cluster structure and survival. Also unclear is how the properties of low-mass clusters, which form from small-scale instabilities in galactic disks and inform much of our understanding of cluster formation and star-formation efficiency, differ from those of more massive clusters, which probably formed in starburst events driven by fast accretion at high redshift, or colliding gas flows in merging galaxies. Modeling cluster formation requires simulating many simultaneous physical processes, placing stringent demands on both software and hardware. Simulations of galaxies evolving in cosmological contexts usually lack the numerical resolution to simulate star formation in detail. They do not include detailed treatments of important physical effects such as magnetic fields, radiation pressure, ionization, and supernova feedback. Simulations of smaller clusters include these effects, but fall far short of the mass of even single young globular clusters. With major advances in computing power and software, we can now directly address this problem. We propose to model the formation of massive star clusters by integrating the FLASH adaptive mesh refinement magnetohydrodynamics (MHD) code into the Astrophysical Multi-purpose Software Environment (AMUSE) framework, to work with existing stellar-dynamical and stellar evolution modules in AMUSE. All software will be freely distributed on-line, allowing open access to state-of- the-art simulation techniques within a modern, modular software environment. We will follow the gravitational collapse of 0.1-10 million-solar mass gas clouds through star formation and coalescence into a star cluster, modeling in detail the coupling of the gas and the newborn stars. We will study the effects of star formation by detecting accreting regions of gas in self-gravitating, turbulent, MHD, FLASH models that we will translate into collisional dynamical systems of stars modeled with an N-body code, coupled together in the AMUSE framework. Our FLASH models will include treatments of radiative transfer from the newly formed stars, including heating and radiative acceleration of the surrounding gas. Specific questions to be addressed are: (1) How efficiently does the gas in a star forming region form stars, how does this depend on mass, metallicity, and other parameters, and what terminates star formation? What observational predictions can be made to constrain our models? (2) How important are different mechanisms for driving turbulence and removing gas from a cluster: accretion, radiative feedback, and mechanical feedback? (3) How does the infant mortality rate of young clusters depend on the initial properties of the parent cloud? (4) What are the characteristic formation timescales of massive star clusters, and what observable imprints does the assembly process leave on their structure at an age of 10-20 Myr, when formation is essentially complete and many clusters can be observed? These studies are directly relevant to NASA missions at many electromagnetic wavelengths, including Chandra, GALEX, Hubble, and Spitzer. Each traces different aspects of cluster formation and evolution: X-rays trace supernovae, ultraviolet traces young stars, visible colors can distinguish between young blue stars and older red stars, and the infrared directly shows young embedded star clusters.

Light clusters and pasta phases in warm and dense nuclear matter

NASA Astrophysics Data System (ADS)

Avancini, Sidney S.; Ferreira, Márcio; Pais, Helena; Providência, Constança; Röpke, Gerd

2017-04-01

The pasta phases are calculated for warm stellar matter in a framework of relativistic mean-field models, including the possibility of light cluster formation. Results from three different semiclassical approaches are compared with a quantum statistical calculation. Light clusters are considered as point-like particles, and their abundances are determined from the minimization of the free energy. The couplings of the light clusters to mesons are determined from experimental chemical equilibrium constants and many-body quantum statistical calculations. The effect of these light clusters on the chemical potentials is also discussed. It is shown that, by including heavy clusters, light clusters are present up to larger nucleonic densities, although with smaller mass fractions.

Distribution of cardiac sodium channels in clusters potentiates ephaptic interactions in the intercalated disc.

PubMed

Hichri, Echrak; Abriel, Hugues; Kucera, Jan P

2018-02-15

It has been proposed that ephaptic conduction, relying on interactions between the sodium (Na + ) current and the extracellular potential in intercalated discs, might contribute to cardiac conduction when gap junctional coupling is reduced, but this mechanism is still controversial. In intercalated discs, Na + channels form clusters near gap junction plaques, but the functional significance of these clusters has never been evaluated. In HEK cells expressing cardiac Na + channels, we show that restricting the extracellular space modulates the Na + current, as predicted by corresponding simulations accounting for ephaptic effects. In a high-resolution model of the intercalated disc, clusters of Na + channels that face each other across the intercellular cleft facilitate ephaptic impulse transmission when gap junctional coupling is reduced. Thus, our simulations reveal a functional role for the clustering of Na + channels in intercalated discs, and suggest that rearrangement of these clusters in disease may influence cardiac conduction. It has been proposed that ephaptic interactions in intercalated discs, mediated by extracellular potentials, contribute to cardiac impulse propagation when gap junctional coupling is reduced. However, experiments demonstrating ephaptic effects on the cardiac Na + current (I Na ) are scarce. Furthermore, Na + channels form clusters around gap junction plaques, but the electrophysiological significance of these clusters has never been investigated. In patch clamp experiments with HEK cells stably expressing human Na v 1.5 channels, we examined how restricting the extracellular space modulates I Na elicited by an activation protocol. In parallel, we developed a high-resolution computer model of the intercalated disc to investigate how the distribution of Na + channels influences ephaptic interactions. Approaching the HEK cells to a non-conducting obstacle always increased peak I Na at step potentials near the threshold of I Na activation and decreased peak I Na at step potentials far above threshold (7 cells, P = 0.0156, Wilcoxon signed rank test). These effects were consistent with corresponding control simulations with a uniform Na + channel distribution. In the intercalated disc computer model, redistributing the Na + channels into a central cluster of the disc potentiated ephaptic effects. Moreover, ephaptic impulse transmission from one cell to another was facilitated by clusters of Na + channels facing each other across the intercellular cleft when gap junctional coupling was reduced. In conclusion, our proof-of-principle experiments demonstrate that confining the extracellular space modulates cardiac I Na , and our simulations reveal the functional role of the aggregation of Na + channels in the perinexus. These findings highlight novel concepts in the physiology of cardiac excitation. © 2017 The Authors. The Journal of Physiology © 2017 The Physiological Society.

Transport and mixing in strongly coupled dusty plasma medium

NASA Astrophysics Data System (ADS)

Dharodi, Vikram; Das, Amita; Patel, Bhavesh

2016-10-01

The generalized hydrodynamic (GHD) fluid model has been employed to study the transport and mixing properties of Dusty plasma medium in strong coupling limit. The response of lighter electron and ion species to the dust motion is taken to be instantaneous i.e. inertia-less. Thus the electron and ion density are presumed to follow the Boltzman relation. In the incompressible limit (i-GHD) the model supports Transverse Shear wave in contrast to the Hydrodynamic fluids. It has been shown that the presence of these waves leads to a better mixing of fluid in this case. Several cases of flow configuration have been considered for the study. The transport and mixing attributes have been quantified by studying the dynamical evolution of tracer particles in the system. The diffusion and clustering of these test particles are directly linked to the mixing characteristic of a medium. The displacement of these particles provides for a quantitative estimate of the diffusion coefficient of the medium. It is shown that these test particles often organize themselves in spatially inhomogeneous pattern leading to the phenomena of clustering.

Galaxies at the Extremes: Ultradiffuse Galaxies in the Virgo Cluster

NASA Astrophysics Data System (ADS)

Mihos, Chris

2017-08-01

The ultradiffuse galaxies (UDGs) recently discovered in massive galaxy clusters presents both challenges and opportunities for our understanding of galaxy evolution in dense clusters. Such large, low density galaxies should be most vulnerable to gravitational destruction within the cluster environment. Thus their presence in cluster cores argues either that they must be stabilized by massive dark halos or else be short-lived objects undergoing rapid transformation, perhaps leading to the formation of ultracompact dwarf galaxies (UCDs) if their destruction leaves only a compact nucleus behind. We propose deep imaging of four Virgo Cluster UDGs to probe their local environment within Virgo via accurate tip of the red giant branch (TRGB) distances. With a distance precision of 1 Mpc, we will accurately place the objects in the Virgo core, cluster outskirts, or intervening field. When coupled with our extant kinematic data, we can determine whether they are infalling objects or instead have already passed through the cluster core. We will also compare their compact nuclei to Virgo UCDs, and study their globular cluster (GC) populations in detail. Probing three magnitudes beyond the turnover in the GC luminosity function, we will construct larger and cleaner GC samples than possible with ground-based imaging, using the total mass and radial extent of the globular cluster systems to estimate the dark halo mass and tidal radius for each UDG. The new information provided by HST about the local environment and intrinsic properties of these Virgo UDGs will be used in conjunction with simulation data to study cluster-driven evolution and transformation of low density galaxies.

Kinematics of the Normal Knee during Dynamic Activities: A Synthesis of Data from Intracortical Pins and Biplane Imaging

PubMed Central

Gasparutto, Xavier; Moissenet, Florent; Lafon, Yoann

2017-01-01

Few studies have provided in vivo tibiofemoral kinematics of the normal knee during dynamic weight-bearing activities. Indeed, gold standard measurement methods (i.e., intracortical pins and biplane imaging) raise ethical and experimental issues. Moreover, the conventions used for the processing of the kinematics show large inconsistencies. This study aims at synthesising the tibiofemoral kinematics measured with gold standard measurement methods. Published kinematic data were transformed in the standard recommended by the International Society of Biomechanics (ISB), and a clustering method was applied to investigate whether the couplings between the degrees of freedom (DoFs) are consistent among the different activities and measurement methods. The synthesised couplings between the DoFs during knee flexion (from 4° of extension to −61° of flexion) included abduction (up to −10°); internal rotation (up to 15°); and medial (up to 10 mm), anterior (up to 25 mm), and proximal (up to 28 mm) displacements. These synthesised couplings appeared mainly partitioned into two clusters that featured all the dynamic weight-bearing activities and all the measurement methods. Thus, the effect of the dynamic activities on the couplings between the tibiofemoral DoFs appeared to be limited. The synthesised data might be used as a reference of normal in vivo knee kinematics for prosthetic and orthotic design and for knee biomechanical model development and validation. PMID:28487620

Chimera states in a multilayer network of coupled and uncoupled neurons

NASA Astrophysics Data System (ADS)

Majhi, Soumen; Perc, Matjaž; Ghosh, Dibakar

2017-07-01

We study the emergence of chimera states in a multilayer neuronal network, where one layer is composed of coupled and the other layer of uncoupled neurons. Through the multilayer structure, the layer with coupled neurons acts as the medium by means of which neurons in the uncoupled layer share information in spite of the absence of physical connections among them. Neurons in the coupled layer are connected with electrical synapses, while across the two layers, neurons are connected through chemical synapses. In both layers, the dynamics of each neuron is described by the Hindmarsh-Rose square wave bursting dynamics. We show that the presence of two different types of connecting synapses within and between the two layers, together with the multilayer network structure, plays a key role in the emergence of between-layer synchronous chimera states and patterns of synchronous clusters. In particular, we find that these chimera states can emerge in the coupled layer regardless of the range of electrical synapses. Even in all-to-all and nearest-neighbor coupling within the coupled layer, we observe qualitatively identical between-layer chimera states. Moreover, we show that the role of information transmission delay between the two layers must not be neglected, and we obtain precise parameter bounds at which chimera states can be observed. The expansion of the chimera region and annihilation of cluster and fully coherent states in the parameter plane for increasing values of inter-layer chemical synaptic time delay are illustrated using effective range measurements. These results are discussed in the light of neuronal evolution, where the coexistence of coherent and incoherent dynamics during the developmental stage is particularly likely.

A complete, multi-level conformational clustering of antibody complementarity-determining regions

PubMed Central

Nikoloudis, Dimitris; Pitts, Jim E.

2014-01-01

Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12,712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation. PMID:25071986

Efficient coupling of high intensity short laser pulses into snow clusters

NASA Astrophysics Data System (ADS)

Palchan, T.; Pecker, S.; Henis, Z.; Eisenmann, S.; Zigler, A.

2007-01-01

Measurements of energy absorption of high intensity laser pulses in snow clusters are reported. Targets consisting of sapphire coated with snow nanoparticles were found to absorb more than 95% of the incident light compared to 50% absorption in flat sapphire targets.

Transport properties of dilute α -Fe (X ) solid solutions (X = C, N, O)

NASA Astrophysics Data System (ADS)

Schuler, Thomas; Nastar, Maylise

2016-06-01

We extend the self-consistent mean field (SCMF) method to the calculation of the Onsager matrix of Fe-based interstitial solid solutions. Both interstitial jumps and substitutional atom-vacancy exchanges are accounted for. A general procedure is introduced to split the Onsager matrix of a dilute solid solution into intrinsic cluster Onsager matrices, and extract from them flux-coupling ratios, mobilities, and association-dissociation rates for each cluster. The formalism is applied to vacancy-interstitial solute pairs in α -Fe (V X pairs, X = C, N, O), with ab initio based thermodynamic and kinetic parameters. Convergence of the cluster mobility contribution gives a controlled estimation of the cluster definition distance, taking into account both its thermodynamic and kinetic properties. Then, the flux-coupling behavior of each V X pair is discussed, and qualitative understanding is achieved from the comparison between various contributions to the Onsager matrix. Also, the effect of low-activation energy second-nearest-neighbor interstitial solute jumps around a vacancy on these results is addressed.

Cluster Synchronization of Diffusively Coupled Nonlinear Systems: A Contraction-Based Approach

NASA Astrophysics Data System (ADS)

Aminzare, Zahra; Dey, Biswadip; Davison, Elizabeth N.; Leonard, Naomi Ehrich

2018-04-01

Finding the conditions that foster synchronization in networked nonlinear systems is critical to understanding a wide range of biological and mechanical systems. However, the conditions proved in the literature for synchronization in nonlinear systems with linear coupling, such as has been used to model neuronal networks, are in general not strict enough to accurately determine the system behavior. We leverage contraction theory to derive new sufficient conditions for cluster synchronization in terms of the network structure, for a network where the intrinsic nonlinear dynamics of each node may differ. Our result requires that network connections satisfy a cluster-input-equivalence condition, and we explore the influence of this requirement on network dynamics. For application to networks of nodes with FitzHugh-Nagumo dynamics, we show that our new sufficient condition is tighter than those found in previous analyses that used smooth or nonsmooth Lyapunov functions. Improving the analytical conditions for when cluster synchronization will occur based on network configuration is a significant step toward facilitating understanding and control of complex networked systems.

Rayleigh-Benard turbulence modified by two-way coupled particles

NASA Astrophysics Data System (ADS)

Park, Hyungwon; O'Keefe, Kevin; Richter, David

2017-11-01

Direct numerical simulation (DNS) with Lagrangian point particles is used to study Rayleigh-Bénard convection to understand modifications due to the interaction of inertial particle, gauged by the turbulent kinetic energy (TKE) and Nusselt number (Nu). The initially dispersed particles experience gravitational settling, and become introduced at the lower wall such that turbulence must overcome the settling velocity for the particles to vertically distribute throughout the domain. The particle properties of interest are inertia, as characterized by the Stokes number, and settling velocity. Furthermore, individual contributions by the momentum-coupling and thermal-coupling are studied to see which most significantly changes Nu and TKE. Our results show that particles with Stokes number of order unity maximize Nu, corresponding to a peak of clustering and attenuation of TKE. It is also shown that particles two-way coupled only through momentum attenuate Nu and weaken TKE, while thermal-only coupling also weakens TKE but enhances Nu. When both couplings are present, however, thermal coupling overwhelms the attenuation caused by momentum coupling and the net result is an enhancement of Nu. NSF - Grant No. AGS-1429921, ONR - Grant No. N00014-16-1-2472, and Notre Dame Center for Research Computing.

A combined gene and cell therapy approach for restoration of conduction.

PubMed

Hofshi, Anat; Itzhaki, Ilanit; Gepstein, Amira; Arbel, Gil; Gross, Gil J; Gepstein, Lior

2011-01-01

Abnormal conduction underlies both bradyarrhythmias and re-entrant tachyarrhythmias. However, no practical way exists for restoring or improving conduction in areas of conduction slowing or block. This study sought to test the feasibility of a novel strategy for conduction repair using genetically engineered cells designed to form biological "conducting cables." An in vitro model of conduction block was established using spatially separated, spontaneously contracting, nonsynchronized human embryonic stem cell-derived cardiomyocytes clusters. Immunostaining, dye transfer, intracellular recordings, and multielectrode array (MEA) studies were performed to evaluate the ability of genetically engineered HEK293 cells, expressing the SCN5A-encoded Na(+) channel, to couple with cultured cardiomyocytes and to synchronize their electrical activity. Connexin-43 immunostaining and calcein dye-transfer experiments confirmed the formation of functional gap junctions between the engineered cells and neighboring cardiomyocytes. MEA and intracellular recordings were performed to assess the ability of the engineered cells to restore conduction in the co-cultures. Synchronization was defined by establishment of fixed local activation time differences between the cardiomyocytes clusters and convergence of their activation cycle lengths. Nontransfected control cells were able to induce synchronization between cardiomyocytes clusters separated by distances up to 300 μm (n = 21). In contrast, the Na(+) channel-expressing cells synchronized contractions between clusters separated by up to 1,050 μm, the longest distance studied (n = 23). Finally, engineered cells expressing the voltage-sensitive K(v)1.3 potassium channel prevented synchronization at any distance. Genetically engineered cells, transfected to express Na(+) channels, can form biological conducting cables bridging and coupling spatially separated cardiomyocytes. This novel cell therapy approach might be useful for the development of therapeutic strategies for both bradyarrhythmias and tachyarrhythmias. Copyright © 2011 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Molecular dynamics simulations and docking studies on 3D models of the heterodimeric and homodimeric 5-HT(2A) receptor subtype.

PubMed

Bruno, Agostino; Beato, Claudia; Costantino, Gabriele

2011-04-01

G-protein coupled receptors may exist as functional homodimers, heterodimers and even as higher aggregates. In this work, we investigate the 5-HT(2A) receptor, which is a known target for antipsychotic drugs. Recently, 5-HT(2A) has been shown to form functional homodimers and heterodimers with the mGluR2 receptor. The objective of this study is to build up 3D models of the 5-HT(2A)/mGluR2 heterodimer and of the 5-HT(2A)-5-HT(2A) homodimer, and to evaluate the impact of the dimerization interface on the shape of the 5-HT(2A) binding pocket by using molecular dynamics simulations and docking studies. The heterodimer, homodimer and monomeric 5-HT(2A) receptors were simulated by molecular dynamics for 40 ns each. The trajectories were clustered and representative structures of six clusters for each system were generated. Inspection of the these representative structures clearly indicate an effect of the dimerization interface on the topology of the binding pocket. Docking studies allowed to generate receiver operating characteristic curves for a set of 5-HT(2A) ligands, indicating that different complexes prefer different classes of 5-HT(2A) ligands. This study clearly indicates that the presence of a dimerization interface must explicitly be considered when studying G-protein coupled receptors known to exist as dimers. Molecular dynamics simulation and cluster analysis are appropriate tools to study the phenomenon.

A local framework for calculating coupled cluster singles and doubles excitation energies (LoFEx-CCSD)

DOE PAGES

Baudin, Pablo; Bykov, Dmytro; Liakh, Dmitry I.; ...

2017-02-22

Here, the recently developed Local Framework for calculating Excitation energies (LoFEx) is extended to the coupled cluster singles and doubles (CCSD) model. In the new scheme, a standard CCSD excitation energy calculation is carried out within a reduced excitation orbital space (XOS), which is composed of localised molecular orbitals and natural transition orbitals determined from time-dependent Hartree–Fock theory. The presented algorithm uses a series of reduced second-order approximate coupled cluster singles and doubles (CC2) calculations to optimise the XOS in a black-box manner. This ensures that the requested CCSD excitation energies have been determined to a predefined accuracy compared tomore » a conventional CCSD calculation. We present numerical LoFEx-CCSD results for a set of medium-sized organic molecules, which illustrate the black-box nature of the approach and the computational savings obtained for transitions that are local compared to the size of the molecule. In fact, for such local transitions, the LoFEx-CCSD scheme can be applied to molecular systems where a conventional CCSD implementation is intractable.« less

Exploration of dynamical regimes of irradiated small protonated water clusters

NASA Astrophysics Data System (ADS)

Ndongmouo Taffoti, U. F.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.; Wang, Z. P.

2010-05-01

We explore from a theoretical perspective the dynamical response of small water clusters, (H2O)nH3O+ with n=1,2,3, to a short laser pulse for various frequencies, from infrared (IR) to ultra-violet (UV) and intensities (from 6×10^{13} W/cm^2 to 5×10^{14} W/cm^2). To that end, we use time-dependent local-density approximation for the electrons, coupled to molecular dynamics for the atomic cores (TDLDA-MD). The local-density approximation is augmented by a self-interaction correction (SIC) to allow for a correct description of electron emission. For IR frequencies, we see a direct coupling of the laser field to the very light H+ ions in the clusters. Resonant coupling (in the UV) and/or higher intensities lead to fast ionization with subsequent Coulomb explosion. The stability against Coulomb pressure increases with system size. Excitation to lower ionization stages induced strong ionic vibrations. The latter maintain a rather harmonic pattern in spite of the sizeable amplitudes (often 10% of the bond length).

Density-based clustering: A 'landscape view' of multi-channel neural data for inference and dynamic complexity analysis.

PubMed

Baglietto, Gabriel; Gigante, Guido; Del Giudice, Paolo

2017-01-01

Two, partially interwoven, hot topics in the analysis and statistical modeling of neural data, are the development of efficient and informative representations of the time series derived from multiple neural recordings, and the extraction of information about the connectivity structure of the underlying neural network from the recorded neural activities. In the present paper we show that state-space clustering can provide an easy and effective option for reducing the dimensionality of multiple neural time series, that it can improve inference of synaptic couplings from neural activities, and that it can also allow the construction of a compact representation of the multi-dimensional dynamics, that easily lends itself to complexity measures. We apply a variant of the 'mean-shift' algorithm to perform state-space clustering, and validate it on an Hopfield network in the glassy phase, in which metastable states are largely uncorrelated from memories embedded in the synaptic matrix. In this context, we show that the neural states identified as clusters' centroids offer a parsimonious parametrization of the synaptic matrix, which allows a significant improvement in inferring the synaptic couplings from the neural activities. Moving to the more realistic case of a multi-modular spiking network, with spike-frequency adaptation inducing history-dependent effects, we propose a procedure inspired by Boltzmann learning, but extending its domain of application, to learn inter-module synaptic couplings so that the spiking network reproduces a prescribed pattern of spatial correlations; we then illustrate, in the spiking network, how clustering is effective in extracting relevant features of the network's state-space landscape. Finally, we show that the knowledge of the cluster structure allows casting the multi-dimensional neural dynamics in the form of a symbolic dynamics of transitions between clusters; as an illustration of the potential of such reduction, we define and analyze a measure of complexity of the neural time series.

Density functional calculations of (55)Mn, (14)N and (13)C electron paramagnetic resonance parameters support an energetically feasible model system for the S(2) state of the oxygen-evolving complex of photosystem II.

PubMed

Schinzel, Sandra; Schraut, Johannes; Arbuznikov, Alexei V; Siegbahn, Per E M; Kaupp, Martin

2010-09-10

Metal and ligand hyperfine couplings of a previously suggested, energetically feasible Mn(4)Ca model cluster (SG2009(-1)) for the S(2) state of the oxygen-evolving complex (OEC) of photosystem II (PSII) have been studied by broken-symmetry density functional methods and compared with other suggested structural and spectroscopic models. This was carried out explicitly for different spin-coupling patterns of the S=1/2 ground state of the Mn(III)(Mn(IV))(3) cluster. By applying spin-projection techniques and a scaling of the manganese hyperfine couplings, computation of the hyperfine and nuclear quadrupole coupling parameters allows a direct evaluation of the proposed models in comparison with data obtained from the simulation of EPR, ENDOR, and ESEEM spectra. The computation of (55)Mn hyperfine couplings (HFCs) for SG2009(-1) gives excellent agreement with experiment. However, at the current level of spin projection, the (55)Mn HFCs do not appear sufficiently accurate to distinguish between different structural models. Yet, of all the models studied, SG2009(-1) is the only one with the Mn(III) site at the Mn(C) center, which is coordinated by histidine (D1-His332). The computed histidine (14)N HFC anisotropy for SG2009(-1) gives much better agreement with ESEEM data than the other models, in which Mn(C) is an Mn(IV) site, thus supporting the validity of the model. The (13)C HFCs of various carboxylates have been compared with (13)C ENDOR data for PSII preparations with (13)C-labelled alanine.

Accelerating the coupled-cluster singles and doubles method using the chain-of-sphere approximation

NASA Astrophysics Data System (ADS)

Dutta, Achintya Kumar; Neese, Frank; Izsák, Róbert

2018-06-01

In this paper, we present a chain-of-sphere implementation of the external exchange term, the computational bottleneck of coupled-cluster calculations at the singles and doubles level. This implementation is compared to standard molecular orbital, atomic orbital and resolution of identity implementations of the same term within the ORCA package and turns out to be the most efficient one for larger molecules, with a better accuracy than the resolution-of-identity approximation. Furthermore, it becomes possible to perform a canonical CC calculation on a tetramer of nucleobases in 17 days, 20 hours.

A Massively Parallel Tensor Contraction Framework for Coupled-Cluster Computations

DTIC Science & Technology

2014-08-02

CCSDT The CCSD model [41], where T = T1 + T2 (i.e. n = 2 in Equation 2), is one of the most widely used coupled-cluster methods as it provides a good...derived from response theory. Extending this to CCSDT [30, 35], where T = T1 + T2 + T3 ( n = 3), gives an even more accurate method (often capable of...CCSD and CCSDT have leading-order costs of O(n2on 4 v) and O( n 3 on 5 v), where no and nv are the number of occupied and virtual orbitals, respectively

Communication: Acceleration of coupled cluster singles and doubles via orbital-weighted least-squares tensor hypercontraction

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

Parrish, Robert M.; Sherrill, C. David, E-mail: sherrill@gatech.edu; Hohenstein, Edward G.

2014-05-14

We apply orbital-weighted least-squares tensor hypercontraction decomposition of the electron repulsion integrals to accelerate the coupled cluster singles and doubles (CCSD) method. Using accurate and flexible low-rank factorizations of the electron repulsion integral tensor, we are able to reduce the scaling of the most vexing particle-particle ladder term in CCSD from O(N{sup 6}) to O(N{sup 5}), with remarkably low error. Combined with a T{sub 1}-transformed Hamiltonian, this leads to substantial practical accelerations against an optimized density-fitted CCSD implementation.

Coupled-cluster treatment of molecular strong-field ionization

NASA Astrophysics Data System (ADS)

Jagau, Thomas-C.

2018-05-01

Ionization rates and Stark shifts of H2, CO, O2, H2O, and CH4 in static electric fields have been computed with coupled-cluster methods in a basis set of atom-centered Gaussian functions with a complex-scaled exponent. Consideration of electron correlation is found to be of great importance even for a qualitatively correct description of the dependence of ionization rates and Stark shifts on the strength and orientation of the external field. The analysis of the second moments of the molecular charge distribution suggests a simple criterion for distinguishing tunnel and barrier suppression ionization in polyatomic molecules.

Is the ground state of 5d4 double-perovskite Iridate Ba2YIrO6 magnetic or nonmagnetic?

NASA Astrophysics Data System (ADS)

Gong, Hoshin; Kim, Kyoo; Kim, Beom Hyun; Kim, Bongjae; Kim, Junwon; Min, B. I.

2018-05-01

We have investigated electronic structures and magnetic properties of double perovskite Iridate Ba2YIrO6 with 5d4 configuration, employing the exact diagonalization method for multi-site clusters. We have considered a many-body Hamiltonian for all d states (eg and t2g) including all relevant physical parameters such as the Coulomb correlation, spin-orbit coupling, crystal-field effect, and Hund coupling. We have found that the ground state of Ba2YIrO6 is nonmagnetic and that the Hund coupling plays an important role in the magnetic properties of the 5d4 systems, unlike the well-studied 5d5 systems.

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

Wouters, Denis; Brun, Pierre, E-mail: denis.wouters@cea.fr, E-mail: pierre.brun@cea.fr

Axion-like particles (ALPs) belong to a class of new pseudoscalar particles that generically couple to photons, opening the possibility of oscillations from photons into ALPs in an external magnetic field. Having witnessed the turbulence of their magnetic fields, these oscillations are expected to imprint irregularities on a limited energy range of the spectrum of astrophysical sources. In this study, Chandra observations of the Hydra galaxy cluster are used to constrain the value of the coupling of ALPs to photons. We consider the conversion of X-ray photons from the central source Hydra A in the magnetic field of the cluster. Themore » magnetic field strength and structure are well determined observationally, which adds to the robustness of the analysis. The absence of anomalous irregularities in the X-ray spectrum of Hydra A conservatively provides the most competitive constraints on the coupling constant for ALP masses below 7 Multiplication-Sign 10{sup -12} eV at the level of g{sub {gamma}a} < 8.3 Multiplication-Sign 10{sup -12} GeV{sup -1} at the 95% confidence level. Because of the specific phenomenology involved, these constraints actually hold more generally for very light pseudo-Nambu-Goldstone bosons.« less

Generalized quantum kinetic expansion: Higher-order corrections to multichromophoric Förster theory

NASA Astrophysics Data System (ADS)

Wu, Jianlan; Gong, Zhihao; Tang, Zhoufei

2015-08-01

For a general two-cluster energy transfer network, a new methodology of the generalized quantum kinetic expansion (GQKE) method is developed, which predicts an exact time-convolution equation for the cluster population evolution under the initial condition of the local cluster equilibrium state. The cluster-to-cluster rate kernel is expanded over the inter-cluster couplings. The lowest second-order GQKE rate recovers the multichromophoric Förster theory (MCFT) rate. The higher-order corrections to the MCFT rate are systematically included using the continued fraction resummation form, resulting in the resummed GQKE method. The reliability of the GQKE methodology is verified in two model systems, revealing the relevance of higher-order corrections.

Stochastic process of pragmatic information for 2D spiral wave turbulence in globally and locally coupled Alief-Panfilov oscillators

NASA Astrophysics Data System (ADS)

Kuwahara, Jun; Miyata, Hajime; Konno, Hidetoshi

2017-09-01

Recently, complex dynamics of globally coupled oscillators have been attracting many researcher's attentions. In spite of their numerous studies, their features of nonlinear oscillator systems with global and local couplings in two-dimension (2D) are not understood fully. The paper focuses on 2D states of coherent, clustered and chaotic oscillation especially under the effect of negative global coupling (NGC) in 2D Alief-Panfilov model. It is found that the tuning NGC can cause various new coupling-parameter dependency on the features of oscillations. Then quantitative characterization of various states of oscillations (so called spiral wave turbulence) is examined by using the pragmatic information (PI) which have been utilized in analyzing multimode laser, solar activity and neuronal systems. It is demonstrated that the dynamics of the PI for various oscillations can be characterized successfully by the Hyper-Gamma stochastic process.

Carbohydrate Cluster Microarrays Fabricated on 3-Dimensional Dendrimeric Platforms for Functional Glycomics Exploration

PubMed Central

Zhou, Xichun; Turchi, Craig; Wang, Denong

2009-01-01

We reported here a novel, ready-to-use bioarray platform and methodology for construction of sensitive carbohydrate cluster microarrays. This technology utilizes a 3-dimensional (3-D) poly(amidoamine) starburst dendrimer monolayer assembled on glass surface, which is functionalized with terminal aminooxy and hydrazide groups for site-specific coupling of carbohydrates. A wide range of saccharides, including monosaccharides, oligosaccharides and polysaccharides of diverse structures, are applicable for the 3-D bioarray platform without prior chemical derivatization. The process of carbohydrate coupling is effectively accelerated by microwave radiation energy. The carbohydrate concentration required for microarray fabrication is substantially reduced using this technology. Importantly, this bioarray platform presents sugar chains in defined orientation and cluster configurations. It is, thus, uniquely useful for exploration of the structural and conformational diversities of glyco-epitope and their functional properties. PMID:19791771

In vitro motility evaluation of aggregated cancer cells by means of automatic image processing.

PubMed

De Hauwer, C; Darro, F; Camby, I; Kiss, R; Van Ham, P; Decaesteker, C

1999-05-01

Set up of an automatic image processing based method that enables the motility of in vitro aggregated cells to be evaluated for a number of hours. Our biological model included the PC-3 human prostate cancer cell line growing as a monolayer on the bottom of Falcon plastic dishes containing conventional culture media. Our equipment consisted of an incubator, an inverted phase contrast microscope, a Charge Coupled Device (CCD) video camera, and a computer equipped with an image processing software developed in our laboratory. This computer-assisted microscope analysis of aggregated cells enables global cluster motility to be evaluated. This analysis also enables the trajectory of each cell to be isolated and parametrized within a given cluster or, indeed, the trajectories of individual cells outside a cluster. The results show that motility inside a PC-3 cluster is not restricted to slight motion due to cluster expansion, but rather consists of a marked cell movement within the cluster. The proposed equipment enables in vitro aggregated cell motility to be studied. This method can, therefore, be used in pharmacological studies in order to select anti-motility related compounds. The compounds selected by the equipment described could then be tested in vivo as potential anti-metastatic.

Comparing Effects of Cluster-Coupled Patterns on Opinion Dynamics

NASA Astrophysics Data System (ADS)

Liu, Yun; Si, Xia-Meng; Zhang, Yan-Chao

2012-07-01

Community structure is another important feature besides small-world and scale-free property of complex networks. Communities can be coupled through specific fixed links between nodes, or occasional encounter behavior. We introduce a model for opinion evolution with multiple cluster-coupled patterns, in which the interconnectivity denotes the coupled degree of communities by fixed links, and encounter frequency controls the coupled degree of communities by encounter behaviors. Considering the complicated cognitive system of people, the CODA (continuous opinions and discrete actions) update rules are used to mimic how people update their decisions after interacting with someone. It is shown that, large interconnectivity and encounter frequency both can promote consensus, reduce competition between communities and propagate some opinion successfully across the whole population. Encounter frequency is better than interconnectivity at facilitating the consensus of decisions. When the degree of social cohesion is same, small interconnectivity has better effects on lessening the competence between communities than small encounter frequency does, while large encounter frequency can make the greater degree of agreement across the whole populations than large interconnectivity can.

Version 4.0 of code Java for 3D simulation of the CCA model

NASA Astrophysics Data System (ADS)

Fan, Linyu; Liao, Jianwei; Zuo, Junsen; Zhang, Kebo; Li, Chao; Xiong, Hailing

2018-07-01

This paper presents a new version Java code for the three-dimensional simulation of Cluster-Cluster Aggregation (CCA) model to replace the previous version. Many redundant traverses of clusters-list in the program were totally avoided, so that the consumed simulation time is significantly reduced. In order to show the aggregation process in a more intuitive way, we have labeled different clusters with varied colors. Besides, a new function is added for outputting the particle's coordinates of aggregates in file to benefit coupling our model with other models.

Pendulum Motion in Main Parachute Clusters

NASA Technical Reports Server (NTRS)

Ray, Eric S.; Machin, Ricardo A.

2015-01-01

The coupled dynamics of a cluster of parachutes to a payload are notoriously difficult to predict. Often the payload is designed to be insensitive to the range of attitude and rates that might occur, but spacecraft generally do not have the mass and volume budgeted for this robust of a design. The National Aeronautics and Space Administration (NASA) Orion Capsule Parachute Assembly System (CPAS) implements a cluster of three mains for landing. During testing of the Engineering Development Unit (EDU) design, it was discovered that with a cluster of two mains (a fault tolerance required for human rating) the capsule coupled to the parachute cluster could get into a limit cycle pendulum motion which would exceed the spacecraft landing capability. This pendulum phenomenon could not be predicted with the existing models and simulations. A three phased effort has been undertaken to understand the consequence of the pendulum motion observed, and explore potential design changes that would mitigate this phenomenon. This paper will review the early analysis that was performed of the pendulum motion observed during EDU testing, summarize the analysis ongoing to understand the root cause of the pendulum phenomenon, and discuss the modeling and testing that is being pursued to identify design changes that would mitigate the risk.

Ab initio Bogoliubov coupled cluster theory for open-shell nuclei

DOE PAGES

Signoracci, Angelo J.; Duguet, Thomas; Hagen, Gaute; ...

2015-06-29

Background: Ab initio many-body methods have been developed over the past 10 yr to address closed-shell nuclei up to mass A≈130 on the basis of realistic two- and three-nucleon interactions. A current frontier relates to the extension of those many-body methods to the description of open-shell nuclei. Several routes to address open-shell nuclei are currently under investigation, including ideas that exploit spontaneous symmetry breaking. Purpose: Singly open-shell nuclei can be efficiently described via the sole breaking of U(1) gauge symmetry associated with particle-number conservation as a way to account for their superfluid character. While this route was recently followed withinmore » the framework of self-consistent Green's function theory, the goal of the present work is to formulate a similar extension within the framework of coupled cluster theory. Methods: We formulate and apply Bogoliubov coupled cluster (BCC) theory, which consists of representing the exact ground-state wave function of the system as the exponential of a quasiparticle excitation cluster operator acting on a Bogoliubov reference state. Equations for the ground-state energy and the cluster amplitudes are derived at the singles and doubles level (BCCSD) both algebraically and diagrammatically. The formalism includes three-nucleon forces at the normal-ordered two-body level. The first BCC code is implemented in m scheme, which will permit the treatment of doubly open-shell nuclei via the further breaking of SU(2) symmetry associated with angular momentum conservation. Results: Proof-of-principle calculations in an N max=6 spherical harmonic oscillator basis for 16,18O and 18Ne in the BCCD approximation are in good agreement with standard coupled cluster results with the same chiral two-nucleon interaction, while 20O and 20Mg display underbinding relative to experiment. The breaking of U(1) symmetry, monitored by computing the variance associated with the particle-number operator, is relatively constant for all five nuclei, in both the Hartree-Fock-Bogoliubov and BCCD approximations. Conclusions: The newly developed many-body formalism increases the potential span of ab initio calculations based on single-reference coupled cluster techniques tremendously, i.e., potentially to reach several hundred additional midmass nuclei. The new formalism offers a wealth of potential applications and further extensions dedicated to the description of ground and excited states of open-shell nuclei. Short-term goals include the implementation of three-nucleon forces at the normal-ordered two-body level. Midterm extensions include the approximate treatment of triples corrections and the development of the equation-of-motion methodology to treat both excited states and odd nuclei. Long-term extensions include exact restoration of U(1) and SU(2) symmetries.« less

Clustering of Helicobacter pylori infection in couples: differences between high- and low-prevalence population groups.

PubMed

Brenner, Hermann; Weyermann, Maria; Rothenbacher, Dietrich

2006-07-01

Several mostly small-scale studies reported clustering of Helicobacter pylori infections as a possible indicator of conjugal transmission, but results have been inconsistent. We assessed clustering of H pylori infections in a large community-based study from Germany that included both high-prevalence and low-prevalence population subgroups. Current H pylori infection was determined among 670 couples by means of carbon-13-urea breath test ((13)C-UBT) breath test and a monoclonal antigen immunoassay for H pylori in stool. Prevalences of infection among women were 34.9% (51 of 146 women) if the partner was infected and 14.5% (76 of 524 women) if the partner was not infected. Stratification by nationality showed a strong association of infection for partners with other than German nationality (adjusted odds ratio [OR], 6.05; 95% confidence interval [CI], 1.31-17.96), for whom prevalence of infection was greater than 50%, whereas no association was seen for German partners born in Germany (OR, 1.10; 95% CI, 0.47-2.61), for whom infection prevalence was approximately 10% (p for interaction = 0.048). Conjugal transmission of infection caused by H pylori is unlikely to be of relevance in low-prevalence population groups. Our results are consistent with the hypothesis of a potential role of conjugal transmission of H pylori infection in high-prevalence population groups.

Rapidly differentiating grape seeds from different sources based on characteristic fingerprints using direct analysis in real time coupled with time-of-flight mass spectrometry combined with chemometrics.

PubMed

Song, Yuqiao; Liao, Jie; Dong, Junxing; Chen, Li

2015-09-01

The seeds of grapevine (Vitis vinifera) are a byproduct of wine production. To examine the potential value of grape seeds, grape seeds from seven sources were subjected to fingerprinting using direct analysis in real time coupled with time-of-flight mass spectrometry combined with chemometrics. Firstly, we listed all reported components (56 components) from grape seeds and calculated the precise m/z values of the deprotonated ions [M-H](-) . Secondly, the experimental conditions were systematically optimized based on the peak areas of total ion chromatograms of the samples. Thirdly, the seven grape seed samples were examined using the optimized method. Information about 20 grape seed components was utilized to represent characteristic fingerprints. Finally, hierarchical clustering analysis and principal component analysis were performed to analyze the data. Grape seeds from seven different sources were classified into two clusters; hierarchical clustering analysis and principal component analysis yielded similar results. The results of this study lay the foundation for appropriate utilization and exploitation of grape seed samples. Due to the absence of complicated sample preparation methods and chromatographic separation, the method developed in this study represents one of the simplest and least time-consuming methods for grape seed fingerprinting. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Excited states of 4He

NASA Astrophysics Data System (ADS)

Aoyama, Shigeyoshi

2013-04-01

The study of the 4He nucleus is important because it is the most basic sub-unit (cluster) in nuclei. We have investigated the structures and the reaction mechanisms in 4He by using the correlated Gaussian basis function with the global vector representation. In order to treat the boundary condition for the ab-initio calculation of the four nucleons, we employ the Microscopic R-matrix Method (MRM) and the Complex Scaling Method (CSM) . Elastic-scattering phase shifts for four-nucleon systems are studied in an ab-initio type cluster model with MRM in order to clarify the role of the tensor force and to investigate cluster distortions in low energy d+d and t+p scattering. For 1S0, the calculated phase shifts show that the t+p and h+n channels are strongly coupled to the d+d channel for the case of the realistic interaction.

Pilot-in-the-Loop CFD Method Development

DTIC Science & Technology

2014-06-16

CFD analysis. Coupled simulations will be run at PSU on the COCOA -4 cluster, a high performance computing cluster. The CRUNCH CFD software has...been installed on the COCOA -4 servers and initial software tests are being conducted. Initial efforts will use the Generic Frigate Shape SFS-2 to

The devil is in the tails: the role of globular cluster mass evolution on stream properties

NASA Astrophysics Data System (ADS)

Balbinot, Eduardo; Gieles, Mark

2018-02-01

We present a study of the effects of collisional dynamics on the formation and detectability of cold tidal streams. A semi-analytical model for the evolution of the stellar mass function was implemented and coupled to a fast stellar stream simulation code, as well as the synthetic cluster evolution code EMACSS for the mass evolution as a function of a globular cluster orbit. We find that the increase in the average mass of the escaping stars for clusters close to dissolution has a major effect on the observable stream surface density. As an example, we show that Palomar 5 would have undetectable streams (in an SDSS-like survey) if it was currently three times more massive, despite the fact that a more massive cluster loses stars at a higher rate. This bias due to the preferential escape of low-mass stars is an alternative explanation for the absence of tails near massive clusters, than a dark matter halo associated with the cluster. We explore the orbits of a large sample of Milky Way globular clusters and derive their initial masses and remaining mass fraction. Using properties of known tidal tails, we explore regions of parameter space that favour the detectability of a stream. A list of high-probability candidates is discussed.

Role of a Water Network around the Mn4CaO5 Cluster in Photosynthetic Water Oxidation: A Fourier Transform Infrared Spectroscopy and Quantum Mechanics/Molecular Mechanics Calculation Study.

PubMed

Nakamura, Shin; Ota, Kai; Shibuya, Yuichi; Noguchi, Takumi

2016-01-26

Photosynthetic water oxidation takes place at the Mn4CaO5 cluster in photosystem II. Around the Mn4CaO5 cluster, a hydrogen bond network is formed by several water molecules, including four water ligands. To clarify the role of this water network in the mechanism of water oxidation, we investigated the effects of the removal of Ca(2+) and substitution with metal ions on the vibrations of water molecules coupled to the Mn4CaO5 cluster by means of Fourier transform infrared (FTIR) difference spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. The OH stretching vibrations of nine water molecules forming a network between D1-D61 and YZ were calculated using the QM/MM method. On the the calculated normal modes, a broad positive feature at 3200-2500 cm(-1) in an S2-minus-S1 FTIR spectrum was attributed to the vibrations of strongly hydrogen-bonded OH bonds of water involving the vibrations of water ligands to a Mn ion and the in-phase coupled vibration of a water network connected to YZ, while bands in the 3700-3500 cm(-1) region were assigned to the coupled vibrations of weakly hydrogen-bonded OH bonds of water. All the water bands were lost upon Ca(2+) depletion and Ba(2+) substitution, which inhibit the S2 → S3 transition, indicating that a solid water network was broken by these treatments. By contrast, Sr(2+) substitution slightly altered the water bands around 3600 cm(-1), reflecting minor modification in water interactions, consistent with the retention of water oxidation activity with a decreased efficiency. These results suggest that the water network around the Mn4CaO5 cluster plays an essential role in the water oxidation mechanism particularly in a concerted process of proton transfer and water insertion during the S2 → S3 transition.

Structures of Aln (n= 27, 28, 29, and 30) clusters with double-tetrahedron structures

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

Zhang, W.; Lu, W. C.; Sun, J.

2008-01-31

Global search for lowest-energy structures of neutral aluminum clusters Al{sub n} (n = 27, 28, 29 and 30) was performed using a genetic algorithm (GA) coupled with a tight-binding (TB) method. Structural candidates obtained from our GA search were further optimized with first-principles calculations. It is found that the medium-sized aluminum clusters Al{sub 27} to Al{sub 30} favor double-tetrahedron structures.

The cD galaxy in Abell cluster 1775

NASA Technical Reports Server (NTRS)

Hayes, J. J. E.; Bhattacharya, B.

1990-01-01

Over the last 20 years, a number of workers have studied the multiple nuclei cD galaxy in the rich Abell cluster 1775, trying to discover its nature. In all the cases though, very little has been published concerning its morphology. The majority of arguments about the nature of this object have been based on the relative radial velocities of the 2 components with each other and with the other galaxies in the cluster, or its radio morphology. Very little work has been done on the optical morphology. To rectify that lack of data, the authors have obtained charge coupled device (CCD) images of the cD. The authors find from the CCD data that the cD is unlikely to be a bound object and that there is strong evidence for a collision.

Infrared spectroscopy reveals both qualitative and quantitative differences in equine subchondral bone during maturation

NASA Astrophysics Data System (ADS)

Kobrina, Yevgeniya; Isaksson, Hanna; Sinisaari, Miikka; Rieppo, Lassi; Brama, Pieter A.; van Weeren, René; Helminen, Heikki J.; Jurvelin, Jukka S.; Saarakkala, Simo

2010-11-01

The collagen phase in bone is known to undergo major changes during growth and maturation. The objective of this study is to clarify whether Fourier transform infrared (FTIR) microspectroscopy, coupled with cluster analysis, can detect quantitative and qualitative changes in the collagen matrix of subchondral bone in horses during maturation and growth. Equine subchondral bone samples (n = 29) from the proximal joint surface of the first phalanx are prepared from two sites subjected to different loading conditions. Three age groups are studied: newborn (0 days old), immature (5 to 11 months old), and adult (6 to 10 years old) horses. Spatial collagen content and collagen cross-link ratio are quantified from the spectra. Additionally, normalized second derivative spectra of samples are clustered using the k-means clustering algorithm. In quantitative analysis, collagen content in the subchondral bone increases rapidly between the newborn and immature horses. The collagen cross-link ratio increases significantly with age. In qualitative analysis, clustering is able to separate newborn and adult samples into two different groups. The immature samples display some nonhomogeneity. In conclusion, this is the first study showing that FTIR spectral imaging combined with clustering techniques can detect quantitative and qualitative changes in the collagen matrix of subchondral bone during growth and maturation.

Exploring gay couples' experience with sexual dysfunction after radical prostatectomy: a qualitative study.

PubMed

Hartman, Mary-Ellen; Irvine, Jane; Currie, Kristen L; Ritvo, Paul; Trachtenberg, Lianne; Louis, Alyssa; Trachtenberg, John; Jamnicky, Leah; Matthew, Andrew G

2014-01-01

This exploratory study examines the experience of three gay couples managing sexual dysfunction as a result of undergoing a radical prostatectomy. Semi-structured interviews were conducted as part of a larger study at an urban hospital in Toronto, Ontario, Canada. Interview transcripts were transcribed verbatim, and analyzed using interpretative phenomenological analysis. The authors clustered 18 subordinate themes under 3 superordinate themes: (a) acknowledging change in sexual experience (libido, erectile function, sexual activity, orgasmic function); (b) accommodating change in sexual experience (strategies: emphasizing intimacy, embracing plan B, focus on the other; barriers: side-effect concerns, loss of naturalness, communication breakdown, failure to initiate, trial and failure, partner confounds); and (c) accepting change in sexual experience (indicators: emphasizing health, age attributions, finding a new normal; barriers: uncertain outcomes, treatment regrets). Although gay couples and heterosexual couples share many similar challenges, we discovered that gay men have particular sexual roles and can engage in novel accommodation practices, such as open relationships, that have not been noted in heterosexual couples. All couples, regardless of their level of sexual functioning, highlighted the need for more extensive programming related to sexual rehabilitation. Equitable rehabilitative support is critical to assist homosexual couples manage distress associated with prostatectomy-related sexual dysfunction.

A multi-point perspective on the formation of polar cap arcs: kinetic modeling and observations by Cluster and TIMED

NASA Astrophysics Data System (ADS)

de Keyser, J. M.; Maggiolo, R.; Echim, M.; Simon, C.; Zhang, Y.; Trotignon, J.

2010-12-01

On April 1st, 2004 the GUVI imager onboard the TIMED spacecraft spots an isolated and elongated polar cap arc. Simultaneously, the Cluster spacecraft detects an isolated upflowing ion beam above the polar cap. Cluster observations show that the ions are accelerated upward by a quasi-stationary electric field. The field-aligned potential drop is estimated to about 600 V and the upflowing ions are accompanied by a tenuous population of isotropic protons with a temperature of about 300eV. The footprint of the magnetic field line on which the Cluster spacecraft are situated, is located just outside the GUVI field of view in the prolongation of the polar cap arc. This suggests that the upflowing ion beam and the polar cap arc may be different signatures of the same phenomenon, as suggested by a recent statistical study of polar cap ion beams using Cluster data. We use Cluster observations at high altitude as input to a quasi-stationary magnetosphere-ionosphere (MI) coupling model. Using a Knight-type current-voltage relationship and the current continuity at the topside ionosphere, the model computes the energy spectrum of precipitating electrons at ionospheric altitudes corresponding to the generator electric field observed by Cluster. The MI coupling model provides a field-aligned potential drop in agreement with Cluster observations of upflowing ions and a spatial scale of the polar cap arc consistent with the optical observations by TIMED. The energy spectrum of the precipitating electrons provided by the model is introduced as input to the Trans4 ionospheric transport code. This 1-D model, based on Boltzmann's kinetic formalism, takes into account ionospheric processes like photoionisation and electron/proton precipitation, and computes the optical and UV emissions due to precipitating electrons. The emission rates provided by the Trans4 code are then compared to the optical observations by TIMED. Data and modeling results are consistent with quasi-static acceleration of precipitating magnetospheric electrons. We also discuss possible implications of our modeling results for optical observations of polar cap arcs.

Spatiotemporal coding of inputs for a system of globally coupled phase oscillators

NASA Astrophysics Data System (ADS)

Wordsworth, John; Ashwin, Peter

2008-12-01

We investigate the spatiotemporal coding of low amplitude inputs to a simple system of globally coupled phase oscillators with coupling function g(ϕ)=-sin(ϕ+α)+rsin(2ϕ+β) that has robust heteroclinic cycles (slow switching between cluster states). The inputs correspond to detuning of the oscillators. It was recently noted that globally coupled phase oscillators can encode their frequencies in the form of spatiotemporal codes of a sequence of cluster states [P. Ashwin, G. Orosz, J. Wordsworth, and S. Townley, SIAM J. Appl. Dyn. Syst. 6, 728 (2007)]. Concentrating on the case of N=5 oscillators we show in detail how the spatiotemporal coding can be used to resolve all of the information that relates the individual inputs to each other, providing that a long enough time series is considered. We investigate robustness to the addition of noise and find a remarkable stability, especially of the temporal coding, to the addition of noise even for noise of a comparable magnitude to the inputs.

Monothiol glutaredoxins and A-type proteins: partners in Fe-S cluster trafficking.

PubMed

Mapolelo, Daphne T; Zhang, Bo; Randeniya, Sajini; Albetel, Angela-Nadia; Li, Haoran; Couturier, Jérémy; Outten, Caryn E; Rouhier, Nicolas; Johnson, Michael K

2013-03-07

Monothiol glutaredoxins (Grxs) are proposed to function in Fe-S cluster storage and delivery, based on their ability to exist as apo monomeric forms and dimeric forms containing a subunit-bridging [Fe(2)S(2)](2+) cluster, and to accept [Fe(2)S(2)](2+) clusters from primary scaffold proteins. In addition yeast cytosolic monothiol Grxs interact with Fra2 (Fe repressor of activation-2), to form a heterodimeric complex with a bound [Fe(2)S(2)](2+) cluster that plays a key role in iron sensing and regulation of iron homeostasis. In this work, we report on in vitro UV-visible CD studies of cluster transfer between homodimeric monothiol Grxs and members of the ubiquitous A-type class of Fe-S cluster carrier proteins ((Nif)IscA and SufA). The results reveal rapid, unidirectional, intact and quantitative cluster transfer from the [Fe(2)S(2)](2+) cluster-bound forms of A. thaliana GrxS14, S. cerevisiae Grx3, and A. vinelandii Grx-nif homodimers to A. vinelandii(Nif)IscA and from A. thaliana GrxS14 to A. thaliana SufA1. Coupled with in vivo evidence for interaction between monothiol Grxs and A-type Fe-S cluster carrier proteins, the results indicate that these two classes of proteins work together in cellular Fe-S cluster trafficking. However, cluster transfer is reversed in the presence of Fra2, since the [Fe(2)S(2)](2+) cluster-bound heterodimeric Grx3-Fra2 complex can be formed by intact [Fe(2)S(2)](2+) cluster transfer from (Nif)IscA. The significance of these results for Fe-S cluster biogenesis or repair and the cellular regulation of the Fe-S cluster status are discussed.

Finer Distinctions: Variability in Satisfied Older Couples' Problem-Solving Behaviors.

PubMed

Rauer, Amy; Williams, Leah; Jensen, Jakob

2017-06-01

This study utilized observational and self-report data from 64 maritally satisfied and stable older couples to explore if there were meaningful differences in how couples approached marital disagreements. Using a typology approach to classify couples based on their behaviors in a 15-minute problem-solving interaction, findings revealed four types of couples: (1) problem solvers (characterized by both spouses' higher problem-solving skills and warmth), (2) supporters (characterized by both spouses' notable warmth), (3) even couples (characterized by both spouses' moderate problem-solving skills and warmth), and (4) cool couples (characterized by both spouses' greater negativity and lower problem-solving skills and warmth). Despite the differences in these behaviors, all couples had relatively high marital satisfaction and functioning. However, across nearly all indices, spouses in the cool couple cluster reported poorer marital functioning, particularly when compared to the problem solvers and supporters. These findings suggest that even modest doses of negativity (e.g., eye roll) may be problematic for some satisfied couples later in life. The implications of these typologies are discussed as they pertain to practitioners' efforts to tailor their approaches to a wider swath of the population. © 2015 Family Process Institute.

IMPLICATIONS OF RAPID CORE ROTATION IN RED GIANTS FOR INTERNAL ANGULAR MOMENTUM TRANSPORT IN STARS

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

Tayar, Jamie; Pinsonneault, Marc H., E-mail: tayar.1@osu.edu

2013-09-20

Core rotation rates have been measured for red giant stars using asteroseismology. These data, along with helioseismic measurements and open cluster spin-down studies, provide powerful clues about the nature and timescale for internal angular momentum transport in stars. We focus on two cases: the metal-poor red giant KIC 7341231 ({sup O}tto{sup )} and intermediate-mass core helium burning stars. For both, we examine limiting case studies for angular momentum coupling between cores and envelopes under the assumption of rigid rotation on the main sequence. We discuss the expected pattern of core rotation as a function of mass and radius. In themore » case of Otto, strong post-main-sequence coupling is ruled out and the measured core rotation rate is in the range of 23-33 times the surface value expected from standard spin-down models. The minimum coupling timescale (0.17-0.45 Gyr) is significantly longer than that inferred for young open cluster stars. This implies ineffective internal angular momentum transport in early first ascent giants. By contrast, the core rotation rates of evolved secondary clump stars are found to be consistent with strong coupling given their rapid main-sequence rotation. An extrapolation to the white dwarf regime predicts rotation periods between 330 and 0.0052 days, depending on mass and decoupling time. We identify two key ingredients that explain these features: the presence of a convective core and inefficient angular momentum transport in the presence of larger mean molecular weight gradients. Observational tests that can disentangle these effects are discussed.« less

Electronic structure of the Mn4OxCa cluster in the S0 and S2 states of the oxygen-evolving complex of photosystem II based on pulse 55Mn-ENDOR and EPR spectroscopy.

PubMed

Kulik, Leonid V; Epel, Boris; Lubitz, Wolfgang; Messinger, Johannes

2007-11-07

The heart of the oxygen-evolving complex (OEC) of photosystem II is a Mn4OxCa cluster that cycles through five different oxidation states (S0 to S4) during the light-driven water-splitting reaction cycle. In this study we interpret the recently obtained 55Mn hyperfine coupling constants of the S0 and S2 states of the OEC [Kulik et al. J. Am. Chem. Soc. 2005, 127, 2392-2393] on the basis of Y-shaped spin-coupling schemes with up to four nonzero exchange coupling constants, J. This analysis rules out the presence of one or more Mn(II) ions in S0 in methanol (3%) containing samples and thereby establishes that the oxidation states of the manganese ions in S0 and S2 are, at 4 K, Mn4(III, III, III, IV) and Mn4(III, IV, IV, IV), respectively. By applying a "structure filter" that is based on the recently reported single-crystal EXAFS data on the Mn4OxCa cluster [Yano et al. Science 2006, 314, 821-825] we (i) show that this new structural model is fully consistent with EPR and 55Mn-ENDOR data, (ii) assign the Mn oxidation states to the individual Mn ions, and (iii) propose that the known shortening of one 2.85 A Mn-Mn distance in S0 to 2.75 A in S1 [Robblee et al. J. Am. Chem. Soc. 2002, 124, 7459-7471] corresponds to a deprotonation of a mu-hydroxo bridge between MnA and MnB, i.e., between the outer Mn and its neighboring Mn of the mu3-oxo bridged moiety of the cluster. We summarize our results in a molecular model for the S0 --> S1 and S1 --> S2 transitions.

Electron spectra of xenon clusters irradiated with a laser-driven plasma soft-x-ray laser pulse

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

Namba, S.; Takiyama, K.; Hasegawa, N.

Xenon clusters were irradiated with plasma soft-x-ray laser pulses (having a wavelength of 13.9 nm, time duration of 7 ps, and intensities of up to 10 GW/cm{sup 2}). The laser photon energy was high enough to photoionize 4d core electrons. The cross section is large due to a giant resonance. The interaction was investigated by measuring the electron energy spectra. The photoelectron spectra for small clusters indicate that the spectral width due to the 4d hole significantly broadens with increasing cluster size. For larger clusters, the electron energy spectra evolve into a Maxwell-Boltzmann distribution, as a strongly coupled cluster nanoplasmamore » is generated.« less

The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

NASA Astrophysics Data System (ADS)

Förner, Wolfgang

1992-03-01

Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

Simulation of the photodetachment spectrum of HHfO- using coupled-cluster calculations

NASA Astrophysics Data System (ADS)

Mok, Daniel K. W.; Dyke, John M.; Lee, Edmond P. F.

2016-12-01

The photodetachment spectrum of HHfO- was simulated using restricted-spin coupled-cluster single-double plus perturbative triple {RCCSD(T)} calculations performed on the ground electronic states of HHfO and HHfO-, employing basis sets of up to quintuple-zeta quality. The computed RCCSD(T) electron affinity of 1.67 ± 0.02 eV at the complete basis set limit, including Hf 5s25p6 core correlation and zero-point energy corrections, agrees well with the experimental value of 1.70 ± 0.05 eV from a recent photodetachment study [X. Li et al., J. Chem. Phys. 136, 154306 (2012)]. For the simulation, Franck-Condon factors were computed which included allowances for anharmonicity and Duschinsky rotation. Comparisons between simulated and experimental spectra confirm the assignments of the molecular carrier and electronic states involved but suggest that the experimental vibrational structure has suffered from poor signal-to-noise ratio. An alternative assignment of the vibrational structure to that suggested in the experimental work is presented.

Investigation of a Diagnostic for Perturbation Theory: Comparison to the T(sub 1) Diagnostic of Coupled-Cluster Theory

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Head-Gordon, Martin; Rendell, Alistair P.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

A diagnostic for perturbation theory calculations, S(sub 2), is defined and numerical results are compared to the established T(sub 1) diagnostic from coupled-cluster theory. S(sub 2) is the lowest order non-zero contribution to a perturbation expansion of T(sub 1). S(sub 2) is a reasonable estimate of the importance of non-dynamical electron correlation, although not as reliable as T(sub 1). S(sub 2) values less than or equal to 0.012 suggest that low orders of perturbation theory should yield reasonable results; S(sub 2) values between 0.012-0.015 suggest that caution is required in interpreting results from low orders of perturbation theory; S(sub 2) values greater than or equal to 0.015 indicate that low orders of perturbation theory are not reliable for accurate results. Although not required mathematically, S(sub 2) is always less than T(sub 1) for the examples studied here.

Equation-of-motion coupled cluster method for the description of the high spin excited states

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

Musiał, Monika, E-mail: musial@ich.us.edu.pl; Lupa, Łukasz; Kucharski, Stanisław A.

2016-04-21

The equation-of-motion (EOM) coupled cluster (CC) approach in the version applicable for the excitation energy (EE) calculations has been formulated for high spin components. The EE-EOM-CC scheme based on the restricted Hartree-Fock reference and standard amplitude equations as used in the Davidson diagonalization procedure yields the singlet states. The triplet and higher spin components require separate amplitude equations. In the case of quintets, the relevant equations are much simpler and easier to solve. Out of 26 diagrammatic terms contributing to the R{sub 1} and R{sub 2} singlet equations in the case of quintets, only R{sub 2} operator survives with 5more » diagrammatic terms present. In addition all terms engaging three body elements of the similarity transformed Hamiltonian disappear. This indicates a substantial simplification of the theory. The implemented method has been applied to the pilot study of the excited states of the C{sub 2} molecule and quintet states of C and Si atoms.« less

Vacuum Ultraviolet Photoionization of Complex Chemical Systems

DOE PAGES

Kostko, Oleg; Bandyopadhyay, Biswajit; Ahmed, Musahid

2016-02-24

Tunable vacuum ultraviolet (VUV) radiation coupled to mass spectrometry is applied to the study of complex chemical systems in this paper. The identification of novel reactive intermediates and radicals is revealed in flame, pulsed photolysis, and pyrolysis reactors, leading to the elucidation of spectroscopy, reaction mechanisms, and kinetics. Mass-resolved threshold photoelectron photoion coincidence measurements provide unprecedented access to vibrationally resolved spectra of free radicals present in high-temperature reactors. Photoionization measurements in water clusters, nucleic acid base dimers, and their complexes with water provide signatures of proton transfer in hydrogen-bonded and π-stacked systems. Experimental and theoretical methods to track ion–molecule reactionsmore » and fragmentation pathways in intermolecular and intramolecular hydrogen-bonded systems in sugars and alcohols are described. Photoionization of laser-ablated molecules, clusters, and their reaction products inform thermodynamics and spectroscopy that are relevant to astrochemistry and catalysis. Finally, new directions in coupling VUV radiation to interrogate complex chemical systems are discussed.« less

Quantum soldering of individual quantum dots.

PubMed

Roy, Xavier; Schenck, Christine L; Ahn, Seokhoon; Lalancette, Roger A; Venkataraman, Latha; Nuckolls, Colin; Steigerwald, Michael L

2012-12-07

Making contact to a quantum dot: Single quantum-dot electronic circuits are fabricated by wiring atomically precise metal chalcogenide clusters with conjugated molecular connectors. These wired clusters can couple electronically to nanoscale electrodes and be tuned to control the charge-transfer characteristics (see picture). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geminal-spanning orbitals make explicitly correlated reduced-scaling coupled-cluster methods robust, yet simple

NASA Astrophysics Data System (ADS)

Pavošević, Fabijan; Neese, Frank; Valeev, Edward F.

2014-08-01

We present a production implementation of reduced-scaling explicitly correlated (F12) coupled-cluster singles and doubles (CCSD) method based on pair-natural orbitals (PNOs). A key feature is the reformulation of the explicitly correlated terms using geminal-spanning orbitals that greatly reduce the truncation errors of the F12 contribution. For the standard S66 benchmark of weak intermolecular interactions, the cc-pVDZ-F12 PNO CCSD F12 interaction energies reproduce the complete basis set CCSD limit with mean absolute error <0.1 kcal/mol, and at a greatly reduced cost compared to the conventional CCSD F12.

Adaptive fixed-time control for cluster synchronisation of coupled complex networks with uncertain disturbances

NASA Astrophysics Data System (ADS)

Jiang, Shengqin; Lu, Xiaobo; Cai, Guoliang; Cai, Shuiming

2017-12-01

This paper focuses on the cluster synchronisation problem of coupled complex networks with uncertain disturbances under an adaptive fixed-time control strategy. To begin with, complex dynamical networks with community structure which are subject to uncertain disturbances are taken into account. Then, a novel adaptive control strategy combined with fixed-time techniques is proposed to guarantee the nodes in the communities to desired states in a settling time. In addition, the stability of complex error systems is theoretically proved based on Lyapunov stability theorem. At last, two examples are presented to verify the effectiveness of the proposed adaptive fixed-time control.

The electron affinity of Al13H cluster: high level ab initio study

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2014-11-01

Al13H clusters have been considered candidates for cluster assembled materials. Here we have carried out benchmark calculations for the Al13H cluster, both neutral and anionic, with the aim of verifying the nature of stationary points on the potential energy surface, studying dynamics of H atom and determining an adiabatic electron affinity. A range of correlated methods applied include second-order perturbation theory (MP2), spin-component-scaled MP2, coupled electron pair (CEPA) and coupled cluster singles and doubles with perturbative triple corrections (CCSD(T)). These methods are used in combination with the correlation consistent basis sets through aug-cc-pVTZ including extrapolation to the complete basis set (CBS) limit. Performance of several different flavours of density functional theory (DFT) such as generalised gradient approximation (GGA), hybrid GGA, meta-GGA and hybrid-meta-GGA is assessed with respect to the ab initio correlated reference data. The harmonic force constant analysis is systematically performed with the MP2 and DFT methods. The MP2 results show that for neutral Al13H only the hollow structure is a potential energy minimum, with the bridged structure being a transition state for the H shift from the hollow site to the adjacent hollow site. The CCSD(T)/aug-cc-pVTZ (CCSD(T)/CBS) estimate of the energy barrier to this H shift is 2.6 (2.9) kcal/mol, implying that the H atom movement over the Al13H cluster surface is facile. By contrast, the DFT force constant analysis results suggest additional terminal and bridged minima structures. For the anion Al13H-, exhibiting 'stiffer' potential energy surface compared to the neutral, the existence of the hollow and terminal isomers is consistent with the earlier photoelectron spectroscopy assignment. The adiabatic electron affinity of Al13H is determined to be 2.00 and 1.95 eV (the latter including the ΔZPE correction) based on the CCSD(T) energies extrapolated to the CBS limit, whereas the respective CCSD(T)/CBS thermodynamic EA values are 2.79 and 2.80 eV.

Influence of Aromatic Molecules on the Structure and Spectroscopy of Water Clusters

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Walsh, Patrick S.; Zwier, Timothy S.

2016-06-01

Isomer-specific resonant ion-dip infrared spectra are presented for benzene-(water)_n, 1-2-diphenoxyethane-(water)_n, and tricyclophane-(water)_n clusters. The IR spectra are modeled with a local mode Hamiltonian that was originally formulated for the analysis of benzene-(water)_n clusters with up to seven waters. The model accounts for stretch-bend Fermi coupling, which can complicate the IR spectra in the 3150-3300 cm-1 region. When the water clusters interact with each of the solutes, the hydrogen bond lengths between the water molecules change in a characteristic way, reflecting the strength of the solute-water interaction. These structural effects are also reflected spectroscopically in the shifts of the local mode OH stretch frequencies. When diphenoxyethane is the solute, the water clusters distort more significantly than when bound to benzene. Tricyclophane's structure provides an aromatic-rich binding pocket for the water clusters. The local mode model is used to extract Hamiltonians for individual water molecules. These monomer Hamiltonians divide into groups based on their local H-bonding architecture, allowing for further classification of the wide variety of water environments encountered in this study.

Plasmaspheric Plumes Observed by the CLUSTER and IMAGE Spacecraft

NASA Technical Reports Server (NTRS)

Fung, S. F.; Benson, R. F.; Garcia, L. N.; Adrian, M. L.; Sandel, B.; Goldstein, M. L.

2008-01-01

Global IMAGE/EUV observations have revealed complex changes in plasmaspheric structures as the plasmasphere responds to geomagnetic activity while remaining under varying degrees of influence by co-rotation, depending on the radial distance. The complex plasmaspheric dynamics, with different scales of variability, is clearly far from being well understood. There is now renewed interest in the plasmasphere due to its apparent connections with the development of the ring current and radiation belt, and loss of ionospheric plasmas. Early in the mission, the Cluster spacecraft only crossed the plasmapause (L - 4) occasionally and made measurements of the outer plasmasphere and plasmaspheric drainage plumes. The study by Darrouzet et al. [2006] provided detailed analyses of in situ Cluster observations and IMAGE EUV observations of three plasmaspheric plumes detected in April-June, 2002. Within the next couple of years, Cluster orbit will change, causing perigee to migrate to lower altitudes, and thus providing excellent opportunities to obtain more detailed measurements of the plasmasphere. In this paper, we report our analyses of the earlier Cluster-IMAGE events by incorporating the different perspectives provided by the IMAGE Radio Plasma Imager (RPI) observations. We will discuss our new understanding of the structure and dynamics of the Cluster-IMAGE events.

Study of atmospheric dynamics and pollution in the coastal area of English Channel using clustering technique

NASA Astrophysics Data System (ADS)

Sokolov, Anton; Dmitriev, Egor; Delbarre, Hervé; Augustin, Patrick; Gengembre, Cyril; Fourmenten, Marc

2016-04-01

The problem of atmospheric contamination by principal air pollutants was considered in the industrialized coastal region of English Channel in Dunkirk influenced by north European metropolitan areas. MESO-NH nested models were used for the simulation of the local atmospheric dynamics and the online calculation of Lagrangian backward trajectories with 15-minute temporal resolution and the horizontal resolution down to 500 m. The one-month mesoscale numerical simulation was coupled with local pollution measurements of volatile organic components, particulate matter, ozone, sulphur dioxide and nitrogen oxides. Principal atmospheric pathways were determined by clustering technique applied to backward trajectories simulated. Six clusters were obtained which describe local atmospheric dynamics, four winds blowing through the English Channel, one coming from the south, and the biggest cluster with small wind speeds. This last cluster includes mostly sea breeze events. The analysis of meteorological data and pollution measurements allows relating the principal atmospheric pathways with local air contamination events. It was shown that contamination events are mostly connected with a channelling of pollution from local sources and low-turbulent states of the local atmosphere.

Tailoring Ion Charge State Distribution in Tetramethyltin Clusters under Influence of Moderate Intensity Picosecond Laser Pulse: Role of Laser Wavelength and Rate of Energy Deposition

NASA Astrophysics Data System (ADS)

Sharma, Pramod; Das, Soumitra; Vatsa, Rajesh K.

2017-07-01

Systematic manipulation of ionic-outcome in laser-cluster interaction process has been realized for studies carried out on tetramethyltin (TMT) clusters under picosecond laser conditions, determined by choice of laser wavelength and intensity. As a function of laser intensity, TMT clusters exhibit gradual enhancement in overall ionization of its cluster constituents, up to a saturation level of ionization, which was distinct for different wavelengths (266, 355, and 532 nm). Simultaneously, systematic appearance of higher multiply charged atomic ions and shift in relative abundance of multiply charged atomic ions towards higher charge state was observed, using time-of-flight mass spectrometer. At saturation level, multiply charged atomic ions up to (C2+, Sn2+) at 266 nm, (C4+, Sn4+) at 355 nm, and (C4+, Sn6+) at 532 nm were detected. In addition, at 355 nm intra-cluster ion chemistry within the ionized cluster leads to generation of molecular hydrogen ion (H2 +) and triatomic molecular hydrogen ion (H3 +). Generation of multiply charged atomic ions is ascribed to efficient coupling of laser pulse with the cluster media, facilitated by inner-ionized electrons produced within the cluster, at the leading edge of laser pulse. Role of inner-ionized electrons is authenticated by measuring kinetic energy distribution of electrons liberated upon disintegration of excessively ionized cluster, under the influence of picosecond laser pulse.

Superresolution Modeling of Calcium Release in the Heart

PubMed Central

Walker, Mark A.; Williams, George S.B.; Kohl, Tobias; Lehnart, Stephan E.; Jafri, M. Saleet; Greenstein, Joseph L.; Lederer, W.J.; Winslow, Raimond L.

2014-01-01

Stable calcium-induced calcium release (CICR) is critical for maintaining normal cellular contraction during cardiac excitation-contraction coupling. The fundamental element of CICR in the heart is the calcium (Ca2+) spark, which arises from a cluster of ryanodine receptors (RyR). Opening of these RyR clusters is triggered to produce a local, regenerative release of Ca2+ from the sarcoplasmic reticulum (SR). The Ca2+ leak out of the SR is an important process for cellular Ca2+ management, and it is critically influenced by spark fidelity, i.e., the probability that a spontaneous RyR opening triggers a Ca2+ spark. Here, we present a detailed, three-dimensional model of a cardiac Ca2+ release unit that incorporates diffusion, intracellular buffering systems, and stochastically gated ion channels. The model exhibits realistic Ca2+ sparks and robust Ca2+ spark termination across a wide range of geometries and conditions. Furthermore, the model captures the details of Ca2+ spark and nonspark-based SR Ca2+ leak, and it produces normal excitation-contraction coupling gain. We show that SR luminal Ca2+-dependent regulation of the RyR is not critical for spark termination, but it can explain the exponential rise in the SR Ca2+ leak-load relationship demonstrated in previous experimental work. Perturbations to subspace dimensions, which have been observed in experimental models of disease, strongly alter Ca2+ spark dynamics. In addition, we find that the structure of RyR clusters also influences Ca2+ release properties due to variations in inter-RyR coupling via local subspace Ca2+ concentration ([Ca2+]ss). These results are illustrated for RyR clusters based on super-resolution stimulated emission depletion microscopy. Finally, we present a believed-novel approach by which the spark fidelity of a RyR cluster can be predicted from structural information of the cluster using the maximum eigenvalue of its adjacency matrix. These results provide critical insights into CICR dynamics in heart, under normal and pathological conditions. PMID:25517166

Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling

PubMed Central

Li, Wenyuan; Dai, Chao; Liu, Chun-Chi

2012-01-01

Abstract Current network analysis methods all focus on one or multiple networks of the same type. However, cells are organized by multi-layer networks (e.g., transcriptional regulatory networks, splicing regulatory networks, protein-protein interaction networks), which interact and influence each other. Elucidating the coupling mechanisms among those different types of networks is essential in understanding the functions and mechanisms of cellular activities. In this article, we developed the first computational method for pattern mining across many two-layered graphs, with the two layers representing different types yet coupled biological networks. We formulated the problem of identifying frequent coupled clusters between the two layers of networks into a tensor-based computation problem, and proposed an efficient solution to solve the problem. We applied the method to 38 two-layered co-transcription and co-splicing networks, derived from 38 RNA-seq datasets. With the identified atlas of coupled transcription-splicing modules, we explored to what extent, for which cellular functions, and by what mechanisms transcription-splicing coupling takes place. PMID:22697243

Unsupervised learning on scientific ocean drilling datasets from the South China Sea

NASA Astrophysics Data System (ADS)

Tse, Kevin C.; Chiu, Hon-Chim; Tsang, Man-Yin; Li, Yiliang; Lam, Edmund Y.

2018-06-01

Unsupervised learning methods were applied to explore data patterns in multivariate geophysical datasets collected from ocean floor sediment core samples coming from scientific ocean drilling in the South China Sea. Compared to studies on similar datasets, but using supervised learning methods which are designed to make predictions based on sample training data, unsupervised learning methods require no a priori information and focus only on the input data. In this study, popular unsupervised learning methods including K-means, self-organizing maps, hierarchical clustering and random forest were coupled with different distance metrics to form exploratory data clusters. The resulting data clusters were externally validated with lithologic units and geologic time scales assigned to the datasets by conventional methods. Compact and connected data clusters displayed varying degrees of correspondence with existing classification by lithologic units and geologic time scales. K-means and self-organizing maps were observed to perform better with lithologic units while random forest corresponded best with geologic time scales. This study sets a pioneering example of how unsupervised machine learning methods can be used as an automatic processing tool for the increasingly high volume of scientific ocean drilling data.

Analytical Energy Gradients for Excited-State Coupled-Cluster Methods

NASA Astrophysics Data System (ADS)

Wladyslawski, Mark; Nooijen, Marcel

The equation-of-motion coupled-cluster (EOM-CC) and similarity transformed equation-of-motion coupled-cluster (STEOM-CC) methods have been firmly established as accurate and routinely applicable extensions of single-reference coupled-cluster theory to describe electronically excited states. An overview of these methods is provided, with emphasis on the many-body similarity transform concept that is the key to a rationalization of their accuracy. The main topic of the paper is the derivation of analytical energy gradients for such non-variational electronic structure approaches, with an ultimate focus on obtaining their detailed algebraic working equations. A general theoretical framework using Lagrange's method of undetermined multipliers is presented, and the method is applied to formulate the EOM-CC and STEOM-CC gradients in abstract operator terms, following the previous work in [P.G. Szalay, Int. J. Quantum Chem. 55 (1995) 151] and [S.R. Gwaltney, R.J. Bartlett, M. Nooijen, J. Chem. Phys. 111 (1999) 58]. Moreover, the systematics of the Lagrange multiplier approach is suitable for automation by computer, enabling the derivation of the detailed derivative equations through a standardized and direct procedure. To this end, we have developed the SMART (Symbolic Manipulation and Regrouping of Tensors) package of automated symbolic algebra routines, written in the Mathematica programming language. The SMART toolkit provides the means to expand, differentiate, and simplify equations by manipulation of the detailed algebraic tensor expressions directly. The Lagrangian multiplier formulation establishes a uniform strategy to perform the automated derivation in a standardized manner: A Lagrange multiplier functional is constructed from the explicit algebraic equations that define the energy in the electronic method; the energy functional is then made fully variational with respect to all of its parameters, and the symbolic differentiations directly yield the explicit equations for the wavefunction amplitudes, the Lagrange multipliers, and the analytical gradient via the perturbation-independent generalized Hellmann-Feynman effective density matrix. This systematic automated derivation procedure is applied to obtain the detailed gradient equations for the excitation energy (EE-), double ionization potential (DIP-), and double electron affinity (DEA-) similarity transformed equation-of-motion coupled-cluster singles-and-doubles (STEOM-CCSD) methods. In addition, the derivatives of the closed-shell-reference excitation energy (EE-), ionization potential (IP-), and electron affinity (EA-) equation-of-motion coupled-cluster singles-and-doubles (EOM-CCSD) methods are derived. Furthermore, the perturbative EOM-PT and STEOM-PT gradients are obtained. The algebraic derivative expressions for these dozen methods are all derived here uniformly through the automated Lagrange multiplier process and are expressed compactly in a chain-rule/intermediate-density formulation, which facilitates a unified modular implementation of analytic energy gradients for CCSD/PT-based electronic methods. The working equations for these analytical gradients are presented in full detail, and their factorization and implementation into an efficient computer code are discussed.

Surface critical behavior of thin Ising films at the ‘special point’

NASA Astrophysics Data System (ADS)

Moussa, Najem; Bekhechi, Smaine

2003-03-01

The critical surface phenomena of a magnetic thin Ising film is studied using numerical Monte-Carlo method based on Wolff cluster algorithm. With varying the surface coupling, js= Js/ J, the phase diagram exhibits a special surface coupling jsp at which all the films have a unique critical temperature Tc for an arbitrary thickness n. In spite of this, the critical exponent of the surface magnetization at the special point is found to increase with n. Moreover, non-universal features as well as dimensionality crossover from two- to three-dimensional behavior are found at this point.

TOSCA-based orchestration of complex clusters at the IaaS level

NASA Astrophysics Data System (ADS)

Caballer, M.; Donvito, G.; Moltó, G.; Rocha, R.; Velten, M.

2017-10-01

This paper describes the adoption and extension of the TOSCA standard by the INDIGO-DataCloud project for the definition and deployment of complex computing clusters together with the required support in both OpenStack and OpenNebula, carried out in close collaboration with industry partners such as IBM. Two examples of these clusters are described in this paper, the definition of an elastic computing cluster to support the Galaxy bioinformatics application where the nodes are dynamically added and removed from the cluster to adapt to the workload, and the definition of an scalable Apache Mesos cluster for the execution of batch jobs and support for long-running services. The coupling of TOSCA with Ansible Roles to perform automated installation has resulted in the definition of high-level, deterministic templates to provision complex computing clusters across different Cloud sites.

Insight from first principles into the stability and magnetism of alkali-metal superoxide nanoclusters

NASA Astrophysics Data System (ADS)

Arcelus, Oier; Suaud, Nicolas; Katcho, Nebil A.; Carrasco, Javier

2017-05-01

Alkali-metal superoxides are gaining increasing interest as 2p magnetic materials for information and energy storage. Despite significant research efforts on bulk materials, gaps in our knowledge of the electronic and magnetic properties at the nanoscale still remain. Here, we focused on the role that structural details play in determining stability, electronic structure, and magnetic couplings of (MO2)n (M = Li, Na, and K, with n = 2-8) clusters. Using first-principles density functional theory based on the Perdew-Burke-Ernzerhof and Heyd-Scuseria-Ernzerhof functionals, we examined the effect of atomic structure on the relative stability of different polymorphs within each investigated cluster size. We found that small clusters prefer to form planar-ring structures, whereas non-planar geometries become more stable when increasing the cluster size. However, the crossover point depends on the nature of the alkali metal. Our analysis revealed that electrostatic interactions govern the highly ionic M-O2 bonding and ultimately control the relative stability between 2-D and 3-D geometries. In addition, we analyzed the weak magnetic couplings between superoxide molecules in (NaO2)4 clusters comparing model Hamiltonian methods based on Wannier function projections onto πg states with wave function-based multi-reference calculations.

Incompatibility and preferred morphology in the self-accommodation microstructure of β-titanium shape memory alloy

NASA Astrophysics Data System (ADS)

Inamura, T.; Hosoda, H.; Miyazaki, S.

2013-02-01

The frequency distribution of habit plane variant (HPV) clusters and the deviation from twin orientation relationships (ORs) at the junction plane (JP) are investigated by transmission electron microscopy together with theoretical evaluation of the kinematic compatibility (KC) at the JP in a β-titanium shape memory alloy. Even though there are more than 10 types of possible HPV clusters, only three types are formed. V-shaped couplings of HPVs by {111} type I twins (VI: 49%) and by ⟨211⟩ type II twins (VII: 42%) are the predominant types. A triangular morphology due to coupling of {111} type I twins is observed with a frequency of only 9%. These preferred morphologies are well explained by the degree of incompatibility (the rotation necessary for compatible connection of HPVs). The exact twin OR and KC are maintained at the JP in a VI cluster instead of KC at the habit plane (HP), whereas the JP in a VII cluster is incompatible and the ⟨211⟩ type II twin OR shows slight deviation at the JP by about 0.4°. The competition between KC at the JP and KC at the HP (invariant plane) is responsible for the frequency distribution of HPV clusters and the character of the interfaces in the self-accommodation microstructure.

CHARM, a gender equity and family planning intervention for men and couples in rural India: protocol for the cluster randomized controlled trial evaluation.

PubMed

Yore, Jennifer; Dasgupta, Anindita; Ghule, Mohan; Battala, Madhusadana; Nair, Saritha; Silverman, Jay; Saggurti, Niranjan; Balaiah, Donta; Raj, Anita

2016-02-20

Globally, 41% of all pregnancies are unintended, increasing risk for unsafe abortion, miscarriage and maternal and child morbidities and mortality. One in four pregnancies in India (3.3 million pregnancies, annually) are unintended; 2/3 of these occur in the context of no modern contraceptive use. In addition, no contraceptive use until desired number and sex composition of children is achieved remains a norm in India. Research shows that globally and in India, the youngest and most newly married wives are least likely to use contraception and most likely to report husband's exclusive family planning decision-making control, suggesting that male engagement and family planning support is important for this group. Thus, the Counseling Husbands to Achieve Reproductive Health and Marital Equity (CHARM) intervention was developed in recognition of the need for more male engagement family planning models that include gender equity counseling and focus on spacing contraception use in rural India. For this study, a multi-session intervention delivered to men but inclusive of their wives was developed and evaluated as a two-armed cluster randomized controlled design study conducted across 50 mapped clusters in rural Maharashtra, India. Eligible rural young husbands and their wives (N = 1081) participated in a three session gender-equity focused family planning program delivered to the men (Sessions 1 and 2) and their wives (Session 3) by village health providers in rural India. Survey assessments were conducted at baseline and 9&18 month follow-ups with eligible men and their wives, and pregnancy tests were obtained from wives at baseline and 18-month follow-up. Additional in-depth understanding of how intervention impact occurred was assessed via in-depth interviews at 18 month follow-up with VHPs and a subsample of couples (n = 50, 2 couples per intervention cluster). Process evaluation was conducted to collect feedback from husbands, wives, and VHPs on program quality and to ascertain whether program elements were implemented according to curriculum protocols. Fidelity to intervention protocol was assessed via review of clinical records. All study procedures were completed in February 2015. Findings from this work offer important contributions to the growing field of male engagement in family planning, globally. ClinicalTrial.gov, NCT01593943.

Preliminary analysis of one year long space climate simulation

NASA Astrophysics Data System (ADS)

Facsko, G.; Honkonen, I. J.; Juusola, L.; Viljanen, A.; Vanhamäki, H.; Janhunen, P.; Palmroth, M.; Milan, S. E.

2013-12-01

One full year (155 Cluster orbits, from January 29, 2002 to February 2, 2003) is simulated using the Grand Unified Magnetosphere Ionosphere Coupling simulation (GUMICS) in the European Cluster Assimilation Technology project (ECLAT). This enables us to study the performance of a global magnetospheric model in an unprecedented scale both in terms of the amount of available observations and the length of the timeseries that can be compared. The solar wind for the simulated period, obtained from OMNIWeb, is used as input to GUMICS. We present an overview of various comparisons of GUMICS results to observations for the simulated year. Results along the Cluster reference spacecraft orbit to are compared to Cluster measurements. The Cross Polar Cap Potential (CPCP) results are compared to SuperDARN measurements. The IMAGE electrojet indicators (IU, IL) calculated from the ionospheric currents of GUMICS are compared to observations. Finally, Geomagnetically Induced Currents (GIC) calculated from GUMICS results along the Finnish mineral gas pipeline at Mätsälä are also compared to measurements.

Mapping the dynamics of force transduction at cell–cell junctions of epithelial clusters

PubMed Central

Ng, Mei Rosa; Besser, Achim; Brugge, Joan S; Danuser, Gaudenz

2014-01-01

Force transduction at cell-cell adhesions regulates tissue development, maintenance and adaptation. We developed computational and experimental approaches to quantify, with both sub-cellular and multi-cellular resolution, the dynamics of force transmission in cell clusters. Applying this technology to spontaneously-forming adherent epithelial cell clusters, we found that basal force fluctuations were coupled to E-cadherin localization at the level of individual cell-cell junctions. At the multi-cellular scale, cell-cell force exchange depended on the cell position within a cluster, and was adaptive to reconfigurations due to cell divisions or positional rearrangements. Importantly, force transmission through a cell required coordinated modulation of cell-matrix adhesion and actomyosin contractility in the cell and its neighbors. These data provide insights into mechanisms that could control mechanical stress homeostasis in dynamic epithelial tissues, and highlight our methods as a resource for the study of mechanotransduction in cell-cell adhesions. DOI: http://dx.doi.org/10.7554/eLife.03282.001 PMID:25479385

Social aggregation as a cooperative game

NASA Astrophysics Data System (ADS)

Vilone, Daniele; Guazzini, Andrea

2011-07-01

A new approach for the description of phenomena of social aggregation is suggested. On the basis of psychological concepts (as for instance social norms and cultural coordinates), we deduce a general mechanism for social aggregation in which different clusters of individuals can merge according to cooperation among the agents. In their turn, the agents can cooperate or defect according to the clusters' distribution inside the system. The fitness of an individual increases with the size of its cluster, but decreases with the work the individual had to do in order to join it. In order to test the reliability of such a new approach, we introduce a couple of simple toy models with the features illustrated above. We see, from this preliminary study, how cooperation is the most convenient strategy only in the presence of very large clusters, while on the other hand it is not necessary to have one hundred percent of cooperators for reaching a totally ordered configuration with only one megacluster filling the whole system.

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.

Validity of the classical monte carlo method to model the magnetic properties of a large transition-metal cluster: Mn19.

PubMed

Lima, Nicola; Caneschi, Andrea; Gatteschi, Dante; Kritikos, Mikael; Westin, L Gunnar

2006-03-20

The susceptibility of the large transition-metal cluster [Mn19O12(MOE)14(MOEH)10].MOEH (MOE = OC2H2O-CH3) has been fitted through classical Monte Carlo simulation, and an estimation of the exchange coupling constants has been done. With these results, it has been possible to perform a full-matrix diagonalization of the cluster core, which was used to provide information on the nature of the low-lying levels.

A technique for efficiently generating bimetallic clusters

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

Wagner, R.L.; Vann, W.D.; Castleman, A.W. , Jr.

1997-08-01

Reactivities of bimetallic clusters can be controlled by varying their composition, making them potentially valuable as catalysts and for use in elucidating the reactivities of such subnanoscale surfaces. A dual rod laser vaporization source coupled to a fast flow reactor is developed for the study of bimetallic clusters and their reactions. In order to establish the versatility of the technique, the results of studies are presented in which Nb/Al clusters are formed in two plasmas induced by the second harmonic (532 nm photons) of a single Nd:YAG laser and then detected by a quadrupole mass spectrometer. The beam from themore » laser is split and then focused onto each rod, allowing the mixing ratio within the cluster to vary by altering the laser fluence on each rod. With a low fluence on the Nb rod and a high fluence on the Al rod, an Al rich cluster distribution is formed, NbAl{sub m}{sup {minus}} (m=2{endash}20), and Al{sub m}{sup {minus}} (m=5{endash}31). By increasing the fluence on the Nb rod and decreasing the fluence on the Al rod, a Nb rich cluster distribution is formed, Nb{sub n}Al{sub m}{sup {minus}} (n=3{endash}8 and m=1{endash}3), Nb{sub n}OAl{sub m}{sup {minus}} (n=3{endash}8 and m=1{endash}5), and Nb{sub n}O{sup {minus}} (n=3{endash}8). Additional characterization is also performed on V/Al clusters. {copyright} {ital 1997 American Institute of Physics.}« less

Study of CP(N-1) theta-vacua by cluster simulation of SU(N) quantum spin ladders.

PubMed

Beard, B B; Pepe, M; Riederer, S; Wiese, U-J

2005-01-14

D-theory provides an alternative lattice regularization of the 2D CP(N-1) quantum field theory in which continuous classical fields emerge from the dimensional reduction of discrete SU(N) quantum spins. Spin ladders consisting of n transversely coupled spin chains lead to a CP(N-1) model with a vacuum angle theta=npi. In D-theory no sign problem arises and an efficient cluster algorithm is used to investigate theta-vacuum effects. At theta=pi there is a first order phase transition with spontaneous breaking of charge conjugation symmetry for CP(N-1) models with N>2.

Hyperfine coupling constants of the nitrogen and phosphorus atoms: A challenge for exact-exchange density-functional and post-Hartree-Fock methods

NASA Astrophysics Data System (ADS)

Kaupp, Martin; Arbuznikov, Alexei V.; Heßelmann, Andreas; Görling, Andreas

2010-05-01

The isotropic hyperfine coupling constants of the free N(S4) and P(S4) atoms have been evaluated with high-level post-Hartree-Fock and density-functional methods. The phosphorus hyperfine coupling presents a significant challenge to both types of methods. With large basis sets, MP2 and coupled-cluster singles and doubles calculations give much too small values for the phosphorus atom. Triple excitations are needed in coupled-cluster calculations to achieve reasonable agreement with experiment. None of the standard density functionals reproduce even the correct sign of this hyperfine coupling. Similarly, the computed hyperfine couplings depend crucially on the self-consistent treatment in exact-exchange density-functional theory within the optimized effective potential (OEP) method. Well-balanced auxiliary and orbital basis sets are needed for basis-expansion exact-exchange-only OEP approaches to come close to Hartree-Fock or numerical OEP data. Results from the localized Hartree-Fock and Krieger-Li-Iafrate approximations deviate notably from exact OEP data in spite of very similar total energies. Of the functionals tested, only full exact-exchange methods augmented by a correlation functional gave at least the correct sign of the P(S4) hyperfine coupling but with too low absolute values. The subtle interplay between the spin-polarization contributions of the different core shells has been analyzed, and the influence of even very small changes in the exchange-correlation potential could be identified.

The preBötzinger complex as a hub for network activity along the ventral respiratory column in the neonate rat.

PubMed

Gourévitch, Boris; Mellen, Nicholas

2014-09-01

In vertebrates, respiratory control is ascribed to heterogeneous respiration-modulated neurons along the Ventral Respiratory Column (VRC) in medulla, which includes the preBötzinger Complex (preBötC), the putative respiratory rhythm generator. Here, the functional anatomy of the VRC was characterized via optical recordings in the sagittaly sectioned neonate rat hindbrain, at sampling rates permitting coupling estimation between neuron pairs, so that each neuron was described using unitary, neuron-system, and coupling attributes. Structured coupling relations in local networks, significantly oriented coupling in the peri-inspiratory interval detected in pooled data, and significant correlations between firing rate and expiratory duration in subsets of neurons revealed network regulation at multiple timescales. Spatially averaged neuronal attributes, including coupling vectors, revealed a sharp boundary at the rostral margin of the preBötC, as well as other functional anatomical features congruent with identified structures, including the parafacial respiratory group and the nucleus ambiguus. Cluster analysis of attributes identified two spatially compact, homogenous groups: the first overlapped with the preBötC, and was characterized by strong respiratory modulation and dense bidirectional coupling with itself and other groups, consistent with a central role for the preBötC in respiratory control; the second lay between preBötC and the facial nucleus, and was characterized by weak respiratory modulation and weak coupling with other respiratory neurons, which is congruent with cardiovascular regulatory networks that are found in this region. Other groups identified using cluster analysis suggested that networks along VRC regulated expiratory duration, and the transition to and from inspiration, but these groups were heterogeneous and anatomically dispersed. Thus, by recording local networks in parallel, this study found evidence for respiratory regulation at multiple timescales along the VRC, as well as a role for the preBötC in the integration of functionally disparate respiratory neurons. Copyright © 2014 Elsevier Inc. All rights reserved.

Recent advances in spin-free state-specific and state-universal multi-reference coupled cluster formalisms: A unitary group adapted approach

NASA Astrophysics Data System (ADS)

Maitra, Rahul; Sinha, Debalina; Sen, Sangita; Shee, Avijit; Mukherjee, Debashis

2012-06-01

We present here the formulations and implementations of Mukherjee's State-Specific and State-Universal Multi-reference Coupled Cluster theories, which are explicitly spin free being obtained via the Unitary Group Adapted (UGA) approach, and thus, do not suffer from spin-contamination. We refer to them as UGA-SSMRCC and UGASUMRCC respectively. We propose a new multi-exponential cluster Ansatz analogous to but different from the one suggested by Jeziorski and Monkhorst (JM). Unlike the JM Ansatz, our choice involves spin-free unitary generators for the cluster operators and we replace the traditional exponential structure for the wave-operator by a suitable normal ordered exponential. We sketch the consequences of choosing our Ansatz, which leads to fully spin-free finite power series structure of the direct term of the MRCC equations. The UGA-SUMRCC follows from a suitable hierarchical generation of the cluster amplitudes of increasing rank, while the UGA-SSMRCC requires suitable sufficiency conditions to arrive at a well-defined set of equations for the cluster amplitudes. We discuss two distinct and inequivalent sufficiency conditions and their pros and cons. We also discuss a variant of the UGA-SSMRCC, where the number of cluster amplitudes can be drastically reduced by internal contraction of the two-body inactive cluster amplitudes. These are the most numerous, and thus a spin-free internally contracted description will lead to a high speed-up factor. We refer to this as ICID-UGA-SSMRCC. Essentially the same mathematical manipulations provide us with the UGA-SUMRCC theory as well. Pilot numerical results are presented to indicate the promise and the efficacy of all the three methods.

Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry

PubMed Central

Sampath, Rangarajan; Mulholland, Niveen; Blyn, Lawrence B.; Massire, Christian; Whitehouse, Chris A.; Waybright, Nicole; Harter, Courtney; Bogan, Joseph; Miranda, Mary Sue; Smith, David; Baldwin, Carson; Wolcott, Mark; Norwood, David; Kreft, Rachael; Frinder, Mark; Lovari, Robert; Yasuda, Irene; Matthews, Heather; Toleno, Donna; Housley, Roberta; Duncan, David; Li, Feng; Warren, Robin; Eshoo, Mark W.; Hall, Thomas A.; Hofstadler, Steven A.; Ecker, David J.

2012-01-01

Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have closely related near-neighbor organisms that are harmless. The biothreat agent, along with its near neighbors, can be thought of as a biothreat cluster or a biocluster for short. The ability to comprehensively detect the important biothreat clusters with resolution sufficient to distinguish the near neighbors with an extremely low false positive rate is required. A technological solution to this problem can be achieved by coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS). The biothreat assay described here detects ten bacterial and four viral biothreat clusters on the NIAID priority pathogen and HHS/USDA select agent lists. Detection of each of the biothreat clusters was validated by analysis of a broad collection of biothreat organisms and near neighbors prepared by spiking biothreat nucleic acids into nucleic acids extracted from filtered environmental air. Analytical experiments were carried out to determine breadth of coverage, limits of detection, linearity, sensitivity, and specificity. Further, the assay breadth was demonstrated by testing a diverse collection of organisms from each biothreat cluster. The biothreat assay as configured was able to detect all the target organism clusters and did not misidentify any of the near-neighbor organisms as threats. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry. PMID:22768032

Modifiers of Neighbors' Bystander Intervention in Intimate Partner Violence: A Concept Mapping Study.

PubMed

Wee, Sara; Todd, Mary-Justine; Oshiro, Michael; Greene, Emily; Frye, Victoria

2016-03-01

Encouraging bystander intervention in intimate partner violence (IPV) against women is potentially an important method of reducing the prevalence of such violence in urban communities. Most existing research has been conducted on campuses and in relation to sexual violence among teens or young adults. Our understanding of which bystander behaviors are feasible is nascent, and our knowledge of which situational factors influence neighbors' self-reported willingness to intervene is underdeveloped. We conducted a concept mapping study to identify potential bystander intervention behaviors in IPV among neighbors in urban settings; we also assessed whether perceived feasibility and effectiveness of those behaviors varied by situational characteristics. Using data collected from 41 residents of a low-income New York City neighborhood in late 2011, concept mapping was used to create a conceptual map of the 74 behaviors identified by participants. We examined participant differences in mean feasibility (i.e., that the participants "could" or "would" enact a behavior), feasibility given two situational characteristics (if the couple was perceived to have a history of IPV, and if children were believed to be involved or present), and perceived effectiveness of bystander behaviors. Differences across select sociodemographic factors of participants were also analyzed. A 13-cluster solution emerged, with clusters of bystander behaviors grouped into four larger cluster areas: victim focused, parenting/education focused, perpetrator focused, and community involvement focused. Bivariate analyses revealed that participants rated the four cluster areas as more feasible when a child was believed to be involved. Male participants rated intervention as less feasible when the couple was believed to have a history of IPV. Participants who reported a history of IPV victimization rated all four cluster areas as less effective on average, as compared with participants without a history of IPV. This study explored bystander intervention into IPV outside of a college context and among urban adults living in high-poverty areas. Results suggest that the presence of children and perceived history of IPV may affect bystander intervention. Specific recommendations to build the research base on bystander intervention in adult IPV as well as what situational, sociodemographic, and other factors mitigate against intervention among potential responders are offered.

Adding Spice to Vanilla LCDM simulations: Alternative Cosmologies & Lighting up Simulations

NASA Astrophysics Data System (ADS)

Jahan Elahi, Pascal

2015-08-01

Cold Dark Matter simulations have formed the backbone of our theoretical understanding of cosmological structure formation. Predictions from the Lambda Cold Dark Matter (LCDM) cosmology, where the Universe contains two dark components, namely Dark Matter & Dark Energy, are in excellent agreement with the Large-Scale Structures observed, i.e., the distribution of galaxies across cosmic time. However, this paradigm is in tension with observations at small-scales, from the number and properties of satellite galaxies around galaxies such as the Milky Way and Andromeda, to the lensing statistics of massive galaxy clusters. I will present several alternative models of cosmology (from Warm Dark Matter to coupled Dark Matter-Dark Energy models) and how they compare to vanilla LCDM by studying formation of groups and clusters dark matter only and adiabatic hydrodynamical zoom simulations. I will show how modifications to the dark sector can lead to some surprising results. For example, Warm Dark Matter, so often examined on small satellite galaxies scales, can be probed observationally using weak lensing at cluster scales. Coupled dark sectors, where dark matter decays into dark energy and experiences an effective gravitational potential that differs from that experienced by normal matter, is effectively hidden away from direct observations of galaxies. Studies like these are vital if we are to pinpoint observations which can look for unique signatures of the physics that governs the hidden Universe. Finally, I will discuss how all of these predictions are affected by uncertain galaxy formation physics. I will present results from a major comparison study of numerous hydrodynamical codes, the nIFTY cluster comparison project. This comparison aims to understand the code-to-code scatter in the properties of dark matter haloes and the galaxies that reside in them. We find that even in purely adiabatic simulations, different codes form clusters with very different X-ray profiles. The galaxies that form in these simulations, which all use codes that attempt to reproduce the observed galaxy population via not unreasonable subgrid physics, vary in stellar mass, morphology and gas fraction, sometimes by an order of magnitude. I will end with a discussion of precision cosmology in light of these results.

The Atacama Cosmology Telescope: Physical Properties and Purity of a Galaxy Cluster Sample Selected Via the Sunyaev-Zel'Dovich Effect

NASA Technical Reports Server (NTRS)

Menanteau, Felipe; Gonzalez, Jorge; Juin, Jean-Baptiste; Marriage, Tobias; Reese, Erik D.; Acquaviva, Viviana; Aguirre, Paula; Appel, John Willam; Baker, Andrew J.; Barrientos, L. Felipe;

Role of spin-orbit coupling in the Kugel-Khomskii model on the honeycomb lattice

NASA Astrophysics Data System (ADS)

Koga, Akihisa; Nakauchi, Shiryu; Nasu, Joji

2018-03-01

We study the effective spin-orbital model for honeycomb-layered transition metal compounds, applying the second-order perturbation theory to the three-orbital Hubbard model with the anisotropic hoppings. This model is reduced to the Kitaev model in the strong spin-orbit coupling limit. Combining the cluster mean-field approximations with the exact diagonalization, we treat the Kugel-Khomskii type superexchange interaction and spin-orbit coupling on an equal footing to discuss ground-state properties. We find that a zigzag ordered state is realized in the model within nearest-neighbor interactions. We clarify how the ordered state competes with the nonmagnetic state, which is adiabatically connected to the quantum spin liquid state realized in a strong spin-orbit coupling limit. Thermodynamic properties are also addressed. The present paper should provide another route to account for the Kitaev-based magnetic properties in candidate materials.

Magnetic Ordering in Gold Nanoclusters

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

Agrachev, Mikhail; Antonello, Sabrina; Dainese, Tiziano

Here, several research groups have observed magnetism in monolayer-protected gold-cluster samples, but the results were often contradictory and thus a clear understanding of this phenomenon is still missing. We used Au 25(SCH 2CH 2Ph) 18 0, which is a paramagnetic cluster that can be prepared with atomic precision and whose structure is known precisely. Previous magnetometry studies only detected paramagnetism. We used samples representing a range of crystallographic orders and studied their magnetic behaviors by electron paramagnetic resonance (EPR). As a film, Au 25(SCH 2CH 2Ph) 18 0 displays paramagnetic behavior but, at low temperature, ferromagnetic interactions are detectable. Onemore » or few single crystals undergo physical reorientation with the applied field and display ferromagnetism, as detected through hysteresis experiments. A large collection of microcrystals is magnetic even at room temperature and shows distinct paramagnetic, superparamagnetic, and ferromagnetic behaviors. Simulation of the EPR spectra shows that both spin-orbit coupling and crystal distortion are important to determine the observed magnetic behaviors. DFT calculations carried out on single cluster and periodic models predict values of spin6orbit coupling and crystal6splitting effects in agreement with the EPR derived quantities. Magnetism in gold nanoclusters is thus demonstrated to be the outcome of a very delicate balance of factors. To obtain reproducible results, the samples must be (i) controlled for composition and thus be monodispersed with atomic precision, (ii) of known charge state, and (iii) well defined also in terms of crystallinity and experimental conditions. This study highlights the efficacy of EPR spectroscopy to provide a molecular understanding of these phenomena« less

Magnetic Ordering in Gold Nanoclusters

DOE PAGES

Agrachev, Mikhail; Antonello, Sabrina; Dainese, Tiziano; ...

2017-06-12

Here, several research groups have observed magnetism in monolayer-protected gold-cluster samples, but the results were often contradictory and thus a clear understanding of this phenomenon is still missing. We used Au 25(SCH 2CH 2Ph) 18 0, which is a paramagnetic cluster that can be prepared with atomic precision and whose structure is known precisely. Previous magnetometry studies only detected paramagnetism. We used samples representing a range of crystallographic orders and studied their magnetic behaviors by electron paramagnetic resonance (EPR). As a film, Au 25(SCH 2CH 2Ph) 18 0 displays paramagnetic behavior but, at low temperature, ferromagnetic interactions are detectable. Onemore » or few single crystals undergo physical reorientation with the applied field and display ferromagnetism, as detected through hysteresis experiments. A large collection of microcrystals is magnetic even at room temperature and shows distinct paramagnetic, superparamagnetic, and ferromagnetic behaviors. Simulation of the EPR spectra shows that both spin-orbit coupling and crystal distortion are important to determine the observed magnetic behaviors. DFT calculations carried out on single cluster and periodic models predict values of spin6orbit coupling and crystal6splitting effects in agreement with the EPR derived quantities. Magnetism in gold nanoclusters is thus demonstrated to be the outcome of a very delicate balance of factors. To obtain reproducible results, the samples must be (i) controlled for composition and thus be monodispersed with atomic precision, (ii) of known charge state, and (iii) well defined also in terms of crystallinity and experimental conditions. This study highlights the efficacy of EPR spectroscopy to provide a molecular understanding of these phenomena« less

Spectroscopic and functional characterization of iron-sulfur cluster-bound forms of Azotobacter vinelandii (Nif)IscA.

PubMed

Mapolelo, Daphne T; Zhang, Bo; Naik, Sunil G; Huynh, Boi Hanh; Johnson, Michael K

2012-10-16

The mechanism of [4Fe-4S] cluster assembly on A-type Fe-S cluster assembly proteins, in general, and the specific role of (Nif)IscA in the maturation of nitrogen fixation proteins are currently unknown. To address these questions, in vitro spectroscopic studies (UV-visible absorption/CD, resonance Raman and Mössbauer) have been used to investigate the mechanism of [4Fe-4S] cluster assembly on Azotobacter vinelandii(Nif)IscA, and the ability of (Nif)IscA to accept clusters from NifU and to donate clusters to the apo form of the nitrogenase Fe-protein. The results show that (Nif)IscA can rapidly and reversibly cycle between forms containing one [2Fe-2S](2+) and one [4Fe-4S](2+) cluster per homodimer via DTT-induced two-electron reductive coupling of two [2Fe-2S](2+) clusters and O(2)-induced [4Fe-4S](2+) oxidative cleavage. This unique type of cluster interconversion in response to cellular redox status and oxygen levels is likely to be important for the specific role of A-type proteins in the maturation of [4Fe-4S] cluster-containing proteins under aerobic growth or oxidative stress conditions. Only the [4Fe-4S](2+)-(Nif)IscA was competent for rapid activation of apo-nitrogenase Fe protein under anaerobic conditions. Apo-(Nif)IscA was shown to accept clusters from [4Fe-4S] cluster-bound NifU via rapid intact cluster transfer, indicating a potential role as a cluster carrier for delivery of clusters assembled on NifU. Overall the results support the proposal that A-type proteins can function as carrier proteins for clusters assembled on U-type proteins and suggest that they are likely to supply [2Fe-2S] clusters rather than [4Fe-4S] for the maturation of [4Fe-4S] cluster-containing proteins under aerobic or oxidative stress growth conditions.

Spectroscopic and Functional Characterization of Iron-Sulfur Cluster-Bound Forms of Azotobacter vinelandii NifIscA†

PubMed Central

Mapolelo, Daphne T.; Zhang, Bo; Naik, Sunil G.; Huynh, Boi Hanh; Johnson, Michael K.

2012-01-01

The mechanism of [4Fe-4S] cluster assembly on A-type Fe-S cluster assembly proteins, in general, and the specific role of NifIscA in the maturation of nitrogen fixation proteins are currently unknown. To address these questions, in vitro spectroscopic studies (UV–visible absorption/CD, resonance Raman and Mössbauer) have been used to investigate the mechanism of [4Fe-4S] cluster assembly on Azotobacter vinelandii NifIscA, and the ability of NifIscA to accept clusters from NifU and to donate clusters to the apo form of the nitrogenase Fe-protein. The results show that NifIscA can rapidly and reversibly cycle between forms containing one [2Fe-2S]2+ and one [4Fe-4S]2+ cluster per homodimer via DTT-induced two-electron reductive coupling of two [2Fe-2S]2+ clusters and O2-induced [4Fe-4S]2+ oxidative cleavage. This unique type of cluster interconversion in response to cellular redox status and oxygen levels is likely to be important for the specific role of A-type proteins in the maturation of [4Fe-4S] cluster-containing proteins under aerobic growth or oxidative stress conditions. Only the [4Fe-4S]2+-NifIscA was competent for rapid activation of apo-nitrogenase Fe protein under anaerobic conditions. Apo-NifIscA was shown to accept clusters from [4Fe-4S] cluster-bound NifU via rapid intact cluster transfer, indicating a potential role as a cluster carrier for delivery of clusters assembled on NifU. Overall the results support the proposal that A-type proteins can function as carrier proteins for clusters assembled on U-type proteins and suggest that they are likely to supply [2Fe-2S] clusters rather than [4Fe-4S] for the maturation of [4Fe-4S] cluster-containing proteins under aerobic or oxidative stress growth conditions. PMID:23003323

Iron-sulfur cluster biogenesis in mammalian cells: new insights into the molecular mechanisms of cluster delivery

PubMed Central

Maio, Nunziata; Rouault, Tracey. A.

2014-01-01

Iron-sulfur (Fe-S) clusters are ancient, ubiquitous cofactors composed of iron and inorganic sulfur. The combination of the chemical reactivity of iron and sulfur, together with many variations of cluster composition, oxidation states and protein environments, enables Fe-S clusters to participate in numerous biological processes. Fe-S clusters are essential to redox catalysis in nitrogen fixation, mitochondrial respiration and photosynthesis, to regulatory sensing in key metabolic pathways (i. e. cellular iron homeostasis and oxidative stress response), and to the replication and maintenance of the nuclear genome. Fe-S cluster biogenesis is a multistep process that involves a complex sequence of catalyzed protein- protein interactions and coupled conformational changes between the components of several dedicated multimeric complexes. Intensive studies of the assembly process have clarified key points in the biogenesis of Fe-S proteins. However several critical questions still remain, such as: what is the role of frataxin? Why do some defects of Fe-S cluster biogenesis cause mitochondrial iron overload? How are specific Fe-S recipient proteins recognized in the process of Fe-S transfer? This review focuses on the basic steps of Fe-S cluster biogenesis, drawing attention to recent advances achieved on the identification of molecular features that guide selection of specific subsets of nascent Fe-S recipients by the cochaperone HSC20. Additionally, it outlines the distinctive phenotypes of human diseases due to mutations in the components of the basic pathway. PMID:25245479

New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins Involved in Iron Sulfur Cluster Biogenesis

PubMed Central

Fantini, Marco; Malinverni, Duccio; De Los Rios, Paolo; Pastore, Annalisa

2017-01-01

Direct coupling analysis (DCA) is a powerful statistical inference tool used to study protein evolution. It was introduced to predict protein folds and protein-protein interactions, and has also been applied to the prediction of entire interactomes. Here, we have used it to analyze three proteins of the iron-sulfur biogenesis machine, an essential metabolic pathway conserved in all organisms. We show that DCA can correctly reproduce structural features of the CyaY/frataxin family (a protein involved in the human disease Friedreich's ataxia) despite being based on the relatively small number of sequences allowed by its genomic distribution. This result gives us confidence in the method. Its application to the iron-sulfur cluster scaffold protein IscU, which has been suggested to function both as an ordered and a disordered form, allows us to distinguish evolutionary traces of the structured species, suggesting that, if present in the cell, the disordered form has not left evolutionary imprinting. We observe instead, for the first time, direct indications of how the protein can dimerize head-to-head and bind 4Fe4S clusters. Analysis of the alternative scaffold protein IscA provides strong support to a coordination of the cluster by a dimeric form rather than a tetramer, as previously suggested. Our analysis also suggests the presence in solution of a mixture of monomeric and dimeric species, and guides us to the prevalent one. Finally, we used DCA to analyze interactions between some of these proteins, and discuss the potentials and limitations of the method. PMID:28664160

A Well-Posed, Objective and Dynamic Two-Fluid Model

NASA Astrophysics Data System (ADS)

Chetty, Krishna; Vaidheeswaran, Avinash; Sharma, Subash; Clausse, Alejandro; Lopez de Bertodano, Martin

The transition from dispersed to clustered bubbly flows due to wake entrainment is analyzed with a well-posed and objective one-dimensional (1-D) Two-Fluid Model, derived from variational principles. Modeling the wake entrainment force using the variational technique requires formulation of the inertial coupling coefficient, which defines the kinetic coupling between the phases. The kinetic coupling between a pair of bubbles and the liquid is obtained from potential flow over two-spheres and the results are validated by comparing the virtual mass coefficients with existing literature. The two-body interaction kinetic coupling is then extended to a lumped parameter model for viscous flow over two cylindrical bubbles, to get the Two-Fluid Model for wake entrainment. Linear stability analyses comprising the characteristics and the dispersion relation and non-linear numerical simulations are performed with the 1-D variational Two-Fluid Model to demonstrate the wake entrainment instability leading to clustering of bubbles. Finally, the wavelengths, amplitudes and propagation velocities of the void waves from non-linear simulations are compared with the experimental data.

Dynamic Transition and Resonance in Coupled Oscillators Under Symmetry-Breaking Fields

NASA Astrophysics Data System (ADS)

Choi, J.; Choi, M. Y.; Chung, M. S.; Yoon, B.-G.

2013-06-01

We investigate numerically the dynamic properties of a system of globally coupled oscillators driven by periodic symmetry-breaking fields in the presence of noise. The phase distribution of the oscillators is computed and a dynamic transition is disclosed. It is further found that the stochastic resonance is closely related to the behavior of the dynamic order parameter, which is in turn explained by the formation of a bi-cluster in the system. Here noise tends to symmetrize the motion of the oscillators, facilitating the bi-cluster formation. The observed resonance appears to be of the same class as the resonance present in the two-dimensional Ising model under oscillating fields.

Implementation of High-Order Multireference Coupled-Cluster Methods on Intel Many Integrated Core Architecture.

PubMed

Aprà, E; Kowalski, K

2016-03-08

In this paper we discuss the implementation of multireference coupled-cluster formalism with singles, doubles, and noniterative triples (MRCCSD(T)), which is capable of taking advantage of the processing power of the Intel Xeon Phi coprocessor. We discuss the integration of two levels of parallelism underlying the MRCCSD(T) implementation with computational kernels designed to offload the computationally intensive parts of the MRCCSD(T) formalism to Intel Xeon Phi coprocessors. Special attention is given to the enhancement of the parallel performance by task reordering that has improved load balancing in the noniterative part of the MRCCSD(T) calculations. We also discuss aspects regarding efficient optimization and vectorization strategies.

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

Zaporozhets, Irina A.; Ivanov, Vladimir V.; Lyakh, Dmitry I.

The earlier proposed multi-reference state-specific coupled-cluster theory with the complete active space reference suffered from a problem of energy discontinuities when the formal reference state was changing in the calculation of the potential energy curve (PEC). A simple remedy to the discontinuity problem is found and is presented in this work. It involves using natural complete active space self-consistent field active orbitals in the complete active space coupled-cluster calculations. As a result, the approach gives smooth PECs for different types of dissociation problems, as illustrated in the calculations of the dissociation of the single bond in the hydrogen fluorine moleculemore » and of the symmetric double-bond dissociation in the water molecule.« less

Adding Spice to Vanilla LCDM simulations: From Alternative Cosmologies to Lighting up Galaxies

NASA Astrophysics Data System (ADS)

Jahan Elahi, Pascal

2015-08-01

Cold Dark Matter simulations have formed the backbone of our theoretical understanding of cosmological structure formation. Predictions from the Lambda Cold Dark Matter (LCDM) cosmology, in which the Universe contains two major dark components, namely Dark Matter and Dark Energy, are in excellent agreement with the Large-Scale Structures observed, i.e., the distribution of galaxies across cosmic time. However, this paradigm is in tension with observations at small-scales, from the number and properties of satellite galaxies around galaxies such as the Milky Way and Andromeda, to the lensing statistics of massive galaxy clusters. I will present several alternative models of cosmology (from Warm Dark Matter to coupled Dark Matter-Dark Energy models) and how they compare to vanilla LCDM by studying formation of groups and clusters dark matter only and adiabatic hydrodynamical zoom simulations. I will show how modifications to the dark sector can lead to some surprising results. For example, Warm Dark Matter, so often examined on small satellite galaxies scales, can be probed observationally using weak lensing at cluster scales. Coupled dark sectors, where dark matter decays into dark energy and experiences an effective gravitational potential that differs from that experienced by normal matter, is effectively hidden away from direct observations of galaxies. Studies like these are vital if we are to pinpoint observations which can look for unique signatures of the physics that governs the hidden Universe. Of course, all of these predictions are unfortunately affected by uncertain galaxy formation physics. I will end by presenting results from a comparison study of numerous hydrodynamical codes, the nIFTY cluster comparison project, and how even how purely adiabatic simulations run with different codes give in quite different galaxy populations. The galaxies that form in these simulations, which all attempt to reproduce the observed galaxy population via not unreasonable subgrid physics, can and do vary in stellar mass, morphology and gas fraction.

Putting out the fire: what terminates calcium-induced calcium release in cardiac muscle?

PubMed

Stern, Michael D; Cheng, Heping

2004-06-01

The majority of contractile calcium in cardiac muscle is released from stores in the sarcoplasmic reticulum (SR), by a process of calcium-induced calcium release (CICR) through ryanodine receptors. Because CICR is intrinsically self-reinforcing, the stability of and graded regulation of cardiac EC coupling appear paradoxical. It is now well established that this gradation results from the stochastic recruitment of varying numbers of elementary local release events, which may themselves be regenerative, and which can be directly observed as calcium sparks. Ryanodine receptors (RyRs) are clustered in dense lattices, and most calcium sparks are now believed to involve activation of multiple RyRs. This implies that local CICR is regenerative, requiring a mechanism to terminate it. It was initially assumed that this mechanism was inactivation of the RyR, but during the decade since the discovery of sparks, no sufficiently strong inactivation mechanism has been demonstrated in vitro and all empirically determined gating schemes for the RyR give unstable EC coupling in Monte Carlo simulations. We consider here possible release termination mechanisms. Stochastic attrition is the spontaneous decay of active clusters due to random channel closure; calculations show that it is much too slow unless assisted by another process. Calcium-dependent RyR inactivation involving third-party proteins remains a viable but speculative mechanism; current candidates include calmodulin and sorcin. Local depletion of SR release terminal calcium could terminate release, however calculations and measurements leave it uncertain whether a sufficient diffusion resistance exists within the SR to sustain such depletion. Depletion could be assisted by dependence of RyR activity on SR lumenal [Ca(2+)]. There is substantial evidence for such lumenal activation, but it is not clear if it is a strong enough effect to account for the robust termination of sparks. The existence of direct interactions among clustered RyRs might account for the discrepancy between the inactivation properties of isolated RyRs and intact clusters. Such coupled gating remains controversial. Determining the mechanism of release termination is the outstanding unsolved problem of cardiac EC coupling, and will probably require extensive genetic manipulation of the EC coupling apparatus in its native environment to unravel the solution.

Photo-induced transformation process at gold clusters-semiconductor interface: Implications for the complexity of gold clusters-based photocatalysis

NASA Astrophysics Data System (ADS)

Liu, Siqi; Xu, Yi-Jun

2016-03-01

The recent thrust in utilizing atomically precise organic ligands protected gold clusters (Au clusters) as photosensitizer coupled with semiconductors for nano-catalysts has led to the claims of improved efficiency in photocatalysis. Nonetheless, the influence of photo-stability of organic ligands protected-Au clusters at the Au/semiconductor interface on the photocatalytic properties remains rather elusive. Taking Au clusters-TiO2 composites as a prototype, we for the first time demonstrate the photo-induced transformation of small molecular-like Au clusters to larger metallic Au nanoparticles under different illumination conditions, which leads to the diverse photocatalytic reaction mechanism. This transformation process undergoes a diffusion/aggregation mechanism accompanied with the onslaught of Au clusters by active oxygen species and holes resulting from photo-excited TiO2 and Au clusters. However, such Au clusters aggregation can be efficiently inhibited by tuning reaction conditions. This work would trigger rational structural design and fine condition control of organic ligands protected-metal clusters-semiconductor composites for diverse photocatalytic applications with long-term photo-stability.

Clustering stock market companies via chaotic map synchronization

NASA Astrophysics Data System (ADS)

Basalto, N.; Bellotti, R.; De Carlo, F.; Facchi, P.; Pascazio, S.

2005-01-01

A pairwise clustering approach is applied to the analysis of the Dow Jones index companies, in order to identify similar temporal behavior of the traded stock prices. To this end, the chaotic map clustering algorithm is used, where a map is associated to each company and the correlation coefficients of the financial time series to the coupling strengths between maps. The simulation of a chaotic map dynamics gives rise to a natural partition of the data, as companies belonging to the same industrial branch are often grouped together. The identification of clusters of companies of a given stock market index can be exploited in the portfolio optimization strategies.

Role of radial nonuniformities in the interaction of an intense laser with atomic clusters

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

Holkundkar, Amol R.; Gupta, N. K.

A model for the interaction of an intense laser with atomic clusters is presented. The model takes into account the spatial nonuniformities of the cluster as it evolves in time. The cluster is treated as a stratified sphere having an arbitrary number of layers. Electric and magnetic fields are obtained by solving the vector Helmholtz equation coupled with one-dimensional Lagrangian hydrodynamics. Results are compared with the uniform density nanoplasma model. Enhancement in the amount of energy absorbed is seen over the uniform density model. In some cases the absorbed energy increases by as much as a factor of 40.

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.

The new ClusterTrap setup

NASA Astrophysics Data System (ADS)

Martinez, F.; Marx, G.; Schweikhard, L.; Vass, A.; Ziegler, F.

2011-07-01

ClusterTrap has been designed to investigate properties of atomic clusters in the gas phase with particular emphasis on the dependence on the cluster size and charge state. The combination of cluster source, Penning trap and time-of-flight mass spectrometry allows a variety of experimental schemes including collision-induced dissociation, photo-dissociation, further ionization by electron impact, and electron attachment. Due to the storage capability of the trap extended-delay reaction experiments can be performed. Several recent modifications have resulted in an improved setup. In particular, an electrostatic quadrupole deflector allows the coupling of several sources or detectors to the Penning trap. Furthermore, a linear radio-frequency quadrupole trap has been added for accumulation and ion bunching and by switching the potential of a drift tube the kinetic energy of the cluster ions can be adjusted on their way towards or from the Penning trap. Recently, experiments on multiply negatively charged clusters have been resumed.

Coupled cluster investigation on the thermochemistry of dimethyl sulphide, dimethyl disulphide and their dissociation products: the problem of the enthalpy of formation of atomic sulphur

NASA Astrophysics Data System (ADS)

Denis, Pablo A.

2014-04-01

By means of coupled cluster theory and correlation consistent basis sets we investigated the thermochemistry of dimethyl sulphide (DMS), dimethyl disulphide (DMDS) and four closely related sulphur-containing molecules: CH3SS, CH3S, CH3SH and CH3CH2SH. For the four closed-shell molecules studied, their enthalpies of formation (EOFs) were derived using bomb calorimetry. We found that the deviation of the EOF with respect to experiment was 0.96, 0.65, 1.24 and 1.29 kcal/mol, for CH3SH, CH3CH2SH, DMS and DMDS, respectively, when ΔHf,0 = 65.6 kcal/mol was utilised (JANAF value). However, if the recently proposed ΔHf,0 = 66.2 kcal/mol was used to estimate EOF, the errors dropped to 0.36, 0.05, 0.64 and 0.09 kcal/mol, respectively. In contrast, for the CH3SS radical, a better agreement with experiment was obtained if the 65.6 kcal/mol value was used. To compare with experiment avoiding the problem of the ΔHf,0 (S), we determined the CH3-S and CH3-SS bond dissociation energies (BDEs) in CH3S and CH3SS. At the coupled cluster with singles doubles and perturbative triples correction level of theory, these values are 48.0 and 71.4 kcal/mol, respectively. The latter BDEs are 1.5 and 1.2 kcal/mol larger than the experimental values. The agreement can be considered to be acceptable if we take into consideration that these two radicals present important challenges when determining their EOFs. It is our hope that this work stimulates new studies which help elucidate the problem of the EOF of atomic sulphur.

Cognitive-behavioral conjoint therapy for PTSD improves various PTSD symptoms and trauma-related cognitions: Results from a randomized controlled trial.

PubMed

Macdonald, Alexandra; Pukay-Martin, Nicole D; Wagner, Anne C; Fredman, Steffany J; Monson, Candice M

2016-02-01

Numerous studies document an association between posttraumatic stress disorder (PTSD) and impairments in intimate relationship functioning, and there is evidence that PTSD symptoms and associated impairments are improved by cognitive-behavioral conjoint therapy for PTSD (CBCT for PTSD; Monson & Fredman, 2012). The present study investigated changes across treatment in clinician-rated PTSD symptom clusters and patient-rated trauma-related cognitions in a randomized controlled trial comparing CBCT for PTSD with waitlist in a sample of 40 individuals with PTSD and their partners (N = 40; Monson et al., 2012). Compared with waitlist, patients who received CBCT for PTSD immediately demonstrated greater improvements in all PTSD symptom clusters, trauma-related beliefs, and guilt cognitions (Hedge's gs -.33 to -1.51). Results suggest that CBCT for PTSD improves all PTSD symptom clusters and trauma-related cognitions among individuals with PTSD and further supports the value of utilizing a couple-based approach to the treatment of PTSD. (c) 2016 APA, all rights reserved).

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

Endogenous field feedback promotes the detectability for exogenous electric signal in the hybrid coupled population.

PubMed

Wei, Xile; Zhang, Danhong; Lu, Meili; Wang, Jiang; Yu, Haitao; Che, Yanqiu

2015-01-01

This paper presents the endogenous electric field in chemical or electrical synaptic coupled networks, aiming to study the role of endogenous field feedback in the signal propagation in neural systems. It shows that the feedback of endogenous fields to network activities can reduce the required energy of the noise and enhance the transmission of input signals in hybrid coupled populations. As a common and important nonsynaptic interactive method among neurons, particularly, the endogenous filed feedback can not only promote the detectability of exogenous weak signal in hybrid coupled neural population but also enhance the robustness of the detectability against noise. Furthermore, with the increasing of field coupling strengths, the endogenous field feedback is conductive to the stochastic resonance by facilitating the transition of cluster activities from the no spiking to spiking regions. Distinct from synaptic coupling, the endogenous field feedback can play a role as internal driving force to boost the population activities, which is similar to the noise. Thus, it can help to transmit exogenous weak signals within the network in the absence of noise drive via the stochastic-like resonance.

The dynamics of cyclone clustering in re-analysis and a high-resolution climate model

NASA Astrophysics Data System (ADS)

Priestley, Matthew; Pinto, Joaquim; Dacre, Helen; Shaffrey, Len

2017-04-01

Extratropical cyclones have a tendency to occur in groups (clusters) in the exit of the North Atlantic storm track during wintertime, potentially leading to widespread socioeconomic impacts. The Winter of 2013/14 was the stormiest on record for the UK and was characterised by the recurrent clustering of intense extratropical cyclones. This clustering was associated with a strong, straight and persistent North Atlantic 250 hPa jet with Rossby wave-breaking (RWB) on both flanks, pinning the jet in place. Here, we provide for the first time an analysis of all clustered events in 36 years of the ERA-Interim Re-analysis at three latitudes (45˚ N, 55˚ N, 65˚ N) encompassing various regions of Western Europe. The relationship between the occurrence of RWB and cyclone clustering is studied in detail. Clustering at 55˚ N is associated with an extended and anomalously strong jet flanked on both sides by RWB. However, clustering at 65(45)˚ N is associated with RWB to the south (north) of the jet, deflecting the jet northwards (southwards). A positive correlation was found between the intensity of the clustering and RWB occurrence to the north and south of the jet. However, there is considerable spread in these relationships. Finally, analysis has shown that the relationships identified in the re-analysis are also present in a high-resolution coupled global climate model (HiGEM). In particular, clustering is associated with the same dynamical conditions at each of our three latitudes in spite of the identified biases in frequency and intensity of RWB.

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.

Application of the finite-field coupled-cluster method to calculate molecular properties relevant to electron electric-dipole-moment searches

NASA Astrophysics Data System (ADS)

Abe, M.; Prasannaa, V. S.; Das, B. P.

2018-03-01

Heavy polar diatomic molecules are currently among the most promising probes of fundamental physics. Constraining the electric dipole moment of the electron (e EDM ), in order to explore physics beyond the standard model, requires a synergy of molecular experiment and theory. Recent advances in experiment in this field have motivated us to implement a finite-field coupled-cluster (FFCC) approach. This work has distinct advantages over the theoretical methods that we had used earlier in the analysis of e EDM searches. We used relativistic FFCC to calculate molecular properties of interest to e EDM experiments, that is, the effective electric field (Eeff) and the permanent electric dipole moment (PDM). We theoretically determine these quantities for the alkaline-earth monofluorides (AEMs), the mercury monohalides (Hg X ), and PbF. The latter two systems, as well as BaF from the AEMs, are of interest to e EDM searches. We also report the calculation of the properties using a relativistic finite-field coupled-cluster approach with single, double, and partial triples' excitations, which is considered to be the gold standard of electronic structure calculations. We also present a detailed error estimate, including errors that stem from our choice of basis sets, and higher-order correlation effects.

Modeling Photoelectron Spectra of CuO, Cu2O, and CuO2 Anions with Equation-of-Motion Coupled-Cluster Methods: An Adventure in Fock Space.

PubMed

Orms, Natalie; Krylov, Anna I

2018-04-12

The experimental photoelectron spectra of di- and triatomic copper oxide anions have been reported previously. We present an analysis of the experimental spectra of the CuO - , Cu 2 O - , and CuO 2 - anions using equation-of-motion coupled-cluster (EOM-CC) methods. The open-shell electronic structure of each molecule demands a unique combination of EOM-CC methods to achieve an accurate and balanced representation of the multiconfigurational anionic- and neutral-state manifolds. Analysis of the Dyson orbitals associated with photodetachment from CuO - reveals the strong non-Koopmans character of the CuO states. For the lowest detachment energy, a good agreement between theoretical and experimental values is obtained with CCSD(T) (coupled-cluster with single and double excitations and perturbative account of triple excitations). The (T) correction is particularly important for Cu 2 O - . Use of a relativistic pseudopotential and matching basis set improves the quality of results in most cases. EOM-DIP-CCSD analysis of the low-lying states of CuO 2 - reveals multiple singlet and triplet anionic states near the triplet ground state, adding an extra layer of complexity to the interpretation of the experimental CuO 2 - photoelectron spectrum.

Increasing Black Hole Feedback-induced Quenching with Anisotropic Thermal Conduction

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

Kannan, Rahul; Vogelsberger, Mark; Pfrommer, Christoph

Feedback from central supermassive black holes is often invoked to explain the low star formation rates (SFRs) in the massive galaxies at the centers of galaxy clusters. However, the detailed physics of the coupling of the injected feedback energy with the intracluster medium (ICM) is still unclear. Using high-resolution magnetohydrodynamic cosmological simulations of galaxy cluster formation, we investigate the role of anisotropic thermal conduction in shaping the thermodynamic structure of clusters, and in particular, in modifying the impact of black hole feedback. Stratified anisotropically conducting plasmas are formally always unstable, and thus more prone to mixing, an expectation borne outmore » by our results. The increased mixing efficiently isotropizes the injected feedback energy, which in turn significantly improves the coupling between the feedback energy and the ICM. This facilitates an earlier disruption of the cool-core, reduces the SFR by more than an order of magnitude, and results in earlier quenching despite an overall lower amount of feedback energy injected into the cluster core. With conduction, the metallicity gradients and dispersions are lowered, aligning them better with observational constraints. These results highlight the important role of thermal conduction in establishing and maintaining the quiescence of massive galaxies.« less

Extensive regularization of the coupled cluster methods based on the generating functional formalism: application to gas-phase benchmarks and to the S(N)2 reaction of CHCl3 and OH- in water

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

Kowalski, Karol; Valiev, Marat

2009-12-21

The recently introduced energy expansion based on the use of generating functional (GF) [K. Kowalski, P.D. Fan, J. Chem. Phys. 130, 084112 (2009)] provides a way of constructing size-consistent non-iterative coupled-cluster (CC) corrections in terms of moments of the CC equations. To take advantage of this expansion in a strongly interacting regime, the regularization of the cluster amplitudes is required in order to counteract the effect of excessive growth of the norm of the CC wavefunction. Although proven to be effcient, the previously discussed form of the regularization does not lead to rigorously size-consistent corrections. In this paper we addressmore » the issue of size-consistent regularization of the GF expansion by redefning the equations for the cluster amplitudes. The performance and basic features of proposed methodology is illustrated on several gas-phase benchmark systems. Moreover, the regularized GF approaches are combined with QM/MM module and applied to describe the SN2 reaction of CHCl3 and OH- in aqueous solution.« less

UV laser photoactivation of hexachloroplatinate bound to individual nucleobases in vacuo as molecular level probes of a model photopharmaceutical.

PubMed

Matthews, Edward; Sen, Ananya; Yoshikawa, Naruo; Bergström, Ed; Dessent, Caroline E H

2016-06-01

Isolated molecular clusters of adenine, cytosine, thymine and uracil bound to hexachloroplatinate, PtCl6(2-), have been studied using laser electronic photodissociation spectroscopy to investigate photoactivation of a platinum complex in the vicinity of a nucleobase. These metal complex-nucleobase clusters represent model systems for identifying the fundamental photochemical processes occurring in photodynamic platinum drug therapies that target DNA. This is the first study to explore the specific role of a strongly photoactive platinum compound in the aggregate complex. Each of the clusters studied displays a broadly similar absorption spectra, with a strong λmax ∼ 4.6 eV absorption band and a subsequent increase in the absorption intensity towards higher spectral-energy. The absorption bands are traced to ligand-to-metal-charge-transfer excitations on the PtCl6(2-) moiety within the cluster, and result in Cl(-)·nucleobase and PtCl5(-) as primary photofragments. These results demonstrate how selective photoexcitation can drive distinctive photodecay channels for a model photo-pharmaceutical. In addition, cluster absorption due to excitation of nucleobase-centred chromophores is observed in the region around 5 eV. For the uracil cluster, photofragments consistent with ultrafast decay of the excited state and vibrational predissociation on the ground-state surface are observed. However, this decay channel becomes successively weaker on going from thymine to cytosine to adenine, due to differential coupling of the excited states to the electron detachment continuum. These effects demonstrate the distinctive photophysical characteristics of the different nucleobases, and are discussed in the context of the recently recorded photoelectron spectra of theses clusters.

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

NASA Astrophysics Data System (ADS)

Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F.; Neese, Frank

2016-01-01

Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate previous implementation.

Decaying vector dark matter as an explanation for the 3.5 keV line from galaxy clusters

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

Farzan, Yasaman; Akbarieh, Amin Rezaei, E-mail: yasaman@theory.ipm.ac.ir, E-mail: am_rezaei@physics.sharif.ir

2014-11-01

We present a Vector Dark Matter (VDM) model that explains the 3.5 keV line recently observed in the XMM-Newton observatory data from galaxy clusters. In this model, dark matter is composed of two vector bosons, V and V', which couple to the photon through an effective generalized Chern-Simons coupling, g{sub V}. V' is slightly heavier than V with a mass splitting m{sub V'} – m{sub V} ≅ 3.5 keV. The decay of V' to V and a photon gives rise to the 3.5 keV line. The production of V and V' takes place in the early universe within the freeze-in framework through the effectivemore » g{sub V} coupling when m{sub V'} < T < Λ, Λ being the cut-off above which the effective g{sub V} coupling is not valid. We introduce a high energy model that gives rise to the g{sub V} coupling at low energies. To do this, V and V' are promoted to gauge bosons of spontaneously broken new U(1){sub V} and U(1){sub V'} gauge symmetries, respectively. The high energy sector includes milli-charged chiral fermions that lead to the g{sub V} coupling at low energy via triangle diagrams.« less

Influence of topology in the mobility enhancement of pulse-coupled oscillator synchronization

NASA Astrophysics Data System (ADS)

Beardo, A.; Prignano, L.; Sagarra, O.; Díaz-Guilera, A.

2017-12-01

In this work we revisit the nonmonotonic behavior (NMB) of synchronization time with velocity reported for systems of mobile pulse-coupled oscillators (PCOs). We devise a control parameter that allows us to predict in which range of velocities NMB may occur, also uncovering the conditions allowing us to establish the emergence of NMB based on specific features of the connectivity rule. Specifically, our results show that if the connectivity rule is such that the interaction patterns are sparse and, more importantly, include a large fraction of nonreciprocal interactions, then the system will display NMB. We furthermore provide a microscopic explanation relating the presence of such features of the connectivity patterns to the existence of local clusters unable to synchronize, termed frustrated clusters, for which we also give a precise definition in terms of simple graph concepts. We conclude that, if the probability of finding a frustrated cluster in a system of moving PCOs is high enough, NMB occurs in a predictable range of velocities.

Properties of coupled-cluster equations originating in excitation sub-algebras

NASA Astrophysics Data System (ADS)

Kowalski, Karol

2018-03-01

In this paper, we discuss properties of single-reference coupled cluster (CC) equations associated with the existence of sub-algebras of excitations that allow one to represent CC equations in a hybrid fashion where the cluster amplitudes associated with these sub-algebras can be obtained by solving the corresponding eigenvalue problem. For closed-shell formulations analyzed in this paper, the hybrid representation of CC equations provides a natural way for extending active-space and seniority number concepts to provide an accurate description of electron correlation effects. Moreover, a new representation can be utilized to re-define iterative algorithms used to solve CC equations, especially for tough cases defined by the presence of strong static and dynamical correlation effects. We will also explore invariance properties associated with excitation sub-algebras to define a new class of CC approximations referred to in this paper as the sub-algebra-flow-based CC methods. We illustrate the performance of these methods on the example of ground- and excited-state calculations for commonly used small benchmark systems.

Spectroscopic insights into the oxygen-tolerant membrane-associated [NiFe] hydrogenase of Ralstonia eutropha H16.

PubMed

Saggu, Miguel; Zebger, Ingo; Ludwig, Marcus; Lenz, Oliver; Friedrich, Bärbel; Hildebrandt, Peter; Lendzian, Friedhelm

2009-06-12

This study provides the first spectroscopic characterization of the membrane-bound oxygen-tolerant [NiFe] hydrogenase (MBH) from Ralstonia eutropha H16 in its natural environment, the cytoplasmic membrane. The H2-converting MBH is composed of a large subunit, harboring the [NiFe] active site, and a small subunit, capable in coordinating one [3Fe4S] and two [4Fe4S] clusters. The hydrogenase dimer is electronically connected to a membrane-integral cytochrome b. EPR and Fourier transform infrared spectroscopy revealed a strong similarity of the MBH active site with known [NiFe] centers from strictly anaerobic hydrogenases. Most redox states characteristic for anaerobic [NiFe] hydrogenases were identified except for one remarkable difference. The formation of the oxygen-inhibited Niu-A state was never observed. Furthermore, EPR data showed the presence of an additional paramagnetic center at high redox potential (+290 mV), which couples magnetically to the [3Fe4S] center and indicates a structural and/or redox modification at or near the proximal [4Fe4S] cluster. Additionally, significant differences regarding the magnetic coupling between the Nia-C state and [4Fe4S] clusters were observed in the reduced form of the MBH. The spectroscopic properties are discussed with regard to the unusual oxygen tolerance of this hydrogenase and in comparison with those of the solubilized, dimeric form of the MBH.

Theoretical Study of the IR Spectroscopy of BENZENE-(WATER)_N Clusters

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Kusaka, Ryoji; Walsh, Patrick S.; Zwier, Timothy S.

2015-06-01

The local mode Hamiltonian that assigns RIDIR spectra for Bz-(H_2O)_6 and Bz-(H_2O)_7 is explored in detail for Bz-(H_2O)_n with n=3-7. In addition to contributions from OH stretches, the Hamiltonian includes the anharmonic coupling of each water monomer's bend overtone and its OH stretch fundamentals, which is necessary for accurately modeling 3150-3300 cm-1 region of the spectra. The parameters of the Hamiltonian can be calculated using either MP2 or density functional theory. The relative strengths and weaknesses of these two electronic structure approaches are examined to gain further physical understanding. Initial assignments of Bz-(H_2O)_6 and Bz-(H_2O)_7 were based on a linear scaling of M06-2X harmonic frequencies. In most cases, counterpoise-corrected MP2 calculations obtain similar frequencies (across all cluster sizes) if stretch anharmonicity is taken into account. Individual ``monomer Hamiltonians'' are constructed via the application of fourth order Van Vleck perturbation theory to MP2 potential energy surfaces. These calculations elucidate the sensitivity of intra-monomer couplings to chemical environment. The presence of benzene has particularly important consequences for the spectra of the Bz-(H_2O)3-5 clusters, in which the symmetry of the water cycles is broken by π-H-bonding to benzene. The nature of these perturbations is discussed.

Effect of H bond removal and changes in the position of the iron–sulphur head domain on the spin–lattice relaxation properties of the [2Fe–2S]2+ Rieske cluster in cytochrome bc1† †Electronic supplementary information (ESI) available: Fig. S1: results of equilibrium redox titration of the Fe–S cluster for different forms of cytochrome bc1; Fig. S2: selected results of simulations of X-band CW EPR spectra of the Rieske cluster recorded at 25 K using a single-component model; Fig. S3: temperature dependence of the spin–lattice relaxation rate (1/T1) of the Rieske cluster for the tds-inhibited WT in linearized form for Raman and Orbach processes; Table S1: values of g and g-strain components determined from fitting the two-component model to X-band CW EPR spectra (25 K) for different forms of cytochrome bc1. See DOI: 10.1039/c5cp02815a

PubMed Central

Sarewicz, Marcin; Dutka, Małgorzata; Pietras, Rafał; Borek, Arkadiusz

2015-01-01

Here, comparative electron spin–lattice relaxation studies of the 2Fe–2S iron–sulphur (Fe–S) cluster embedded in a large membrane protein complex – cytochrome bc1 – are reported. Structural modifications of the local environment alone (mutations S158A and Y160W removing specific H bonds between Fe–S and amino acid side chains) or in combination with changes in global protein conformation (mutations/inhibitors changing the position of the Fe–S binding domain within the protein complex) resulted in different redox potentials as well as g-, g-strain and the relaxation rates (T1–1) for the Fe–S cluster. The relaxation rates for T < 25 K were measured directly by inversion recovery, while for T > 60 K they were deduced from simulation of continuous wave EPR spectra of the cluster using a model that included anisotropy of Lorentzian broadening. In all cases, the relaxation rate involved contributions from direct, second-order Raman and Orbach processes, each dominating over different temperature ranges. The analysis of T1–1 (T) over the range 5–120 K yielded the values of the Orbach energy (EOrb), Debye temperature θD and Raman process efficiency CRam for each variant of the protein. As the Orbach energy was generally higher for mutants S158A and Y160W, compared to wild-type protein (WT), it is suggested that H bond removal influences the geometry leading to increased strength of antiferromagnetic coupling between two Fe ions of the cluster. While θD was similar for all variants (∼107 K), the efficiency of the Raman process generally depends on the spin–orbit coupling that is lower for S158A and Y160W mutants, when compared to the WT. However, in several cases CRam did not only correlate with spin–orbit coupling but was also influenced by other factors – possibly the modification of protein rigidity and therefore the vibrational modes around the Fe–S cluster that change upon the movement of the iron–sulphur head domain. PMID:26355649

Photo-induced transformation process at gold clusters-semiconductor interface: Implications for the complexity of gold clusters-based photocatalysis

PubMed Central

Liu, Siqi; Xu, Yi-Jun

2016-01-01

The recent thrust in utilizing atomically precise organic ligands protected gold clusters (Au clusters) as photosensitizer coupled with semiconductors for nano-catalysts has led to the claims of improved efficiency in photocatalysis. Nonetheless, the influence of photo-stability of organic ligands protected-Au clusters at the Au/semiconductor interface on the photocatalytic properties remains rather elusive. Taking Au clusters–TiO2 composites as a prototype, we for the first time demonstrate the photo-induced transformation of small molecular-like Au clusters to larger metallic Au nanoparticles under different illumination conditions, which leads to the diverse photocatalytic reaction mechanism. This transformation process undergoes a diffusion/aggregation mechanism accompanied with the onslaught of Au clusters by active oxygen species and holes resulting from photo-excited TiO2 and Au clusters. However, such Au clusters aggregation can be efficiently inhibited by tuning reaction conditions. This work would trigger rational structural design and fine condition control of organic ligands protected-metal clusters-semiconductor composites for diverse photocatalytic applications with long-term photo-stability. PMID:26947754

bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

PubMed

Alexander, Nathan; Woetzel, Nils; Meiler, Jens

2011-02-01

Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization.

PubMed

Neustetter, M; Jabbour Al Maalouf, E; Limão-Vieira, P; Denifl, S

2016-08-07

Electron ionization of neat tungsten hexacarbonyl (W(CO)6) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO)6 clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO)n (+) (0 ≤ n ≤ 6) and W2(CO)n (+) (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO)n (+) (0 ≤ n ≤ 3) and W2C(CO)n (+) (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.

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

Rizzi, Silvio; Hereld, Mark; Insley, Joseph

In this work we perform in-situ visualization of molecular dynamics simulations, which can help scientists to visualize simulation output on-the-fly, without incurring storage overheads. We present a case study to couple LAMMPS, the large-scale molecular dynamics simulation code with vl3, our parallel framework for large-scale visualization and analysis. Our motivation is to identify effective approaches for covisualization and exploration of large-scale atomistic simulations at interactive frame rates.We propose a system of coupled libraries and describe its architecture, with an implementation that runs on GPU-based clusters. We present the results of strong and weak scalability experiments, as well as future researchmore » avenues based on our results.« less

Ab initio investigation of structure, stability, thermal behavior, bonding, and infrared spectra of ionized water cluster (H2O)6+

NASA Astrophysics Data System (ADS)

Liu, Lei; Hu, Cui-E.; Tang, Mei; Chen, Xiang-Rong; Cai, Ling-Cang

2016-10-01

The low-lying isomers of cationic water cluster (H2O)6+ have been globally explored by using particle swarm optimization algorithm in conjunction with quantum chemical calculations. Compared with previous results, our searching method covers a wide range of structural isomers of (H2O)6+ and therefore turns out to be more effective. With these local minima, geometry optimization and vibrational analysis are performed for the most interesting clusters at second-order Møller-Plesset (MP2)/aug-cc-pVDZ level, and their energies are further refined at MP2/aug-cc-pVTZ and coupled-cluster theory with single, double, and perturbative triple excitations/aug-cc-pVDZ level. The interaction energies using the complete basis set limits at MP2 level are also reported. The relationships between their structure arrangement and their energies are discussed. Based on the results of thermal simulation, structural change from a four-numbered ring to a tree-like structure occurs at T ≈ 45 K, and the relative population of six lowest-free-energy isomers is found to exceed 4% at some point within the studied temperature range. Studies reveal that, among these six isomers, two new-found isomers constitute 10% of isomer population at 180 K, and the experimental spectra can be better explained with inclusions of the two isomers. The molecular orbitals for six representative cationic water clusters are also studied. Through topological and reduced density gradient analysis, we investigated the structural characteristics and the bonding strengths of these water cluster radical cations.

Interplay between oxygen and Fe-S cluster biogenesis: insights from the Suf pathway.

PubMed

Boyd, Eric S; Thomas, Khaleh M; Dai, Yuyuan; Boyd, Jeff M; Outten, F Wayne

2014-09-23

Iron-sulfur (Fe-S) cluster metalloproteins conduct essential functions in nearly all contemporary forms of life. The nearly ubiquitous presence of Fe-S clusters and the fundamental requirement for Fe-S clusters in both aerobic and anaerobic Archaea, Bacteria, and Eukarya suggest that these clusters were likely integrated into central metabolic pathways early in the evolution of life prior to the widespread oxidation of Earth's atmosphere. Intriguingly, Fe-S cluster-dependent metabolism is sensitive to disruption by oxygen because of the decreased bioavailability of ferric iron as well as direct oxidation of sulfur trafficking intermediates and Fe-S clusters by reactive oxygen species. This fact, coupled with the ubiquity of Fe-S clusters in aerobic organisms, suggests that organisms evolved with mechanisms that facilitate the biogenesis and use of these essential cofactors in the presence of oxygen, which gradually began to accumulate around 2.5 billion years ago as oxygenic photosynthesis proliferated and reduced minerals that buffered against oxidation were depleted. This review highlights the most ancient of the Fe-S cluster biogenesis pathways, the Suf system, which likely was present in early anaerobic forms of life. Herein, we use the evolution of the Suf pathway to assess the relationships between the biochemical functions and physiological roles of Suf proteins, with an emphasis on the selective pressure of oxygen toxicity. Our analysis suggests that diversification into oxygen-containing environments disrupted iron and sulfur metabolism and was a main driving force in the acquisition of accessory Suf proteins (such as SufD, SufE, and SufS) by the core SufB-SufC scaffold complex. This analysis provides a new framework for the study of Fe-S cluster biogenesis pathways and Fe-S cluster-containing metalloenzymes and their complicated patterns of divergence in response to oxygen.

Analyzing simulation-based PRA data through traditional and topological clustering: A BWR station blackout case study

DOE PAGES

Maljovec, D.; Liu, S.; Wang, B.; ...

2015-07-14

Here, dynamic probabilistic risk assessment (DPRA) methodologies couple system simulator codes (e.g., RELAP and MELCOR) with simulation controller codes (e.g., RAVEN and ADAPT). Whereas system simulator codes model system dynamics deterministically, simulation controller codes introduce both deterministic (e.g., system control logic and operating procedures) and stochastic (e.g., component failures and parameter uncertainties) elements into the simulation. Typically, a DPRA is performed by sampling values of a set of parameters and simulating the system behavior for that specific set of parameter values. For complex systems, a major challenge in using DPRA methodologies is to analyze the large number of scenarios generated,more » where clustering techniques are typically employed to better organize and interpret the data. In this paper, we focus on the analysis of two nuclear simulation datasets that are part of the risk-informed safety margin characterization (RISMC) boiling water reactor (BWR) station blackout (SBO) case study. We provide the domain experts a software tool that encodes traditional and topological clustering techniques within an interactive analysis and visualization environment, for understanding the structures of such high-dimensional nuclear simulation datasets. We demonstrate through our case study that both types of clustering techniques complement each other for enhanced structural understanding of the data.« less

Implementation of the incremental scheme for one-electron first-order properties in coupled-cluster theory.

PubMed

Friedrich, Joachim; Coriani, Sonia; Helgaker, Trygve; Dolg, Michael

2009-10-21

A fully automated parallelized implementation of the incremental scheme for coupled-cluster singles-and-doubles (CCSD) energies has been extended to treat molecular (unrelaxed) first-order one-electron properties such as the electric dipole and quadrupole moments. The convergence and accuracy of the incremental approach for the dipole and quadrupole moments have been studied for a variety of chemically interesting systems. It is found that the electric dipole moment can be obtained to within 5% and 0.5% accuracy with respect to the exact CCSD value at the third and fourth orders of the expansion, respectively. Furthermore, we find that the incremental expansion of the quadrupole moment converges to the exact result with increasing order of the expansion: the convergence of nonaromatic compounds is fast with errors less than 16 mau and less than 1 mau at third and fourth orders, respectively (1 mau=10(-3)ea(0)(2)); the aromatic compounds converge slowly with maximum absolute deviations of 174 and 72 mau at third and fourth orders, respectively.

Structural and electronic studies of metal carbide clusterfullerene Sc2C2@Cs-C72

NASA Astrophysics Data System (ADS)

Feng, Yongqiang; Wang, Taishan; Wu, Jingyi; Feng, Lai; Xiang, Junfeng; Ma, Yihan; Zhang, Zhuxia; Jiang, Li; Shu, Chunying; Wang, Chunru

2013-07-01

We present a metal carbide clusterfullerene Sc2C2@Cs(10528)-C72, whose structure has been baffling for many years. A motional endohedral Sc2C2 cluster, special molecule geometry and electronic structure were found in Sc2C2@Cs(10528)-C72. The paramagnetic Sc2C2@Cs-C72 anion radical was successfully prepared by a chemical reduction method and hyperfine couplings in the ESR spectrum were observed.We present a metal carbide clusterfullerene Sc2C2@Cs(10528)-C72, whose structure has been baffling for many years. A motional endohedral Sc2C2 cluster, special molecule geometry and electronic structure were found in Sc2C2@Cs(10528)-C72. The paramagnetic Sc2C2@Cs-C72 anion radical was successfully prepared by a chemical reduction method and hyperfine couplings in the ESR spectrum were observed. Electronic supplementary information (ESI) available: Experimental details, HPLC chromatogram, and DFT calculations. CCDC 917712. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c3nr01739g

CLUH couples mitochondrial distribution to the energetic and metabolic status.

PubMed

Wakim, Jamal; Goudenege, David; Perrot, Rodolphe; Gueguen, Naig; Desquiret-Dumas, Valerie; Chao de la Barca, Juan Manuel; Dalla Rosa, Ilaria; Manero, Florence; Le Mao, Morgane; Chupin, Stephanie; Chevrollier, Arnaud; Procaccio, Vincent; Bonneau, Dominique; Logan, David C; Reynier, Pascal; Lenaers, Guy; Khiati, Salim

2017-06-01

Mitochondrial dynamics and distribution are critical for supplying ATP in response to energy demand. CLUH is a protein involved in mitochondrial distribution whose dysfunction leads to mitochondrial clustering, the metabolic consequences of which remain unknown. To gain insight into the role of CLUH on mitochondrial energy production and cellular metabolism, we have generated CLUH-knockout cells using CRISPR/Cas9. Mitochondrial clustering was associated with a smaller cell size and with decreased abundance of respiratory complexes, resulting in oxidative phosphorylation (OXPHOS) defects. This energetic impairment was found to be due to the alteration of mitochondrial translation and to a metabolic shift towards glucose dependency. Metabolomic profiling by mass spectroscopy revealed an increase in the concentration of some amino acids, indicating a dysfunctional Krebs cycle, and increased palmitoylcarnitine concentration, indicating an alteration of fatty acid oxidation, and a dramatic decrease in the concentrations of phosphatidylcholine and sphingomyeline, consistent with the decreased cell size. Taken together, our study establishes a clear function for CLUH in coupling mitochondrial distribution to the control of cell energetic and metabolic status. © 2017. Published by The Company of Biologists Ltd.

Modification degrees at specific sites on heparan sulphate: an approach to measure chemical modifications on biological molecules with stable isotope labelling

PubMed Central

Wu, Zhengliang L.; Lech, Miroslaw

2005-01-01

Chemical modification of biological molecules is a general mechanism for cellular regulation. A quantitative approach has been developed to measure the extent of modification on HS (heparan sulphates). Sulphation on HS by sulphotransferases leads to variable sulphation levels, which allows cells to tune their affinities to various extracellular proteins, including growth factors. With stable isotope labelling and HPLC-coupled MS, modification degrees at various O-sulphation sites could be determined. A bovine kidney HS sample was first saturated in vitro with 34S by an OST (O-sulphotransferase), then digested with nitrous acid and analysed with HPLC-coupled MS. The 34S-labelled oligosaccharides were identified based on their unique isotope clusters. The modification degrees at the sulphotransferase recognition sites were obtained by calculating the intensities of isotopic peaks in the isotope clusters. The modification degrees at 3-OST-1 and 6-OST-1 sites were examined in detail. This approach can also be used to study other types of chemical modifications on biological molecules. PMID:15743272

Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

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

Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S., E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr

2013-11-07

Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality.more » By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.« 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.

Multi-spacecraft studies of the auroral acceleration region: From cluster to nanosatellites

NASA Astrophysics Data System (ADS)

Sadeghi, S.; Emami, M. R.

2017-03-01

This paper discusses the utilization of multiple Cubesats in various formations for studies in the auroral acceleration region. The focus is on the quasi-static properties, spatio-temporal features, electric potential structures, field-aligned currents, and their relationships, all of which are fundamentally important for an understanding of the magnetosphere-ionosphere coupling. It is argued that a multitude of nanosatellites can address some of the relevant outstanding questions in a broader range of spatial, temporal, and geometrical features, with higher redundancy and data consistency, potentially resulting in a shorter mission period and a higher chance of mission success. A number of mission concepts consisting of a cluster of 6-12 Cubesats with their specific onboard payloads are suggested for such missions over a period of as short as two months.

Education-based health inequalities in 18,000 Norwegian couples: the Nord-Trøndelag Health Study (HUNT).

PubMed

Nilsen, Sara Marie; Bjørngaard, Johan Håkon; Ernstsen, Linda; Krokstad, Steinar; Westin, Steinar

2012-11-19

Education-based inequalities in health are well established, but they are usually studied from an individual perspective. However, many individuals are part of a couple. We studied education-based health inequalities from the perspective of couples where indicators of health were measured by subjective health, anxiety and depression. A sample of 35,980 women and men (17,990 couples) was derived from the Norwegian Nord-Trøndelag Health Study 1995-97 (HUNT 2). Educational data and family identification numbers were obtained from Statistics Norway. The dependent variables were subjective health (four-integer scale), anxiety (21-integer scale) and depression (21-integer scale), which were captured using the Hospital Anxiety and Depression Scale. The dependent variables were rescaled from 0 to 100 where 100 was the worst score. Cross-sectional analyses were performed using two-level linear random effect regression models. The variance attributable to the couple level was 42% for education, 16% for subjective health, 19% for anxiety and 25% for depression. A one-year increase in education relative to that of one's partner was associated with an improvement of 0.6 scale points (95% confidence interval = 0.5-0.8) in the subjective health score (within-couple coefficient). A one-year increase in a couple's average education was associated with an improvement of 1.7 scale points (95% confidence interval = 1.6-1.8) in the subjective health score (between-couple coefficient). There were no education-based differences in the anxiety or depression scores when partners were compared, whereas there were substantial education-based differences between couples in all three outcome measures. We found considerable clustering of education and health within couples, which highlighted the importance of the family environment. Our results support previous studies that report the mutual effects of spouses on education-based inequalities in health, suggesting that couples develop their socioeconomic position together.

Singlet Excited States of Cl and Br Molecules: New Theories Applied to the -XO and -XO2 (X=C1 and Br) Chromophores

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Srinivasan, Parthiban; Head-Gordon, Martin; Huo, Winifred (Technical Monitor)

1998-01-01

Electronic excitation energies are determined using single-reference based theories derived from response equations involving perturbation theory and coupled-cluster theory. These methods are applied to the singlet manifold of excited electronic states of the HClO, HBrO, HOClO, HOBrO, HClO2, and HBrO2 molecules. The reliability of the various perturbation theory approaches is assessed by comparison to the linear-response singles and doubles coupled-cluster (LRCCSD) method. The excitation energies for the Y-XO compounds are compared and contrasted for Y=H and HO, and X=Cl and Br. A similar comparison is performed for the H-XO2 compounds.

Coupled cluster calculations for static and dynamic polarizabilities of C60

NASA Astrophysics Data System (ADS)

Kowalski, Karol; Hammond, Jeff R.; de Jong, Wibe A.; Sadlej, Andrzej J.

2008-12-01

New theoretical predictions for the static and frequency dependent polarizabilities of C60 are reported. Using the linear response coupled cluster approach with singles and doubles and a basis set especially designed to treat the molecular properties in external electric field, we obtained 82.20 and 83.62 Å3 for static and dynamic (λ =1064 nm) polarizabilities. These numbers are in a good agreement with experimentally inferred data of 76.5±8 and 79±4 Å3 [R. Antoine et al., J. Chem. Phys.110, 9771 (1999); A. Ballard et al., J. Chem. Phys.113, 5732 (2000)]. The reported results were obtained with the highest wave function-based level of theory ever applied to the C60 system.

Galaxy Transformations In The Cosmic Web

NASA Astrophysics Data System (ADS)

Jablonka, Pascale

2017-06-01

In this talk, I present a new survey, the Spatial Extended EDisCS Survey (SEEDisCS), that aims at understanding how clusters assemble and the level at which galaxies are preprocessed before falling on the cluster cores. SEEDisCS therefore focusses on the changes in galaxy properties along the large scale structures surrounding a couple of z 0.5 medium mass clusters, I first describe how spiral disc stellar populations are affected by the environment,and how we can get constraints on the timescale of star formation quenching. I then present new NOEMA and ALMA CO observations that trace the fate of the galaxy cold gas content along the infalling paths towards the cluster cores.

Polar cap arcs from the magnetosphere to the ionosphere: kinetic modelling and observations by Cluster and TIMED

NASA Astrophysics Data System (ADS)

Maggiolo, R.; Echim, M.; Wedlund, C. Simon; Zhang, Y.; Fontaine, D.; Lointier, G.; Trotignon, J.-G.

2012-02-01

On 1 April 2004 the GUVI imager onboard the TIMED spacecraft spots an isolated and elongated polar cap arc. About 20 min later, the Cluster satellites detect an isolated upflowing ion beam above the polar cap. Cluster observations show that the ions are accelerated upward by a quasi-stationary electric field. The field-aligned potential drop is estimated to about 700 V and the upflowing ions are accompanied by a tenuous population of isotropic protons with a temperature of about 500 eV. The magnetic footpoints of the ion outflows observed by Cluster are situated in the prolongation of the polar cap arc observed by TIMED GUVI. The upflowing ion beam and the polar cap arc may be different signatures of the same phenomenon, as suggested by a recent statistical study of polar cap ion beams using Cluster data. We use Cluster observations at high altitude as input to a quasi-stationary magnetosphere-ionosphere (MI) coupling model. Using a Knight-type current-voltage relationship and the current continuity at the topside ionosphere, the model computes the energy spectrum of precipitating electrons at the top of the ionosphere corresponding to the generator electric field observed by Cluster. The MI coupling model provides a field-aligned potential drop in agreement with Cluster observations of upflowing ions and a spatial scale of the polar cap arc consistent with the optical observations by TIMED. The computed energy spectrum of the precipitating electrons is used as input to the Trans4 ionospheric transport code. This 1-D model, based on Boltzmann's kinetic formalism, takes into account ionospheric processes such as photoionization and electron/proton precipitation, and computes the optical and UV emissions due to precipitating electrons. The emission rates provided by the Trans4 code are compared to the optical observations by TIMED. They are similar in size and intensity. Data and modelling results are consistent with the scenario of quasi-static acceleration of electrons that generate a polar cap arc as they precipitate in the ionosphere. The detailed observations of the acceleration region by Cluster and the large scale image of the polar cap arc provided by TIMED are two different features of the same phenomenon. Combined together, they bring new light on the configuration of the high-latitude magnetosphere during prolonged periods of Northward IMF. Possible implications of the modelling results for optical observations of polar cap arcs are also discussed.

All-electron and relativistic pseudopotential studies for the group 1 element polarizabilities from K to element 119.

PubMed

Lim, Ivan S; Schwerdtfeger, Peter; Metz, Bernhard; Stoll, Hermann

2005-03-08

Two-component and scalar relativistic energy-consistent pseudopotentials for the group 1 elements from K to element 119 are presented using nine electrons for the valence space definition. The accuracy of such an approximation is discussed for dipole polarizabilities and ionization potentials obtained at the coupled-cluster level as compared to experimental and all-electron Douglas-Kroll results.

A Comparison of High- and Low-Distress Marriages that End in Divorce

ERIC Educational Resources Information Center

Amato, Paul R.; Hohmann-Marriott, Bryndl

2007-01-01

We used data from Waves 1 and 2 of the National Survey of Families and Households to study high- and low-distress marriages that end in divorce. A cluster analysis of 509 couples who divorced between waves revealed that about half were in high-distress relationships and the rest in low-distress relationships. These 2 groups were not artifacts of…

Effective fragment potential study of the interaction of DNA bases.

PubMed

Smith, Quentin A; Gordon, Mark S; Slipchenko, Lyudmila V

2011-10-20

Hydrogen-bonded and stacked structures of adenine-thymine and guanine-cytosine nucleotide base pairs, along with their methylated analogues, are examined with the ab inito based general effective fragment potential (EFP2) method. A comparison of coupled cluster with single, double, and perturbative triple (CCSD(T)) energies is presented, along with an EFP2 energy decomposition to illustrate the components of the interaction energy.

Squaring the Project Management Circle: Updating the Cost, Schedule, and Performance Methodology

DTIC Science & Technology

2016-04-30

success is measured as achieving technical performance and/or mission performance goals, coupled with customer (warfighter) satisfaction (De Wit, 1988...studies added criteria such as customer satisfaction , efficiency of execution, and effectiveness of the project organization (Pinto & Slevin, 1998...team and the user customer organization, management policy and project control. This clustering of success factors represents the amalgamation of the

Self-organized emergence of multilayer structure and chimera states in dynamical networks with adaptive couplings

NASA Astrophysics Data System (ADS)

Kasatkin, D. V.; Yanchuk, S.; Schöll, E.; Nekorkin, V. I.

2017-12-01

We report the phenomenon of self-organized emergence of hierarchical multilayered structures and chimera states in dynamical networks with adaptive couplings. This process is characterized by a sequential formation of subnetworks (layers) of densely coupled elements, the size of which is ordered in a hierarchical way, and which are weakly coupled between each other. We show that the hierarchical structure causes the decoupling of the subnetworks. Each layer can exhibit either a two-cluster state, a periodic traveling wave, or an incoherent state, and these states can coexist on different scales of subnetwork sizes.

FEM numerical model study of heating in magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Pearce, John A.; Cook, Jason R.; Hoopes, P. Jack; Giustini, Andrew

2011-03-01

Electromagnetic heating of nanoparticles is complicated by the extremely short thermal relaxation time constants and difficulty of coupling sufficient power into the particles to achieve desired temperatures. Magnetic field heating by the hysteresis loop mechanism at frequencies between about 100 and 300 kHz has proven to be an effective mechanism in magnetic nanoparticles. Experiments at 2.45 GHz show that Fe3O4 magnetite nanoparticle dispersions in the range of 1012 to 1013 NP/mL also heat substantially at this frequency. An FEM numerical model study was undertaken to estimate the order of magnitude of volume power density, Qgen (W m-3) required to achieve significant heating in evenly dispersed and aggregated clusters of nanoparticles. The FEM models were computed using Comsol Multiphysics; consequently the models were confined to continuum formulations and did not include film nano-dimension heat transfer effects at the nanoparticle surface. As an example, the models indicate that for a single 36 nm diameter particle at an equivalent dispersion of 1013 NP/mL located within one control volume (1.0 x 10-19 m3) of a capillary vessel a power density in the neighborhood of 1017 (W m-3) is required to achieve a steady state particle temperature of 52°C - the total power coupled to the particle is 2.44 μW. As a uniformly distributed particle cluster moves farther from the capillary the required power density decreases markedly. Finally, the tendency for particles in vivo to cluster together at separation distances much less than those of the uniform distribution further reduces the required power density.

Comparison and combination of "direct" and fragment based local correlation methods: Cluster in molecules and domain based local pair natural orbital perturbation and coupled cluster theories

NASA Astrophysics Data System (ADS)

Guo, Yang; Becker, Ute; Neese, Frank

2018-03-01

Local correlation theories have been developed in two main flavors: (1) "direct" local correlation methods apply local approximation to the canonical equations and (2) fragment based methods reconstruct the correlation energy from a series of smaller calculations on subsystems. The present work serves two purposes. First, we investigate the relative efficiencies of the two approaches using the domain-based local pair natural orbital (DLPNO) approach as the "direct" method and the cluster in molecule (CIM) approach as the fragment based approach. Both approaches are applied in conjunction with second-order many-body perturbation theory (MP2) as well as coupled-cluster theory with single-, double- and perturbative triple excitations [CCSD(T)]. Second, we have investigated the possible merits of combining the two approaches by performing CIM calculations with DLPNO methods serving as the method of choice for performing the subsystem calculations. Our cluster-in-molecule approach is closely related to but slightly deviates from approaches in the literature since we have avoided real space cutoffs. Moreover, the neglected distant pair correlations in the previous CIM approach are considered approximately. Six very large molecules (503-2380 atoms) were studied. At both MP2 and CCSD(T) levels of theory, the CIM and DLPNO methods show similar efficiency. However, DLPNO methods are more accurate for 3-dimensional systems. While we have found only little incentive for the combination of CIM with DLPNO-MP2, the situation is different for CIM-DLPNO-CCSD(T). This combination is attractive because (1) the better parallelization opportunities offered by CIM; (2) the methodology is less memory intensive than the genuine DLPNO-CCSD(T) method and, hence, allows for large calculations on more modest hardware; and (3) the methodology is applicable and efficient in the frequently met cases, where the largest subsystem calculation is too large for the canonical CCSD(T) method.

Determination of interglycosidic linkages in O-glycosyl flavones by high-performance liquid chromatography/photodiode-array detection coupled to electrospray ionization ion trap mass spectrometry. Its application to Tetragonula carbonaria honey from Australia.

PubMed

Truchado, Pilar; Vit, Patricia; Heard, Tim A; Tomás-Barberán, Francisco A; Ferreres, Federico

2015-05-30

Tetragonula carbonaria pot-honeys are highly valued as a food source and for their biological activities in Australia, and there is a growing interest to know its composition. Phenolic metabolites, which could be related to their beneficial properties, have not been studied in depth yet. Mass spectrometry (MS) coupled to liquid chromatography (LC) is an advanced technique for the study of complex flavonoids present in difficult food matrices that hampers their isolation and purification. This allows the tentative characterization of diglycosides/triglycosides establishing the position of the O-glycosylation on the sugar moiety by the study of the MS data in T. carbonaria pot-honeys from Australia. Their spectra obtained by high-performance liquid chromatography/photodiode-array detection/electrospray ionization ion trap mass spectrometry (HPLC/DAD/ESI-MS(n) ) revealed for the first time 19 quercetin, kaempferol and isorhamnetin O-glycosides. These compounds were clustered in flavonoid triglycosides, diglycosides and monoglycosides. The first cluster contained one flavonoid trihexoside, two -3-O-(2-hexosyl, 6-rhamnosyl)hexosides and their isomers and two -3-O-(2,6-di-rhamnosyl)hexosides. In the second cluster, eleven flavonoid diglycosides such as three -3-O-(2-hexosyl)hexosides, four -3-O-(2-rhamnosyl)hexosides and one -3-O-(6-rhamnosyl)hexoside as well as two -3-O-(2-pentosyl)hexosides and one tentative -3-O-(3-pentosyl)hexoside were detected. In the monoglycoside group, only one flavonoid -3-O-hexoside was identified. The occurrence of this large number of flavonoid glycosides could be due to the low glucosidase activity previously reported in stingless bee honey. Copyright © 2015 John Wiley & Sons, Ltd.

Kramers degeneracy and relaxation in vanadium, niobium and tantalum clusters

NASA Astrophysics Data System (ADS)

Diaz-Bachs, A.; Katsnelson, M. I.; Kirilyuk, A.

2018-04-01

In this work we use magnetic deflection of V, Nb, and Ta atomic clusters to measure their magnetic moments. While only a few of the clusters show weak magnetism, all odd-numbered clusters deflect due to the presence of a single unpaired electron. Surprisingly, for the majority of V and Nb clusters an atomic-like behavior is found, which is a direct indication of the absence of spin–lattice interaction. This is in agreement with Kramers degeneracy theorem for systems with a half-integer spin. This purely quantum phenomenon is surprisingly observed for large systems of more than 20 atoms, and also indicates various quantum relaxation processes, via Raman two-phonon and Orbach high-spin mechanisms. In heavier, Ta clusters, the relaxation is always present, probably due to larger masses and thus lower phonon energies, as well as increased spin–orbit coupling.

Recent development in deciphering the structure of luminescent silver nanodots

NASA Astrophysics Data System (ADS)

Choi, Sungmoon; Yu, Junhua

2017-05-01

Matrix-stabilized silver clusters and stable luminescent few-atom silver clusters, referred to as silver nanodots, show notable difference in their photophysical properties. We present recent research on deciphering the nature of silver clusters and nanodots and understanding the factors that lead to variations in luminescent mechanisms. Due to their relatively simple structure, the matrix-stabilized clusters have been well studied. However, the single-stranded DNA (ssDNA)-stabilized silver nanodots that show the most diverse emission wavelengths and the best photophysical properties remain mysterious species. It is clear that their photophysical properties highly depend on their protection scaffolds. Analyses from combinations of high-performance liquid chromatography, inductively coupled plasma-atomic emission spectroscopy, electrophoresis, and mass spectrometry indicate that about 10 to 20 silver atoms form emissive complexes with ssDNA. However, it is possible that not all of the silver atoms in the complex form effective emission centers. Investigation of the nanodot structure will help us understand why luminescent silver nanodots are stable in aqueous solution and how to further improve their chemical and photophysical properties.

Do Ag{sub n} (up to n = 8) clusters retain their identity on graphite? Insights from first-principles calculations including dispersion interactions

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

Singh, Akansha; Sen, Prasenjit, E-mail: prasen@hri.res.in; Majumder, Chiranjib

Adsorption of pre-formed Ag{sub n} clusters for n = 1 − 8 on a graphite substrate is studied within the density functional theory employing the vdW-DF2 functional to treat dispersion interactions. Top sites above surface layer carbon atoms turn out to be most favorable for a Ag adatom, in agreement with experimental observations. The same feature is observed for clusters of almost all sizes which have the lowest energies when the Ag atoms are positioned over top sites. Most gas phase isomers retain their structures over the substrate, though a couple of them undergo significant distortions. Energetics of the adsorptionmore » can be understood in terms of a competition between energy cost of disturbing Ag–Ag bonds in the cluster and energy gain from Ag–C interactions at the surface. Ag{sub 3} turns out to be an exceptional candidate in this regard that undergoes significant structural distortion and has only two of the Ag atoms close to surface C atoms in its lowest energy structure.« less

Functional analysis of ars gene cluster of Pannonibacter indicus strain HT23(T) (DSM 23407(T)) and identification of a proline residue essential for arsenate reductase activity.

PubMed

Bandyopadhyay, Saumya; Das, Subrata K

2016-04-01

Arsenic is a naturally occurring ubiquitous highly toxic metalloid. In this study, we have identified ars gene cluster in Pannonibacter indicus strain HT23(T) (DSM 23407(T)), responsible for reduction of toxic pentavalent arsenate. The ars gene cluster is comprised of four non-overlapping open reading frames (ORFs) encoding a transcriptional regulator (ArsR), a low molecular weight protein tyrosine phosphatases (LMW-PTPase) with hypothetical function, an arsenite efflux pump (Acr3), and an arsenate reductase (ArsC). Heterologous expression of arsenic inducible ars gene cluster conferred arsenic resistance to Escherichia coli ∆ars mutant strain AW3110. The recombinant ArsC was purified and assayed. Site-directed mutagenesis was employed to ascertain the role of specific amino acids in ArsC catalysis. Pro94X (X = Ala, Arg, Cys, and His) amino acid substitutions led to enzyme inactivation. Circular dichroism spectra analysis suggested Pro94 as an essential amino acid for enzyme catalytic activity as it is indispensable for optimum protein folding in P. indicus Grx-coupled ArsC.

Long-time atomistic dynamics through a new self-adaptive accelerated molecular dynamics method

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

Gao, N.; Yang, L.; Gao, F.

2017-02-27

A self-adaptive accelerated molecular dynamics method is developed to model infrequent atomic- scale events, especially those events that occur on a rugged free-energy surface. Key in the new development is the use of the total displacement of the system at a given temperature to construct a boost-potential, which is slowly increased to accelerate the dynamics. The temperature is slowly increased to accelerate the dynamics. By allowing the system to evolve from one steady-state con guration to another by overcoming the transition state, this self-evolving approach makes it possible to explore the coupled motion of species that migrate on vastly differentmore » time scales. The migrations of single vacancy (V) and small He-V clusters, and the growth of nano-sized He-V clusters in Fe for times in the order of seconds are studied by this new method. An interstitial- assisted mechanism is rst explored for the migration of a helium-rich He-V cluster, while a new two-component Ostwald ripening mechanism is suggested for He-V cluster growth.« less

A combined experimental and theoretical spectroscopic protocol for determination of the structure of heterogeneous catalysts: developing the information content of the resonance Raman spectra of M1 MoVO x .

PubMed

Kubas, Adam; Noak, Johannes; Trunschke, Annette; Schlögl, Robert; Neese, Frank; Maganas, Dimitrios

2017-09-01

Absorption and multiwavelength resonance Raman spectroscopy are widely used to investigate the electronic structure of transition metal centers in coordination compounds and extended solid systems. In combination with computational methodologies that have predictive accuracy, they define powerful protocols to study the spectroscopic response of catalytic materials. In this work, we study the absorption and resonance Raman spectra of the M1 MoVO x catalyst. The spectra were calculated by time-dependent density functional theory (TD-DFT) in conjunction with the independent mode displaced harmonic oscillator model (IMDHO), which allows for detailed bandshape predictions. For this purpose cluster models with up to 9 Mo and V metallic centers are considered to represent the bulk structure of MoVO x . Capping hydrogens were used to achieve valence saturation at the edges of the cluster models. The construction of model structures was based on a thorough bonding analysis which involved conventional DFT and local coupled cluster (DLPNO-CCSD(T)) methods. Furthermore the relationship of cluster topology to the computed spectral features is discussed in detail. It is shown that due to the local nature of the involved electronic transitions, band assignment protocols developed for molecular systems can be applied to describe the calculated spectral features of the cluster models as well. The present study serves as a reference for future applications of combined experimental and computational protocols in the field of solid-state heterogeneous catalysis.

Composite vibrational spectroscopy of the group 12 difluorides: ZnF2, CdF2, and HgF2.

PubMed

Solomonik, Victor G; Smirnov, Alexander N; Navarkin, Ilya S

2016-04-14

The vibrational spectra of group 12 difluorides, MF2 (M = Zn, Cd, Hg), were investigated via coupled cluster singles, doubles, and perturbative triples, CCSD(T), including core correlation, with a series of correlation consistent basis sets ranging in size from triple-zeta through quintuple-zeta quality, which were then extrapolated to the complete basis set (CBS) limit using a variety of extrapolation procedures. The explicitly correlated coupled cluster method, CCSD(T)-F12b, was employed as well. Although exhibiting quite different convergence behavior, the F12b method yielded the CBS limit estimates closely matching more computationally expensive conventional CBS extrapolations. The convergence with respect to basis set size was examined for the contributions entering into composite vibrational spectroscopy, including those from higher-order correlation accounted for through the CCSDT(Q) level of theory, second-order spin-orbit coupling effects assessed within four-component and two-component relativistic formalisms, and vibrational anharmonicity evaluated via a perturbative treatment. Overall, the composite results are in excellent agreement with available experimental values, except for the CdF2 bond-stretching frequencies compared to spectral assignments proposed in a matrix isolation infrared and Raman study of cadmium difluoride vapor species [Loewenschuss et al., J. Chem. Phys. 50, 2502 (1969); Givan and Loewenschuss, J. Chem. Phys. 72, 3809 (1980)]. These assignments are called into question in the light of the composite results.

Composite vibrational spectroscopy of the group 12 difluorides: ZnF2, CdF2, and HgF2

NASA Astrophysics Data System (ADS)

Solomonik, Victor G.; Smirnov, Alexander N.; Navarkin, Ilya S.

2016-04-01

The vibrational spectra of group 12 difluorides, MF2 (M = Zn, Cd, Hg), were investigated via coupled cluster singles, doubles, and perturbative triples, CCSD(T), including core correlation, with a series of correlation consistent basis sets ranging in size from triple-zeta through quintuple-zeta quality, which were then extrapolated to the complete basis set (CBS) limit using a variety of extrapolation procedures. The explicitly correlated coupled cluster method, CCSD(T)-F12b, was employed as well. Although exhibiting quite different convergence behavior, the F12b method yielded the CBS limit estimates closely matching more computationally expensive conventional CBS extrapolations. The convergence with respect to basis set size was examined for the contributions entering into composite vibrational spectroscopy, including those from higher-order correlation accounted for through the CCSDT(Q) level of theory, second-order spin-orbit coupling effects assessed within four-component and two-component relativistic formalisms, and vibrational anharmonicity evaluated via a perturbative treatment. Overall, the composite results are in excellent agreement with available experimental values, except for the CdF2 bond-stretching frequencies compared to spectral assignments proposed in a matrix isolation infrared and Raman study of cadmium difluoride vapor species [Loewenschuss et al., J. Chem. Phys. 50, 2502 (1969); Givan and Loewenschuss, J. Chem. Phys. 72, 3809 (1980)]. These assignments are called into question in the light of the composite results.

Rayleigh-Bénard turbulence modified by two-way coupled inertial, nonisothermal particles

NASA Astrophysics Data System (ADS)

Park, Hyungwon John; O'Keefe, Kevin; Richter, David H.

2018-03-01

Direct numerical simulation (DNS) combined with the Lagrangian point particle model is used to study Rayleigh-Bénard convection in order to understand modifications due to the interaction of inertial, nonisothermal particles with buoyancy-driven turbulence. In this system, turbulence can be altered through direct momentum coupling, as well as through buoyancy modification via thermal coupling between phases. We quantify the effect of the dispersed phase by changes to the total integrated turbulent kinetic energy (TKE) and Nusselt number (Nu). The dispersed particles experience gravitational settling and are introduced at the lower wall so that turbulence must overcome the settling velocity for the particles to vertically distribute throughout the domain. We focus primarily on particle inertia, settling velocity, mass fraction, and the ratio of the particle to fluid specific heat. Furthermore, individual contributions by the momentum coupling and thermal coupling are studied to see which most significantly changes Nu and TKE. Our results show that particles with Stokes number of order unity maximize Nu, corresponding to a peak of clustering and attenuation of TKE. Increased mass fractions lead to a linear increase of Nu and decrease of TKE. With varying specific heat ratio, Nu and TKE exhibit monotonic behaviors, where in the high limit particles become isothermal and depend upon the initialized particle temperature. It is also shown that particles two-way coupled only through momentum attenuate Nu and weaken TKE, while thermal-only coupling also weakens TKE but enhances Nu. When both couplings are present, however, thermal coupling overwhelms the momentum coupling attenuation, and the net result is an enhancement of Nu.

Dioxygen Binding, Activation, and Reduction to H2O by Cu Enzymes.

PubMed

Solomon, Edward I

2016-07-05

Oxygen intermediates in copper enzymes exhibit unique spectroscopic features that reflect novel geometric and electronic structures that are key to reactivity. This perspective will describe: (1) the bonding origin of the unique spectroscopic features of the coupled binuclear copper enzymes and how this overcomes the spin forbiddenness of O2 binding and activates monooxygenase activity, (2) how the difference in exchange coupling in the non-coupled binuclear Cu enzymes controls the reaction mechanism, and (3) how the trinuclear Cu cluster present in the multicopper oxidases leads to a major structure/function difference in enabling the irreversible reductive cleavage of the O-O bond with little overpotential and generating a fully oxidized intermediate, different from the resting enzyme studied by crystallography, that is key in enabling fast PCET in the reductive half of the catalytic cycle.

EarthShape: A Strategy for Investigating the Role of Biota on Surface Processes

NASA Astrophysics Data System (ADS)

Ehlers, T. A.; von Blanckenburg, F.; Übernickel, K.; Paulino, L.

2016-12-01

EarthShape - "Earth surface shaping by biota" is a 6-year priority research program funded by the German science foundation (DFG-SPP 1803) that performs soil- and landscape-scale critical zone research at 4 locations along a climate gradient in the Chilean Coastal Cordillera. This region was selected because of its north-south orientation such that it captures a large ecological and climate gradient ranging from hyper-arid to temperate to humid conditions. The sites comprise granitic, previously unglaciated mountain ranges. EarthShape involves an interdisciplinary collaboration between geologists, geomorphologists, ecologists, soil scientists, microbiologists, geophysicists, geochemists, and hydrogeologists including 18 German and 8 Chilean institutions. EarthShape is composed of 4 research clusters representing the process chain from weathering of substrate to deposition of eroded material. Cluster 1 explores micro-biota as the "weathering engine". Investigations in this cluster quantify different mechanisms of biogenic weathering whereby plants, fungi, and bacteria interact with rock in the production of soil. Cluster 2 explores bio-mediated redistribution of material within the weathering zone. Studies in this cluster focus on soil catenas along hill slope profiles to investigate the modification of matter along its transport path. Cluster 3 explores biotic modulation of erosion and sediment routing at the catchment scale. Investigations in this cluster explore the effects of vegetation cover on solute and sediment transport from hill slopes to the channel network. Cluster 4 explores the depositional legacy of coupled biogenic and Earth surface systems. This cluster investigates records of vegetation-land surface interactions in different depositional settings. A final component of EarthShape lies in the integration of results from these 4 clusters using numerical models to bridging between the diverse times scales used by different disciplines.

Does Each Atom Count in the Reactivity of Vanadia Nanoclusters?

PubMed

Zhang, Mei-Qi; Zhao, Yan-Xia; Liu, Qing-Yu; Li, Xiao-Na; He, Sheng-Gui

2017-01-11

Vanadium oxide cluster anions (V 2 O 5 ) n V x O y - (n = 1-31; x = 0, 1; and x + y ≤ 5) with different oxygen deficiencies (Δ = 2y-1-5x = 0, ± 1, and ±2) have been prepared by laser ablation and reacted to abstract hydrogen atoms from alkane molecules (n-butane) in a fast flow reactor. When the cluster size n is less than 25, the Δ = 1 series [(V 2 O 5 ) n O - clusters] that can contain atomic oxygen radical anions (O •- ) generally have much higher reactivity than the other four cluster series (Δ = -2, -1, 0, and 2), indicating that each atom counts in the hydrogen-atom abstraction (HAA) reactivity. Unexpectedly, all of the five cluster series have similar HAA reactivity when the cluster size is greater than 25. The critical dimension of vanadia particles separating the cluster behavior (each atom counts) from the bulk behavior (each atom contributes a little part) is thus about 1.6 nm (∼V 50 O 125 ). The strong electron-phonon coupling of the vanadia particles has been proposed to create the O •- radicals (V 5+ = O 2- + heat → V 4+ -O •- ) for the n > 25 clusters with Δ = -2, -1, 0, and 2. Such a mechanism is supported by a comparative study with the scandium system [(Sc 2 O 3 ) n Sc x O y - (n = 1-29; x = 0, 1; and x + y ≤ 4)] for which the Δ = 1 series [(Sc 2 O 3 ) n O - clusters] always have much higher HAA reactivity than the other cluster series.

A Typology of Marital Quality of Enduring Marriages in Israel

ERIC Educational Resources Information Center

Cohen, Orna; Geron, Yael; Farchi, Alva

2010-01-01

This article presents a typology of enduring marriages of Israeli couples married for at least 40 years. Based on the view that marital quality is a multidimensional phenomenon, the typology is derived from a cluster analysis of responses of husbands and wives in 51 couples to the ENRICH scale items. Three types of enduring marriages were found:…

Equation-of-motion coupled-cluster method for doubly ionized states with spin-orbit coupling.

PubMed

Wang, Zhifan; Hu, Shu; Wang, Fan; Guo, Jingwei

2015-04-14

In this work, we report implementation of the equation-of-motion coupled-cluster method for doubly ionized states (EOM-DIP-CC) with spin-orbit coupling (SOC) using a closed-shell reference. Double ionization potentials (DIPs) are calculated in the space spanned by 2h and 3h1p determinants with the EOM-DIP-CC approach at the CC singles and doubles level (CCSD). Time-reversal symmetry together with spatial symmetry is exploited to reduce computational effort. To circumvent the problem of unstable dianion references when diffuse basis functions are included, nuclear charges are scaled. Effect of this stabilization potential on DIPs is estimated based on results from calculations using a small basis set without diffuse basis functions. DIPs and excitation energies of some low-lying states for a series of open-shell atoms and molecules containing heavy elements with two unpaired electrons have been calculated with the EOM-DIP-CCSD approach. Results show that this approach is able to afford a reliable description on SOC splitting. Furthermore, the EOM-DIP-CCSD approach is shown to provide reasonable excitation energies for systems with a dianion reference when diffuse basis functions are not employed.

Equation-of-motion coupled-cluster method for doubly ionized states with spin-orbit coupling

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

Wang, Zhifan; Hu, Shu; Guo, Jingwei

2015-04-14

In this work, we report implementation of the equation-of-motion coupled-cluster method for doubly ionized states (EOM-DIP-CC) with spin-orbit coupling (SOC) using a closed-shell reference. Double ionization potentials (DIPs) are calculated in the space spanned by 2h and 3h1p determinants with the EOM-DIP-CC approach at the CC singles and doubles level (CCSD). Time-reversal symmetry together with spatial symmetry is exploited to reduce computational effort. To circumvent the problem of unstable dianion references when diffuse basis functions are included, nuclear charges are scaled. Effect of this stabilization potential on DIPs is estimated based on results from calculations using a small basis setmore » without diffuse basis functions. DIPs and excitation energies of some low-lying states for a series of open-shell atoms and molecules containing heavy elements with two unpaired electrons have been calculated with the EOM-DIP-CCSD approach. Results show that this approach is able to afford a reliable description on SOC splitting. Furthermore, the EOM-DIP-CCSD approach is shown to provide reasonable excitation energies for systems with a dianion reference when diffuse basis functions are not employed.« less

An ab initio study of HCuCO

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1994-01-01

HCuCO is studied using a large Gaussian basis set at the coupled cluster singles and doubles level of theory, including a perturbational estimate of the connected triples (CCSD(T)). In contrast with CuCO, HCuCO is linear. The Cu-CO bond in HCuCO is significantly stronger than in CuCO. These differences between HCuCO and CuCO are discussed in terms of theCu-H bond polarizing the Cu 4s electron away from the CO.

Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes

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

Wehrens, Martijn; Rein ten Wolde, Pieter; Mugler, Andrew, E-mail: amugler@purdue.edu

2014-11-28

Clustering of molecules on biological membranes is a widely observed phenomenon. A key example is the clustering of the oncoprotein Ras, which is known to be important for signal transduction in mammalian cells. Yet, the mechanism by which Ras clusters form and are maintained remains unclear. Recently, it has been discovered that activated Ras promotes further Ras activation. Here we show using particle-based simulation that this positive feedback is sufficient to produce persistent clusters of active Ras molecules at the nanometer scale via a dynamic nucleation mechanism. Furthermore, we find that our cluster statistics are consistent with experimental observations ofmore » the Ras system. Interestingly, we show that our model does not support a Turing regime of macroscopic reaction-diffusion patterning, and therefore that the clustering we observe is a purely stochastic effect, arising from the coupling of positive feedback with the discrete nature of individual molecules. These results underscore the importance of stochastic and dynamic properties of reaction diffusion systems for biological behavior.« less

Education-based health inequalities in 18,000 Norwegian couples: the Nord-Trøndelag Health Study (HUNT)

PubMed Central

2012-01-01

Background Education-based inequalities in health are well established, but they are usually studied from an individual perspective. However, many individuals are part of a couple. We studied education-based health inequalities from the perspective of couples where indicators of health were measured by subjective health, anxiety and depression. Methods A sample of 35,980 women and men (17,990 couples) was derived from the Norwegian Nord-Trøndelag Health Study 1995–97 (HUNT 2). Educational data and family identification numbers were obtained from Statistics Norway. The dependent variables were subjective health (four-integer scale), anxiety (21-integer scale) and depression (21-integer scale), which were captured using the Hospital Anxiety and Depression Scale. The dependent variables were rescaled from 0 to 100 where 100 was the worst score. Cross-sectional analyses were performed using two-level linear random effect regression models. Results The variance attributable to the couple level was 42% for education, 16% for subjective health, 19% for anxiety and 25% for depression. A one-year increase in education relative to that of one’s partner was associated with an improvement of 0.6 scale points (95% confidence interval = 0.5–0.8) in the subjective health score (within-couple coefficient). A one-year increase in a couple’s average education was associated with an improvement of 1.7 scale points (95% confidence interval = 1.6–1.8) in the subjective health score (between-couple coefficient). There were no education-based differences in the anxiety or depression scores when partners were compared, whereas there were substantial education-based differences between couples in all three outcome measures. Conclusions We found considerable clustering of education and health within couples, which highlighted the importance of the family environment. Our results support previous studies that report the mutual effects of spouses on education-based inequalities in health, suggesting that couples develop their socioeconomic position together. PMID:23157803

Hysteretic transitions in the Kuramoto model with inertia.

PubMed

Olmi, Simona; Navas, Adrian; Boccaletti, Stefano; Torcini, Alessandro

2014-10-01

We report finite-size numerical investigations and mean-field analysis of a Kuramoto model with inertia for fully coupled and diluted systems. In particular, we examine, for a gaussian distribution of the frequencies, the transition from incoherence to coherence for increasingly large system size and inertia. For sufficiently large inertia the transition is hysteretic, and within the hysteretic region clusters of locked oscillators of various sizes and different levels of synchronization coexist. A modification of the mean-field theory developed by Tanaka, Lichtenberg, and Oishi [Physica D 100, 279 (1997)] allows us to derive the synchronization curve associated to each of these clusters. We have also investigated numerically the limits of existence of the coherent and of the incoherent solutions. The minimal coupling required to observe the coherent state is largely independent of the system size, and it saturates to a constant value already for moderately large inertia values. The incoherent state is observable up to a critical coupling whose value saturates for large inertia and for finite system sizes, while in the thermodinamic limit this critical value diverges proportionally to the mass. By increasing the inertia the transition becomes more complex, and the synchronization occurs via the emergence of clusters of whirling oscillators. The presence of these groups of coherently drifting oscillators induces oscillations in the order parameter. We have shown that the transition remains hysteretic even for randomly diluted networks up to a level of connectivity corresponding to a few links per oscillator. Finally, an application to the Italian high-voltage power grid is reported, which reveals the emergence of quasiperiodic oscillations in the order parameter due to the simultaneous presence of many competing whirling clusters.

New measurements of radial velocities in clusters of galaxies. II

NASA Astrophysics Data System (ADS)

Proust, D.; Mazure, A.; Sodre, L.; Capelato, H.; Lund, G.

1988-03-01

Heliocentric radial velocities are determined for 100 galaxies in five clusters, on the basis of 380-518-nm observations obtained using a CCD detector coupled by optical fibers to the OCTOPUS multiobject spectrograph at the Cassegrain focus of the 3.6-m telescope at ESO La Silla. The data-reduction procedures and error estimates are discussed, and the results are presented in tables and graphs and briefly characterized.

Homochiral coordination polymers with helixes and metal clusters based on lactate derivatives

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

Xu, Zhong-Xuan, E-mail: xuzhongxuan4201@163.com; Ma, Yu-Lu; Lv, Guo-ling

2017-05-15

Utilizing the lactic acid derivatives (R)-4-(1-carboxyethoxy)benzoic acid (denoted: (R)-H{sub 2}CBA) and (S)-4-(1-carboxyethoxy)benzoic acid (denoted: (S)-H{sub 2}CBA)as chiral linkers to self-assemble with 4, 4′-bipyridine (denoted: BIP) and Cd(II) ions, a couple of three-dimensional homochiral coordination polymers, namely [Cd{sub 3}((R)-CBA){sub 3} (BIP){sub 2}(H{sub 2}O)]·xGuest (1-D) and [Cd{sub 3}((S)-CBA){sub 3}(BIP){sub 2}(H{sub 2}O)]·xGuest (1-L), have been synthesized under solvothermal reaction condition. Single crystal X-ray diffraction analysis reveals the two complexes contain single helical chains based on enantiopure ligands and cadmium clusters. Moreover, some physical characteristics such as PXRD, thermal stability, solid-state circular dichroism (CD) and luminescent were also investigated. - Graphical abstract: Utilizing enantiomericmore » lactic acid derivatives (R)-H{sub 2}CBA and (S)-H{sub 2}CBA to assemble with Cd{sup 2+} ions and ancillary BIP ligands, a couple of 3D homochiral coordination polymers with metal clusters and helical chains have been prepared by hydrothermal reaction. - Highlights: • Chiral lactic acid derivative. • Enantiomeric coordination polymer. • Helical chain. • Trinuclear cadmium cluster.« less

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

Formation, structure and bond dissociation thresholds of gas-phase vanadium oxide cluster ions

NASA Astrophysics Data System (ADS)

Bell, R. C.; Zemski, K. A.; Justes, D. R.; Castleman, A. W.

2001-01-01

The formation and structure of gas-phase vanadium oxide cluster anions are examined using a guided ion beam mass spectrometer coupled with a laser vaporization source. The dominant peaks in the anion total mass distribution correspond to clusters having stoichiometries of the form (VO2)n(VO3)m(O2)q-. Collision-induced dissociation studies of the vanadium oxide species V2O4-6-, V3O6-9-, V4O8-10-, V5O11-13-, V6O13-15-, and V7O16-18- indicate that VO2, VO3, and V2O5 units are the main building blocks of these clusters. There are many similarities between the anion mass distribution and that of the cation distribution studied previously. The principal difference is a shift to higher oxygen content by one additional oxygen atom for the stoichiometric anions (VxOy-) as compared to the cations with the same number of vanadium atoms, which is attributed to the extra pair of electrons of the anionic species. The oxygen-rich clusters, VxOy(O2)-, are shown to more tightly adsorb molecular oxygen than those of the corresponding cationic clusters. In addition, the bond dissociation thresholds for the vanadium oxide clusters ΔE(V+-O)=6.09±0.28 eV, ΔE(OV+-O)=3.51±0.36 eV, and ΔE(O2V--O)=5.43±0.31 eV are determined from the energy-dependent collision-induced dissociation cross sections with Xe as the collision partner. To the best of our knowledge, this is the first bond dissociation energy reported for the breaking of the V-O bond of a vanadium oxide anion.

Laboratory Study of Air Turbulence-Particle Coupling

NASA Astrophysics Data System (ADS)

Petersen, A.; Baker, L.; Coletti, F.

2017-12-01

Inertial particles suspended in a turbulent flow are unable to follow the fluid's rapid velocity fluctuations, leading to high concentrations in regions where fluid strain dominates vorticity. This phenomenon is known as preferential concentration or clustering and is thought to affect natural processes ranging from the collisional growth of raindrops to the formation of planetesimals in proto-planetary nebulas. In the present study, we use a large jet-stirred chamber to generate homogeneous air turbulence into which we drop particles with an aerodynamic response time comparable to the flow time scales. Using laser imaging we find that turbulence can lead to a multi-fold increase of settling velocity compared to still-air conditions. We then employ Voronoi tessellation to examine the particle spatial distribution, finding strong evidence of turbulence-driven particle clustering over a wide range of experimental conditions. We observe individual clusters of a larger size range than seen previously, sometimes beyond the integral length scale of the turbulence. We also investigate cluster topology and find that they (i) exhibit a fractal structure, (ii) have a nearly constant particle concentration over their entire size range, and (iii) are most often vertically oriented. Furthermore, clustered particles tend to fall faster than those outside clusters, and larger clusters fall faster on average than smaller ones. Finally, by simultaneous measurement of particle and air velocity fields, we provide the first experimental evidence of preferential sweeping, a mechanism previously proposed to explain the increase in particle settling velocity found in numerical simulations, and find it especially effective for clustered particles. These results are significant for the micro-scale physics of atmospheric clouds. The large cluster size range has implications for how droplets will influence the local environment through condensation, evaporation, drag and latent heat effects. Our results also suggest that large collections of droplets will interact due to differential settling, possibly enhancing raindrop formation.

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

Particle clustering within a two-phase turbulent pipe jet

NASA Astrophysics Data System (ADS)

Lau, Timothy; Nathan, Graham

2016-11-01

A comprehensive study of the influence of Stokes number on the instantaneous distributions of particles within a well-characterised, two-phase, turbulent pipe jet in a weak co-flow was performed. The experiments utilised particles with a narrow size distribution, resulting in a truly mono-disperse particle-laden jet. The jet Reynolds number, based on the pipe diameter, was in the range 10000 <= ReD <= 40000 , while the exit Stokes number was in the range 0 . 3 <= SkD <= 22 . 4 . The particle mass loading was fixed at ϕ = 0 . 4 , resulting in a flow that was in the two-way coupling regime. Instantaneous particle distributions within a two-dimensional sheet was measured using planar nephelometry while particle clusters were identified and subsequently characterised using an in-house developed technique. The results show that particle clustering is significantly influenced by the exit Stokes number. Particle clustering was found to be significant for 0 . 3 <= SkD <= 5 . 6 , with the degree of clustering increasing as SkD is decreased. The clusters, which typically appeared as filament-like structures with high aspect ratio oriented at oblique angles to the flow, were measured right from the exit plane, suggesting that they were generated inside the pipe. The authors acknowledge the financial contributions by the Australian Research Council (Grant No. DP120102961) and the Australian Renewable Energy Agency (Grant No. USO034).

A phase cell cluster expansion for Euclidean field theories

NASA Astrophysics Data System (ADS)

Battle, Guy A., III; Federbush, Paul

1982-08-01

We adapt the cluster expansion first used to treat infrared problems for lattice models (a mass zero cluster expansion) to the usual field theory situation. The field is expanded in terms of special block spin functions and the cluster expansion given in terms of the expansion coefficients (phase cell variables); the cluster expansion expresses correlation functions in terms of contributions from finite coupled subsets of these variables. Most of the present work is carried through in d space time dimensions (for φ24 the details of the cluster expansion are pursued and convergence is proven). Thus most of the results in the present work will apply to a treatment of φ34 to which we hope to return in a succeeding paper. Of particular interest in this paper is a substitute for the stability of the vacuum bound appropriate to this cluster expansion (for d = 2 and d = 3), and a new method for performing estimates with tree graphs. The phase cell cluster expansions have the renormalization group incorporated intimately into their structure. We hope they will be useful ultimately in treating four dimensional field theories.

Field-induced cluster spin glass and inverse symmetry breaking enhanced by frustration

NASA Astrophysics Data System (ADS)

Schmidt, M.; Zimmer, F. M.; Magalhaes, S. G.

2018-03-01

We consider a cluster disordered model to study the interplay between short- and long-range interactions in geometrically frustrated spin systems under an external magnetic field (h). In our approach, the intercluster long-range disorder (J) is analytically treated to get an effective cluster model that is computed exactly. The clusters follow a checkerboard lattice with first-neighbor (J1) and second-neighbor (J2) interactions. We find a reentrant transition from the cluster spin-glass (CSG) state to a paramagnetic (PM) phase as the temperature decreases for a certain range of h. This inverse symmetry breaking (ISB) appears as a consequence of both quenched disorder with frustration and h, that introduce a CSG state with higher entropy than the polarized PM phase. The competitive scenario introduced by antiferromagnetic (AF) short-range interactions increases the CSG state entropy, leading to continuous ISB transitions and enhancing the ISB regions, mainly in the geometrically frustrated case (J1 =J2). Remarkably, when strong AF intracluster couplings are present, field-induced CSG phases can be found. These CSG regions are strongly related to the magnetization plateaus observed in this cluster disordered system. In fact, it is found that each field-induced magnetization jump brings a CSG region. We notice that geometrical frustration, as well as cluster size, play an important role in the magnetization plateaus and, therefore, are also relevant in the field-induced glassy states. Our findings suggest that competing interactions support ISB and field-induced CSG phases in disordered cluster systems under an external magnetic field.

Dynamic secondary ion mass spectroscopy of Au nanoparticles on Si wafer using Bi3+ as primary ion coupled with surface etching by Ar cluster ion beam: The effect of etching conditions on surface structure

NASA Astrophysics Data System (ADS)

Park, Eun Ji; Choi, Chang Min; Kim, Il Hee; Kim, Jung-Hwan; Lee, Gaehang; Jin, Jong Sung; Ganteför, Gerd; Kim, Young Dok; Choi, Myoung Choul

2018-01-01

Wet-chemically synthesized Au nanoparticles were deposited on Si wafer surfaces, and the secondary ions mass spectra (SIMS) from these samples were collected using Bi3+ with an energy of 30 keV as the primary ions. In the SIMS, Au cluster cations with a well-known, even-odd alteration pattern in the signal intensity were observed. We also performed depth profile SIMS analyses, i.e., etching the surface using an Ar gas cluster ion beam (GCIB), and a subsequent Bi3+ SIMS analysis was repetitively performed. Here, two different etching conditions (Ar1600 clusters of 10 keV energy or Ar1000 of 2.5 keV denoted as "harsh" or "soft" etching conditions, respectively) were used. Etching under harsh conditions induced emission of the Au-Si binary cluster cations in the SIMS spectra of the Bi3+ primary ions. The formation of binary cluster cations can be induced by either fragmentation of Au nanoparticles or alloying of Au and Si, increasing Au-Si coordination on the sample surface during harsh GCIB etching. Alternatively, use of the soft GCIB etching conditions resulted in exclusive emission of pure Au cluster cations with nearly no Au-Si cluster cation formation. Depth profile analyses of the Bi3+ SIMS combined with soft GCIB etching can be useful for studying the chemical environments of atoms at the surface without altering the original interface structure during etching.

Electronic, Magnetic, and Redox Properties of [MFe(3)S(4)] Clusters (M = Cd, Cu, Cr) in Pyrococcus furiosus Ferredoxin.

PubMed

Staples, Christopher R.; Dhawan, Ish K.; Finnegan, Michael G.; Dwinell, Derek A.; Zhou, Zhi Hao; Huang, Heshu; Verhagen, Marc F. J. M.; Adams, Michael W. W.; Johnson, Michael K.

1997-12-03

The ground- and excited-state properties of heterometallic [CuFe(3)S(4)](2+,+), [CdFe(3)S(4)](2+,+), and [CrFe(3)S(4)](2+,+) cubane clusters assembled in Pyrococcus furiosus ferredoxin have been investigated by the combination of EPR and variable-temperature/variable-field magnetic circular dichroism (MCD) studies. The results indicate Cd(2+) incorporation into [Fe(3)S(4)](0,-) cluster fragments to yield S = 2 [CdFe(3)S(4)](2+) and S = (5)/(2) [CdFe(3)S(4)](+) clusters and Cu(+) incorporation into [Fe(3)S(4)](+,0) cluster fragments to yield S = (1)/(2) [CuFe(3)S(4)](2+) and S = 2 [CuFe(3)S(4)](+) clusters. This is the first report of the preparation of cubane type [CrFe(3)S(4)](2+,+) clusters, and the combination of EPR and MCD results indicates S = 0 and S = (3)/(2) ground states for the oxidized and reduced forms, respectively. Midpoint potentials for the [CdFe(3)S(4)](2+,+), [CrFe(3)S(4)](2+,+), and [CuFe(3)S(4)](2+,+) couples, E(m) = -470 +/- 15, -440 +/- 10, and +190 +/- 10 mV (vs NHE), respectively, were determined by EPR-monitored redox titrations or direct electrochemistry at a glassy carbon electrode. The trends in redox potential, ground-state spin, and electron delocalization of [MFe(3)S(4)](2+,+) clusters in P. furiosus ferredoxin are discussed as a function of heterometal (M = Cr, Mn, Fe, Co, Ni, Cu, Zn, Cd, and Tl).

Anion photoelectron spectroscopy of radicals and clusters

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

Travis, Taylor R.

1999-12-01

Anion photoelectron spectroscopy is used to study free radicals and clusters. The low-lying 2Σ and 2π states of C 2nH (n = 1--4) have been studied. The anion photoelectron spectra yielded electron affinities, term values, and vibrational frequencies for these combustion and astrophysically relevant species. Photoelectron angular distributions allowed the author to correctly assign the electronic symmetry of the ground and first excited states and to assess the degree of vibronic coupling in C 2H and C 4H. Other radicals studied include NCN and I 3. The author was able to observe the low-lying singlet and triplet states of NCNmore » for the first time. Measurement of the electron affinity of I 3 revealed that it has a bound ground state and attachment of an argon atom to this moiety enabled him to resolve the symmetric stretching progression.« less

Bolometers for millimeter-wave Cosmology

NASA Astrophysics Data System (ADS)

Bock, James J.

2002-05-01

Bolometers offer high sensitivity for observations of the cosmic microwave background, Sunyaev-Zel'Dovich effect in clusters, and far-infrared galaxies. Near background-limited performance may be realized even under the low background conditions available from a space-borne platform. We discuss the achieved performance of silicon nitride micromesh (`spider web') bolometers readout by NTD Ge thermistors. We are developing arrays of such bolometers coupled to single-mode feedhorns. CMB polarization may be studies using a new absorber geometry allowing simultaneous detection of both linear polarizations in a single feedhorn with two individual detectors. Finally we discuss a new bolometer architecture consisting of an array of slot antennae coupled to filters and bolometers via superconducting microstrip. .

Local-world and cluster-growing weighted networks with controllable clustering

NASA Astrophysics Data System (ADS)

Yang, Chun-Xia; Tang, Min-Xuan; Tang, Hai-Qiang; Deng, Qiang-Qiang

2014-12-01

We constructed an improved weighted network model by introducing local-world selection mechanism and triangle coupling mechanism based on the traditional BBV model. The model gives power-law distributions of degree, strength and edge weight and presents the linear relationship both between the degree and strength and between the degree and the clustering coefficient. Particularly, the model is equipped with an ability to accelerate the speed increase of strength exceeding that of degree. Besides, the model is more sound and efficient in tuning clustering coefficient than the original BBV model. Finally, based on our improved model, we analyze the virus spread process and find that reducing the size of local-world has a great inhibited effect on virus spread.

Nested variant of the method of moments of coupled cluster equations for vertical excitation energies and excited-state potential energy surfaces.

PubMed

Kowalski, Karol

2009-05-21

In this article we discuss the problem of proper balancing of the noniterative corrections to the ground- and excited-state energies obtained with approximate coupled cluster (CC) and equation-of-motion CC (EOMCC) approaches. It is demonstrated that for a class of excited states dominated by single excitations and for states with medium doubly excited component, the newly introduced nested variant of the method of moments of CC equations provides mathematically rigorous way of balancing the ground- and excited-state correlation effects. The resulting noniterative methodology accounting for the effect of triples is tested using its parallel implementation on the systems, for which iterative CC/EOMCC calculations with full inclusion of triply excited configurations or their most important subset are numerically feasible.

Dealing with chemical reaction pathways and electronic excitations in molecular systems via renormalized and active-space coupled-cluster methods

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

Piecuch, Piotr; Li, Wei; Lutz, Jesse J.

Coupled-cluster (CC) theory has become the de facto standard for high-accuracy molecular calculations, but the widely used CC and equation-of-motion (EOM) CC approaches, such as CCSD(T) and EOMCCSD, have difficulties with capturing stronger electron correlations that characterize multi-reference molecular problems. This presentation demonstrates that many of these difficulties can be addressed by exploiting the completely renormalized (CR) CC and EOMCC approaches, such as CR-CC(2,3), CR-EOMCCSD(T), and CR-EOMCC(2,3), and their local correlation counterparts applicable to systems with hundreds of atoms, and the active-space CC/EOMCC approaches, such as CCSDt and EOMCCSDt, and their extensions to valence systems via the electron-attached and ionizedmore » formalisms.« less

Noniterative Multireference Coupled Cluster Methods on Heterogeneous CPU-GPU Systems

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

Bhaskaran-Nair, Kiran; Ma, Wenjing; Krishnamoorthy, Sriram

2013-04-09

A novel parallel algorithm for non-iterative multireference coupled cluster (MRCC) theories, which merges recently introduced reference-level parallelism (RLP) [K. Bhaskaran-Nair, J.Brabec, E. Aprà, H.J.J. van Dam, J. Pittner, K. Kowalski, J. Chem. Phys. 137, 094112 (2012)] with the possibility of accelerating numerical calculations using graphics processing unit (GPU) is presented. We discuss the performance of this algorithm on the example of the MRCCSD(T) method (iterative singles and doubles and perturbative triples), where the corrections due to triples are added to the diagonal elements of the MRCCSD (iterative singles and doubles) effective Hamiltonian matrix. The performance of the combined RLP/GPU algorithmmore » is illustrated on the example of the Brillouin-Wigner (BW) and Mukherjee (Mk) state-specific MRCCSD(T) formulations.« less

Nonlinear dynamics of the complex multi-scale network

NASA Astrophysics Data System (ADS)

Makarov, Vladimir V.; Kirsanov, Daniil; Goremyko, Mikhail; Andreev, Andrey; Hramov, Alexander E.

2018-04-01

In this paper, we study the complex multi-scale network of nonlocally coupled oscillators for the appearance of chimera states. Chimera is a special state in which, in addition to the asynchronous cluster, there are also completely synchronous parts in the system. We show that the increase of nodes in subgroups leads to the destruction of the synchronous interaction within the common ring and to the narrowing of the chimera region.

Targeted replacement: systematic studies of dodecanuclear {MLn} coordination clusters (M = Cr, Co; Ln = Dy, Y).

PubMed

Chen, Sihuai; Mereacre, Valeriu; Zhao, Zhiying; Zhang, Wanwan; Zhang, Mengsi; He, Zhangzhen

2018-06-05

Three dodecanuclear 3d-4f coordination clusters, [CrIII6LnIII6(μ3-OH)8(tbdea)6(C6H5COO)16]·2H2O (Ln = Dy (1), Y (2)) and [CoIII6DyIII6(μ3-OH)8(nbdea)6(m-CH3C6H4COO)16]·2H2O·2CH3CN (3), have been synthesized under solvothermal conditions and characterized. Single-crystal X-ray diffraction analysis revealed that all three compounds possess an analogous {MIII6LnIII6} core (M = Cr, Co; Ln = Dy, Y) and dc magnetic susceptibility studies indicated that the magnetic exchange couplings between DyIII ions are dominant antiferromagnetic, while the CrIII-DyIII interactions are weakly ferromagnetic. Furthermore, the ac magnetic susceptibility measurements showed that both CrIII6DyIII6 compound 1 and CoIIi6DyIII6 compound 3 containing highly anisotropic DyIII ions displayed single-molecule magnetic (SMM) behavior with the energy barrier Ueff increasing from 12.8 K (for 1) to 20.8 K (for 3), indicating that weak 3d-4f exchange couplings enhance the QTM and reduce the energy barrier.

Reduction Potentials of [FeFe]-Hydrogenase Accessory Iron-Sulfur Clusters Provide Insights into the Energetics of Proton Reduction Catalysis.

PubMed

Artz, Jacob H; Mulder, David W; Ratzloff, Michael W; Lubner, Carolyn E; Zadvornyy, Oleg A; LeVan, Axl X; Williams, S Garrett; Adams, Michael W W; Jones, Anne K; King, Paul W; Peters, John W

2017-07-19

An [FeFe]-hydrogenase from Clostridium pasteurianum, CpI, is a model system for biological H 2 activation. In addition to the catalytic H-cluster, CpI contains four accessory iron-sulfur [FeS] clusters in a branched series that transfer electrons to and from the active site. In this work, potentiometric titrations have been employed in combination with electron paramagnetic resonance (EPR) spectroscopy at defined electrochemical potentials to gain insights into the role of the accessory clusters in catalysis. EPR spectra collected over a range of potentials were deconvoluted into individual components attributable to the accessory [FeS] clusters and the active site H-cluster, and reduction potentials for each cluster were determined. The data suggest a large degree of magnetic coupling between the clusters. The distal [4Fe-4S] cluster is shown to have a lower reduction potential (∼ < -450 mV) than the other clusters, and molecular docking experiments indicate that the physiological electron donor, ferredoxin (Fd), most favorably interacts with this cluster. The low reduction potential of the distal [4Fe-4S] cluster thermodynamically restricts the Fd ox /Fd red ratio at which CpI can operate, consistent with the role of CpI in recycling Fd red that accumulates during fermentation. Subsequent electron transfer through the additional accessory [FeS] clusters to the H-cluster is thermodynamically favorable.

Studies of the spin Hamiltonian parameters and local structure for ZnO:Cu2+.

PubMed

Wu, Shao-Yi; Wei, Li-Hua; Zhang, Zhi-Hong; Wang, Xue-Feng; Hu, Yue-Xia

2008-12-15

The spin Hamiltonian parameters (the g factors and the hyperfine structure constants) and local structure for ZnO:Cu2+ are theoretically studied from the perturbation formulas of these parameters for a 3d9 ion under trigonally distorted tetrahedra. The ligand orbital and spin-orbit coupling contributions are taken into account from the cluster approach due to the significant covalency of the [CuO4](6-) cluster. According to the investigations, the impurity Cu2+ is suggested not to locate on the ideal Zn2+ site in ZnO but to undergo a slight outward displacement (approximately 0.01 angstroms) away from the ligand triangle along C3 axis. The calculated spin Hamiltonian parameters are in good agreement with the observed values. The validity of the above impurity displacement is also discussed.

Biochemistry of Catabolic Reductive Dehalogenation.

PubMed

Fincker, Maeva; Spormann, Alfred M

2017-06-20

A wide range of phylogenetically diverse microorganisms couple the reductive dehalogenation of organohalides to energy conservation. Key enzymes of such anaerobic catabolic pathways are corrinoid and Fe-S cluster-containing, membrane-associated reductive dehalogenases. These enzymes catalyze the reductive elimination of a halide and constitute the terminal reductases of a short electron transfer chain. Enzymatic and physiological studies revealed the existence of quinone-dependent and quinone-independent reductive dehalogenases that are distinguishable at the amino acid sequence level, implying different modes of energy conservation in the respective microorganisms. In this review, we summarize current knowledge about catabolic reductive dehalogenases and the electron transfer chain they are part of. We review reaction mechanisms and the role of the corrinoid and Fe-S cluster cofactors and discuss physiological implications.

Influence of stochastic perturbations on the cluster explosive synchronization of second-order Kuramoto oscillators on networks.

PubMed

Cao, Liang; Tian, Changhai; Wang, Zhenhua; Zhang, Xiyun; Liu, Zonghua

2018-02-01

Explosive synchronization in networked second-order Kuramoto oscillators has been well studied recently and it is revealed that the synchronization process is featured by cluster explosive synchronization. However, little attention has been paid to the influence of noise or perturbation. We here study this problem and discuss the influences of noise and perturbation. For the former, we interestingly find that noise has significant influence on the cluster explosive synchronization of those nodes with smaller degrees, i.e., their synchronization will change from the first-order to second-order transition and the critical points for both the forward and backward synchronization depend on the strength of noise. Especially, when the strength of noise is in an optimal range, a synchronization of the nodes with smaller degrees will be induced in the region of coupling strength where they do not display synchronization in the absence of noise. For the latter, we find that the effect of perturbation is similar to that of noise when its duration W is small. However, the perturbation will induce a change from cluster explosive synchronization to explosive synchronization when W is large. Furthermore, a brief theory is provided to explain the influence of perturbations on the critical points.

Conformation, structure and molecular solvation: a spectroscopic and computational study of 2-phenoxy ethanol and its singly and multiply hydrated clusters

NASA Astrophysics Data System (ADS)

Macleod, Neil A.; Simons, John P.

2002-10-01

The conformational landscapes of 2-phenoxy ethanol (POX) and its hydrated clusters have been studied in the gas-phase, providing a model for pharmaceutical β-blockers. A combination of experimental techniques, including resonant two-photon ionisation (R2PI), laser-induced-fluorescence (LIF) and resonant ion-dip infra-red spectroscopy (RIDIRS), coupled with high-level ab initio calculations has allowed the assignment of the individually resolved spectral features to discrete conformational and supra-molecular structures. Assignments were made by comparison of experimental vibrational spectra and partially resolved ultra-violet rotational band contours with those predicted from quantum chemical calculations. The isolated molecule displays a solitary structure with an extended geometry of the side-chain which is stabilised by an intramolecular hydrogen-bond between the alcohol (proton donor) and the ether (proton acceptor) groups of the side-chain. In singly hydrated clusters the water molecule is accommodated by insertion into the intramolecular hydrogen-bond. In the doubly hydrated and higher clusters cyclic structures are generated which incorporate both the water molecules and the terminal OH group of the side-chain; additional (weak) hydrogen bonded interactions with the phenoxy group provide a degree of selectivity but essentially, the water 'droplet' forms on the end of the alcohol side-chain.

Structure-related frustrated magnetism of nanosized polyoxometalates: aesthetics and properties in harmony.

PubMed

Kögerler, Paul; Tsukerblat, Boris; Müller, Achim

2010-01-07

The structural versatility characterizing polyoxometalate chemistry, in combination with the option to deliberately use well-defined building blocks, serves as the foundation for the generation of a large family of magnetic clusters, frequently comprising highly symmetric spin arrays. If the spin centers are coupled by antiferromagnetic exchange, some of these systems exhibit spin frustration, which can result in novel magnetic properties of purely molecular origins. We discuss here the magnetic properties of selected nanosized polyoxometalate clusters featuring spin triangles as their magnetic 'building blocks' or fragments. This includes unique porous Keplerate clusters of the type {(Mo)Mo(5)}(12)M(30) (M = Fe(III), Cr(III), V(IV)) with the spin centers defining a regular icosidodecahedron and the {V(15)As(6)}-type cluster sphere containing a single equilateral spin triangle; these species are widely discussed and studied in the literature for their role in materials science as molecular representations of Kagomé lattices and in relation to quantum computing, respectively. Exhibiting fascinating and unique structural features, these magnetic molecules allow the study of the implications of frustrated spin ordering. Furthermore, this perspective covers the impact of spin frustration on the degeneracy of the ground state and related problems, namely strong magnetic anisotropy and the interplay of antisymmetric exchange and structural Jahn-Teller effects.

Theoretical Study of the H2-ML(+) Binding Energies

NASA Technical Reports Server (NTRS)

Maitre, Philippe; Bauschlicher, Charles W., Jr.

1993-01-01

The cooperative ligand effects are studied in MLH2(+) and the results are compared to the recent experiments of Kemper et al. The bonding in these compounds is principally electrostatic in origin; however, ligand to metal and metal to ligand donations are important, especially for H2. We show that differences arise among the vanadium, cobalt, and copper complexes which are due to 3d donation to H2. Electron correlation is required to describe the dative interaction, and we find that second order Moller-Plesset perturbation theory (MP2) yields a good description of these systems compared with higher levels of correlation (such as the modified coupled pair functional and coupled cluster approaches) and experiment. However, obtaining quantitative results requires higher levels of theory than MP2.

Circadian desynchronization

PubMed Central

Granada, Adrián E.; Cambras, Trinitat; Díez-Noguera, Antoni; Herzel, Hanspeter

2011-01-01

The suprachiasmatic nucleus (SCN) coordinates via multiple outputs physiological and behavioural circadian rhythms. The SCN is composed of a heterogeneous network of coupled oscillators that entrain to the daily light–dark cycles. Outside the physiological entrainment range, rich locomotor patterns of desynchronized rhythms are observed. Previous studies interpreted these results as the output of different SCN neural subpopulations. We find, however, that even a single periodically driven oscillator can induce such complex desynchronized locomotor patterns. Using signal analysis, we show how the observed patterns can be consistently clustered into two generic oscillatory interaction groups: modulation and superposition. In seven of 17 rats undergoing forced desynchronization, we find a theoretically predicted third spectral component. Combining signal analysis with the theory of coupled oscillators, we provide a framework for the study of circadian desynchronization. PMID:22419981

Computational chemistry of modified [MFe3S4] and [M2Fe2S4] clusters: assessment of trends in electronic structure and properties.

PubMed

Jensen, Kasper P; Ooi, Bee-Lean; Christensen, Hans E M

2008-12-18

The aim of this work is to understand the molecular evolution of iron-sulfur clusters in terms of electronic structure and function. Metal-substituted models of biological [Fe(4)S(4)] clusters in oxidation states [M(x)Fe(4-x)S(4)](3+/2+/1+) have been studied by density functional theory (M = Cr, Mn, Fe, Co, Ni, Cu, Zn, and Pd, with x = 1 or 2). Most of these clusters have not been characterized before. For those that have been characterized experimentally, very good agreement is obtained, implying that also the predicted structures and properties of new clusters are accurate. Mean absolute errors are 0.024 A for bond lengths ([Fe(4)S(4)], [NiFe(3)S(4)], [CoFe(3)S(4)]) and 0.09 V for shifts in reduction potentials relative to the [Fe(4)S(4)] cluster. All structures form cuboidal geometries similar to the all-iron clusters, except the Pd-substituted clusters, which instead form highly distorted trigonal and tetragonal local sites in compromised, pseudocuboidal geometries. In contrast to other electron-transfer sites, cytochromes, blue copper proteins, and smaller iron-sulfur clusters, we find that the [Fe(4)S(4)] clusters are very insensitive to metal substitution, displaying quite small changes in reorganization energies and reduction potentials upon substitution. Thus, the [Fe(4)S(4)] clusters have an evolutionary advantage in being robust to pollution from other metals, still retaining function. We analyze in detail the electronic structure of individual clusters and rationalize spin couplings and redox activity. Often, several configurations are very close in energy, implying possible use as spin-crossover systems, and spin states are predicted accurately in all but one case ([CuFe(3)S(4)]). The results are anticipated to be helpful in defining new molecular systems with catalytic and magnetic properties.

High-dimensional neural network potentials for solvation: The case of protonated water clusters in helium

NASA Astrophysics Data System (ADS)

Schran, Christoph; Uhl, Felix; Behler, Jörg; Marx, Dominik

2018-03-01

The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the interactions. We show that this challenge can be met by using a combination of an effective pair potential for the He-He interactions and a flexible high-dimensional neural network potential (NNP) for describing the complex interaction between helium and the solute in a pairwise additive manner. This approach yields an excellent agreement with a mean absolute deviation as small as 0.04 kJ mol-1 for the interaction energy between helium and both hydronium and Zundel cations compared with coupled cluster reference calculations with an energetically converged basis set. The construction and improvement of the potential can be performed in a highly automated way, which opens the door for applications to a variety of reactive molecules to study the effect of solvation on the solute as well as the solute-induced structuring of the solvent. Furthermore, we show that this NNP approach yields very convincing agreement with the coupled cluster reference for properties like many-body spatial and radial distribution functions. This holds for the microsolvation of the protonated water monomer and dimer by a few helium atoms up to their solvation in bulk helium as obtained from path integral simulations at about 1 K.

High-dimensional neural network potentials for solvation: The case of protonated water clusters in helium.

PubMed

Schran, Christoph; Uhl, Felix; Behler, Jörg; Marx, Dominik

2018-03-14

The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the interactions. We show that this challenge can be met by using a combination of an effective pair potential for the He-He interactions and a flexible high-dimensional neural network potential (NNP) for describing the complex interaction between helium and the solute in a pairwise additive manner. This approach yields an excellent agreement with a mean absolute deviation as small as 0.04 kJ mol -1 for the interaction energy between helium and both hydronium and Zundel cations compared with coupled cluster reference calculations with an energetically converged basis set. The construction and improvement of the potential can be performed in a highly automated way, which opens the door for applications to a variety of reactive molecules to study the effect of solvation on the solute as well as the solute-induced structuring of the solvent. Furthermore, we show that this NNP approach yields very convincing agreement with the coupled cluster reference for properties like many-body spatial and radial distribution functions. This holds for the microsolvation of the protonated water monomer and dimer by a few helium atoms up to their solvation in bulk helium as obtained from path integral simulations at about 1 K.

Accurate detection of hierarchical communities in complex networks based on nonlinear dynamical evolution

NASA Astrophysics Data System (ADS)

Zhuo, Zhao; Cai, Shi-Min; Tang, Ming; Lai, Ying-Cheng

2018-04-01

One of the most challenging problems in network science is to accurately detect communities at distinct hierarchical scales. Most existing methods are based on structural analysis and manipulation, which are NP-hard. We articulate an alternative, dynamical evolution-based approach to the problem. The basic principle is to computationally implement a nonlinear dynamical process on all nodes in the network with a general coupling scheme, creating a networked dynamical system. Under a proper system setting and with an adjustable control parameter, the community structure of the network would "come out" or emerge naturally from the dynamical evolution of the system. As the control parameter is systematically varied, the community hierarchies at different scales can be revealed. As a concrete example of this general principle, we exploit clustered synchronization as a dynamical mechanism through which the hierarchical community structure can be uncovered. In particular, for quite arbitrary choices of the nonlinear nodal dynamics and coupling scheme, decreasing the coupling parameter from the global synchronization regime, in which the dynamical states of all nodes are perfectly synchronized, can lead to a weaker type of synchronization organized as clusters. We demonstrate the existence of optimal choices of the coupling parameter for which the synchronization clusters encode accurate information about the hierarchical community structure of the network. We test and validate our method using a standard class of benchmark modular networks with two distinct hierarchies of communities and a number of empirical networks arising from the real world. Our method is computationally extremely efficient, eliminating completely the NP-hard difficulty associated with previous methods. The basic principle of exploiting dynamical evolution to uncover hidden community organizations at different scales represents a "game-change" type of approach to addressing the problem of community detection in complex networks.

Clustered Regularly Interspaced Short Palindromic Repeats: Challenges in Treating Retinal Disease.

PubMed

Chrenek, Micah A; Nickerson, John M; Boatright, Jeffrey H

2016-01-01

Ophthalmic researchers and clinicians arguably have led the way for safe, effective gene therapy, most notably with adeno-associated viral gene supplementation in the treatment for patients with Leber congenital amaurosis type 2 with mutations in the RPE65 gene. These successes notwithstanding, most other genetic retinal disease will be refractory to supplementation. The ideal gene therapy approach would correct gene mutations to restore normal function in the affected cells. Gene editing in which a mutant allele is inactivated or converted to sequence that restores normal function is hypothetically one such approach. Such editing involves site-specific digestion of mutant genomic DNA followed by repair. Previous experimental approaches were hampered by inaccurate and high rates of off-site lesioning and by overall low digestion rates. A new tool, clustered regularly interspaced short palindromic repeats coupled with the nuclease Cas9, may address both shortcomings. Some of the many challenges that must be addressed in moving clustered regularly interspaced short palindromic repeats coupled with the nuclease Cas9 therapies to the ophthalmic clinic are discussed here.

Tailoring magnetic properties of Co nanocluster assembled films using hydrogen

NASA Astrophysics Data System (ADS)

Romero, C. P.; Volodin, A.; Paddubrouskaya, H.; Van Bael, M. J.; Van Haesendonck, C.; Lievens, P.

2018-07-01

Tailoring magnetic properties in nanocluster assembled cobalt (Co) thin films was achieved by admitting a small percentage of H2 gas (∼2%) into the Co gas phase cluster formation chamber prior to deposition. The oxygen content in the films is considerably reduced by the presence of hydrogen during the cluster formation, leading to enhanced magnetic interactions between clusters. Two sets of Co samples were fabricated, one without hydrogen gas and one with hydrogen gas. Magnetic properties of the non-hydrogenated and the hydrogen-treated Co nanocluster assembled films are comparatively studied using magnetic force microscopy and vibrating sample magnetometry. When comparing the two sets of samples the considerably larger coercive field of the H2-treated Co nanocluster film and the extended micrometer-sized magnetic domain structure confirm the enhancement of magnetic interactions between clusters. The thickness of the antiferromagnetic CoO layer is controlled with this procedure and modifies the exchange bias effect in these films. The exchange bias shift is lower for the H2-treated Co nanocluster film, which indicates that a thinner antiferromagnetic CoO reduces the coupling with the ferromagnetic Co. The hydrogen-treatment method can be used to tailor the oxidation levels thus controlling the magnetic properties of ferromagnetic cluster-assembled films.

Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization

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

Neustetter, M.; Jabbour Al Maalouf, E.; Denifl, S., E-mail: Stephan.Denifl@uibk.ac.at, E-mail: plimaovieira@fct.unl.pt

2016-08-07

Electron ionization of neat tungsten hexacarbonyl (W(CO){sub 6}) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO){sub 6} clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO){sub n}{sup +} (0 ≤ n ≤ 6) and W{sub 2}(CO){sub n}{sup +} (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO){sub n}{sup +} (0 ≤more » n ≤ 3) and W{sub 2}C(CO){sub n}{sup +} (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.« less

Skill transfer, affordances and dexterity in different climbing environments.

PubMed

Seifert, L; Wattebled, L; L'hermette, M; Bideault, G; Herault, R; Davids, K

2013-12-01

This study explored how skills in one region of a perceptual-motor landscape of performance, created in part by previous experience in rock climbing, can shape those that emerge in another region (ice climbing). Ten novices in rock climbing and five intermediate rock climbers were observed climbing an icefall. Locations of right and left ice tools and crampons were videotaped from a frontal camera. Inter-individual variability of upper and lower limb couplings and types of action regarding icefall properties were assessed by cluster hierarchical analysis, distinguishing three clusters. Pelvis vertical displacement, duration and number of pelvis pauses were also analyzed. Experienced rock climbers were grouped in the same cluster and showed the highest range and variability of limb angular locations and coordination patterns, the highest vertical displacement and the shortest pelvis plateaux durations. Non-fluent climbers (clusters 2 and 3) showed low range and variability of limb angular locations and coordination patterns. In particular, climbers of cluster 3 exhibited the lowest vertical displacement, the longest plateaux durations and the greatest ratio between tool swinging and definitive anchorage. Our results exemplified the positive influence of skills in rock climbing on ice climbing performance, facilitated by the detection of affordances from environmental properties. Copyright © 2013 Elsevier B.V. All rights reserved.

Clustering and phase synchronization in populations of coupled phase oscillators

NASA Astrophysics Data System (ADS)

Cascallares, Guadalupe; Gleiser, Pablo M.

2015-10-01

In many species daily rhythms are endogenously generated by groups of coupled neurons that play the role of a circadian pacemaker. The adaptation of the circadian clock to environmental and seasonal changes has been proposed to be regulated by a dual oscillator system. In order to gain insight into this model, we analyzed the synchronization properties of two fully coupled groups of Kuramoto oscillators. Each group has an internal coupling parameter and the interaction between the two groups can be controlled by two parameters allowing for symmetric or non-symmetric coupling. We show that even for such a simple model counterintuitive behaviours take place, such as a global decrease in synchrony when the coupling between the groups is increased. Through a detailed analysis of the local synchronization processes we explain this behaviour.

Cloud computing and validation of expandable in silico livers.

PubMed

Ropella, Glen E P; Hunt, C Anthony

2010-12-03

In Silico Livers (ISLs) are works in progress. They are used to challenge multilevel, multi-attribute, mechanistic hypotheses about the hepatic disposition of xenobiotics coupled with hepatic responses. To enhance ISL-to-liver mappings, we added discrete time metabolism, biliary elimination, and bolus dosing features to a previously validated ISL and initiated re-validated experiments that required scaling experiments to use more simulated lobules than previously, more than could be achieved using the local cluster technology. Rather than dramatically increasing the size of our local cluster we undertook the re-validation experiments using the Amazon EC2 cloud platform. So doing required demonstrating the efficacy of scaling a simulation to use more cluster nodes and assessing the scientific equivalence of local cluster validation experiments with those executed using the cloud platform. The local cluster technology was duplicated in the Amazon EC2 cloud platform. Synthetic modeling protocols were followed to identify a successful parameterization. Experiment sample sizes (number of simulated lobules) on both platforms were 49, 70, 84, and 152 (cloud only). Experimental indistinguishability was demonstrated for ISL outflow profiles of diltiazem using both platforms for experiments consisting of 84 or more samples. The process was analogous to demonstration of results equivalency from two different wet-labs. The results provide additional evidence that disposition simulations using ISLs can cover the behavior space of liver experiments in distinct experimental contexts (there is in silico-to-wet-lab phenotype similarity). The scientific value of experimenting with multiscale biomedical models has been limited to research groups with access to computer clusters. The availability of cloud technology coupled with the evidence of scientific equivalency has lowered the barrier and will greatly facilitate model sharing as well as provide straightforward tools for scaling simulations to encompass greater detail with no extra investment in hardware.

GW and Bethe-Salpeter study of small water clusters

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

Blase, Xavier, E-mail: xavier.blase@neel.cnrs.fr; Boulanger, Paul; Bruneval, Fabien

We study within the GW and Bethe-Salpeter many-body perturbation theories the electronic and optical properties of small (H{sub 2}O){sub n} water clusters (n = 1-6). Comparison with high-level CCSD(T) Coupled-Cluster at the Single Double (Triple) levels and ADC(3) Green’s function third order algebraic diagrammatic construction calculations indicates that the standard non-self-consistent G{sub 0}W{sub 0}@PBE or G{sub 0}W{sub 0}@PBE0 approaches significantly underestimate the ionization energy by about 1.1 eV and 0.5 eV, respectively. Consequently, the related Bethe-Salpeter lowest optical excitations are found to be located much too low in energy when building transitions from a non-self-consistent G{sub 0}W{sub 0} description ofmore » the quasiparticle spectrum. Simple self-consistent schemes, with update of the eigenvalues only, are shown to provide a weak dependence on the Kohn-Sham starting point and a much better agreement with reference calculations. The present findings rationalize the theory to experiment possible discrepancies observed in previous G{sub 0}W{sub 0} and Bethe-Salpeter studies of bulk water. The increase of the optical gap with increasing cluster size is consistent with the evolution from gas to dense ice or water phases and results from an enhanced screening of the electron-hole interaction.« less

HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach

PubMed Central

Kiwuwa-Muyingo, Sylvia; Nazziwa, Jamirah; Ssemwanga, Deogratius; Ilmonen, Pauliina; Ndembi, Nicaise; Parry, Chris; Kitandwe, Paul Kato; Gershim, Asiki; Mpendo, Juliet; Neilsen, Leslie; Seeley, Janet; Seppälä, Heikki; Lyagoba, Fred; Kamali, Anatoli; Kaleebu, Pontiano

2017-01-01

Background Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection. Methods Using data from a cohort of HIV-positive individuals aged 13–49 years, enrolled from 5 fishing communities on Lake Victoria between 2009–2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering. Results Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26–1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40–11.68]). Conclusions A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections. PMID:29023474

HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach.

PubMed

Kiwuwa-Muyingo, Sylvia; Nazziwa, Jamirah; Ssemwanga, Deogratius; Ilmonen, Pauliina; Njai, Harr; Ndembi, Nicaise; Parry, Chris; Kitandwe, Paul Kato; Gershim, Asiki; Mpendo, Juliet; Neilsen, Leslie; Seeley, Janet; Seppälä, Heikki; Lyagoba, Fred; Kamali, Anatoli; Kaleebu, Pontiano

2017-01-01

Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection. Using data from a cohort of HIV-positive individuals aged 13-49 years, enrolled from 5 fishing communities on Lake Victoria between 2009-2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering. Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26-1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40-11.68]). A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections.

Independent-Cluster Parametrizations of Wave Functions in Model Field Theories III. The Coupled-Cluster Phase Spaces and Their Geometrical Structure

NASA Astrophysics Data System (ADS)

Arponen, J. S.; Bishop, R. F.

1993-11-01

In this third paper of a series we study the structure of the phase spaces of the independent-cluster methods. These phase spaces are classical symplectic manifolds which provide faithful descriptions of the quantum mechanical pure states of an arbitrary system. They are "superspaces" in the sense that the full physical many-body or field-theoretic system is described by a point of the space, in contrast to "ordinary" spaces for which the state of the physical system is described rather by the whole space itself. We focus attention on the normal and extended coupled-cluster methods (NCCM and ECCM). Both methods provide parametrizations of the Hilbert space which take into account in increasing degrees of completeness the connectivity properties of the associated perturbative diagram structure. This corresponds to an increasing incorporation of locality into the description of the quantum system. As a result the degree of nonlinearity increases in the dynamical equations that govern the temporal evolution and determine the equilibrium state. Because of the nonlinearity, the structure of the manifold becomes geometrically complicated. We analyse the neighbourhood of the ground state of the one-mode anharmonic bosonic field theory and derive the nonlinear expansion beyond the linear response regime. The expansion is given in terms of normal-mode amplitudes, which provide the best local coordinate system close to the ground state. We generalize the treatment to other nonequilibrium states by considering the similarly defined normal coordinates around the corresponding phase space point. It is pointed out that the coupled-cluster method (CCM) maps display such features as (an)holonomy, or geometric phase. For example, a physical state may be represented by a number of different points on the CCM manifold. For this reason the whole phase spaces in the NCCM or ECCM cannot be covered by a single chart. To account for this non-Euclidean nature we introduce a suitable pseudo-Riemannian metric structure which is compatible with an important subset of all canonical transformations. It is then shown that the phase space of the configuration-interaction method is flat, namely the complex Euclidean space; that the NCCM manifold has zero curvature even though its Reimann tensor does not vanish; and that the ECCM manifold is intrinsically curved. It is pointed out that with the present metrization many of the dimensions of the ECCM phase space are effectively compactified and that the overall topological structure of the space is related to the distribution of the zeros of the Bargmann wave function.

Double-well chimeras in 2D lattice of chaotic bistable elements

NASA Astrophysics Data System (ADS)

Shepelev, I. A.; Bukh, A. V.; Vadivasova, T. E.; Anishchenko, V. S.; Zakharova, A.

2018-01-01

We investigate spatio-temporal dynamics of a 2D ensemble of nonlocally coupled chaotic cubic maps in a bistability regime. In particular, we perform a detailed study on the transition ;coherence - incoherence; for varying coupling strength for a fixed interaction radius. For the 2D ensemble we show the appearance of amplitude and phase chimera states previously reported for 1D ensembles of nonlocally coupled chaotic systems. Moreover, we uncover a novel type of chimera state, double-well chimera, which occurs due to the interplay of the bistability of the local dynamics and the 2D ensemble structure. Additionally, we find double-well chimera behavior for steady states which we call double-well chimera death. A distinguishing feature of chimera patterns observed in the lattice is that they mainly combine clusters of different chimera types: phase, amplitude and double-well chimeras.

The effect of side motion in the dynamics of interacting molecular motors

NASA Astrophysics Data System (ADS)

Midha, Tripti; Gupta, Arvind Kumar; Kolomeisky, Anatoly B.

2017-07-01

To mimic the collective motion of interacting molecular motors, we propose and discuss an open two-lane symmetrically coupled interactive TASEP model that incorporates interaction in the thermodynamically consistent fashion. We study the effect of both repulsive and attractive interaction on the system’s dynamical properties using various cluster mean field analysis and extensive Monte Carlo simulations. The interactions bring correlations into the system, which were found to be reduced due to the side motion of particles. We produce the steady-state phase diagrams for symmetrically split interaction strength. The behavior of the maximal particle current with respect to the interaction energy E is analyzed for different coupling rates and interaction splittings. The results suggest that for strong coupling and large splittings, the maximal flow of the motors occurs at a weak attractive interaction strength which matches with the known experimental results on kinesin motor protein.

Summary Diagrams for Coupled Hydrodynamic-Ecosystem Model Skill Assessment

DTIC Science & Technology

2009-01-01

reference point have the smallest unbiased RMSD value (Fig. 3). It would appear that the cluster of model points closest to the reference point may...total RMSD values. This is particularly the case for phyto- plankton absorption (Fig. 3B) where the cluster of points closest to the reference...pattern statistics and the bias (difference of mean values) each magnitude of the total Root-Mean-Square Difference ( RMSD ). An alternative skill score and

Treating Subvalence Correlation Effects in Domain Based Pair Natural Orbital Coupled Cluster Calculations: An Out-of-the-Box Approach.

PubMed

Bistoni, Giovanni; Riplinger, Christoph; Minenkov, Yury; Cavallo, Luigi; Auer, Alexander A; Neese, Frank

2017-07-11

The validity of the main approximations used in canonical and domain based pair natural orbital coupled cluster methods (CCSD(T) and DLPNO-CCSD(T), respectively) in standard chemical applications is discussed. In particular, we investigate the dependence of the results on the number of electrons included in the correlation treatment in frozen-core (FC) calculations and on the main threshold governing the accuracy of DLPNO all-electron (AE) calculations. Initially, scalar relativistic orbital energies for the ground state of the atoms from Li to Rn in the periodic table are calculated. An energy criterion is used for determining the orbitals that can be excluded from the correlation treatment in FC coupled cluster calculations without significant loss of accuracy. The heterolytic dissociation energy (HDE) of a series of metal compounds (LiF, NaF, AlF 3 , CaF 2 , CuF, GaF 3 , YF 3 , AgF, InF 3 , HfF 4 , and AuF) is calculated at the canonical CCSD(T) level, and the dependence of the results on the number of correlated electrons is investigated. Although for many of the studied reactions subvalence correlation effects contribute significantly to the HDE, the use of an energy criterion permits a conservative definition of the size of the core, allowing FC calculations to be performed in a black-box fashion while retaining chemical accuracy. A comparison of the CCSD and the DLPNO-CCSD methods in describing the core-core, core-valence, and valence-valence components of the correlation energy is given. It is found that more conservative thresholds must be used for electron pairs containing at least one core electron in order to achieve high accuracy in AE DLPNO-CCSD calculations relative to FC calculations. With the new settings, the DLPNO-CCSD method reproduces canonical CCSD results in both AE and FC calculations with the same accuracy.

Boundaries Control Collective Dynamics of Inertial Self-Propelled Robots.

PubMed

Deblais, A; Barois, T; Guerin, T; Delville, P H; Vaudaine, R; Lintuvuori, J S; Boudet, J F; Baret, J C; Kellay, H

2018-05-04

Simple ingredients, such as well-defined interactions and couplings for the velocity and orientation of self-propelled objects, are sufficient to produce complex collective behavior in assemblies of such entities. Here, we use assemblies of rodlike robots made motile through self-vibration. When confined in circular arenas, dilute assemblies of these rods act as a gas. Increasing the surface fraction leads to a collective behavior near the boundaries: polar clusters emerge while, in the bulk, gaslike behavior is retained. The coexistence between a gas and surface clusters is a direct consequence of inertial effects as shown by our simulations. A theoretical model, based on surface mediated transport accounts for this coexistence and illustrates the exact role of the boundaries. Our study paves the way towards the control of collective behavior: By using deformable but free to move arenas, we demonstrate that the surface induced clusters can lead to directed motion, while the topology of the surface states can be controlled by biasing the motility of the particles.

A PEG/copper(i) halide cluster as an eco-friendly catalytic system for C-N bond formation.

PubMed

Li, Cheng-An; Ji, Wei; Qu, Jian; Jing, Su; Gao, Fei; Zhu, Dun-Ru

2018-05-22

The catalytic activities of eight copper(i) halide clusters assembled from copper(i) halide and ferrocenyltelluroethers, 1-8, were investigated in C-N formation under various conditions. A catalytic procedure using poly(ethylene glycol) (PEG-400) as a greener alternative organic solvent has been developed. The PEG-400/5 system can achieve 99% targeted yield with a mild reaction temperature and short reaction time. After the isolation of the products by extraction with diethyl ether, this PEG-400/cluster system could be easily recycled. Spectroscopic studies elucidate a stepwise mechanism: firstly, proton-coupled electron transfer (PCET) involving the transfer of an electron from Cu+ and a proton from imidazole results in the formation of a labile penta-coordinated Cu2+ and aryl radical; the following effective electron transfer from the ferrocene unit reduces Cu2+ and forms the target product; finally, the ferrocenium unit is reduced by the I- anion. The merits of this eco-friendly synthesis are the efficient utilization of reagents and easy recyclability.

Experimental investigation of the ordering pathway in a Ni-33 at.%Cr alloy

DOE PAGES

Gwalani, B.; Alam, T.; Miller, C.; ...

2016-06-17

The present study involves a detailed experimental investigation of the concurrent compositional clustering and long-range ordering tendencies in a Ni-33 at.%Cr alloy, carried out by coupling synchrotron-based X-ray diffraction (XRD), transmission electron microscopy (TEM), and atom probe tomography (APT). Synchrotron-based XRD results clearly exhibited progressively increasing lattice contraction in the matrix with increasing isothermal aging time, at 475 degrees C, eventually leading to the development of long-range ordering (LRO) of the Pt2Mo-type. Detailed TEM and APT investigations revealed that this LRO in the matrix is manifested in the form of nanometer-scale ordered domains, and the spatial distribution, size, morphology andmore » compositional evolution of these domains have been carefully investigated. Here, the APT results also revealed the early stages of compositional clustering prior to the onset of long-range ordering in this alloy and such compositional clustering can potentially be correlated to the lattice contraction and previously proposed short-range ordering tendencies.« less

Role of isostaticity and load-bearing microstructure in the elasticity of yielded colloidal gels.

PubMed

Hsiao, Lilian C; Newman, Richmond S; Glotzer, Sharon C; Solomon, Michael J

2012-10-02

We report a simple correlation between microstructure and strain-dependent elasticity in colloidal gels by visualizing the evolution of cluster structure in high strain-rate flows. We control the initial gel microstructure by inducing different levels of isotropic depletion attraction between particles suspended in refractive index matched solvents. Contrary to previous ideas from mode coupling and micromechanical treatments, our studies show that bond breakage occurs mainly due to the erosion of rigid clusters that persist far beyond the yield strain. This rigidity contributes to gel elasticity even when the sample is fully fluidized; the origin of the elasticity is the slow Brownian relaxation of rigid, hydrodynamically interacting clusters. We find a power-law scaling of the elastic modulus with the stress-bearing volume fraction that is valid over a range of volume fractions and gelation conditions. These results provide a conceptual framework to quantitatively connect the flow-induced microstructure of soft materials to their nonlinear rheology.

Boundaries Control Collective Dynamics of Inertial Self-Propelled Robots

NASA Astrophysics Data System (ADS)

Deblais, A.; Barois, T.; Guerin, T.; Delville, P. H.; Vaudaine, R.; Lintuvuori, J. S.; Boudet, J. F.; Baret, J. C.; Kellay, H.

2018-05-01

Simple ingredients, such as well-defined interactions and couplings for the velocity and orientation of self-propelled objects, are sufficient to produce complex collective behavior in assemblies of such entities. Here, we use assemblies of rodlike robots made motile through self-vibration. When confined in circular arenas, dilute assemblies of these rods act as a gas. Increasing the surface fraction leads to a collective behavior near the boundaries: polar clusters emerge while, in the bulk, gaslike behavior is retained. The coexistence between a gas and surface clusters is a direct consequence of inertial effects as shown by our simulations. A theoretical model, based on surface mediated transport accounts for this coexistence and illustrates the exact role of the boundaries. Our study paves the way towards the control of collective behavior: By using deformable but free to move arenas, we demonstrate that the surface induced clusters can lead to directed motion, while the topology of the surface states can be controlled by biasing the motility of the particles.

Eye-hand coupling during closed-loop drawing: evidence of shared motor planning?

PubMed

Reina, G Anthony; Schwartz, Andrew B

2003-04-01

Previous paradigms have used reaching movements to study coupling of eye-hand kinematics. In the present study, we investigated eye-hand kinematics as curved trajectories were drawn at normal speeds. Eye and hand movements were tracked as a monkey traced ellipses and circles with the hand in free space while viewing the hand's position on a computer monitor. The results demonstrate that the movement of the hand was smooth and obeyed the 2/3 power law. Eye position, however, was restricted to 2-3 clusters along the hand's trajectory and fixed approximately 80% of the time in one of these clusters. The eye remained stationary as the hand moved away from the fixation for up to 200 ms and saccaded ahead of the hand position to the next fixation along the trajectory. The movement from one fixation cluster to another consistently occurred just after the tangential hand velocity had reached a local minimum, but before the next segment of the hand's trajectory began. The next fixation point was close to an area of high curvature along the hand's trajectory even though the hand had not reached that point along the path. A visuo-motor illusion of hand movement demonstrated that the eye movement was influenced by hand movement and not simply by visual input. During the task, neural activity of pre-motor cortex (area F4) was recorded using extracellular electrodes and used to construct a population vector of the hand's trajectory. The results suggest that the saccade onset is correlated in time with maximum curvature in the population vector trajectory for the hand movement. We hypothesize that eye and arm movements may have common, or shared, information in forming their motor plans.

Proximity effect assisted absorption enhancement in thin film with locally clustered nanoholes.

PubMed

Wu, Shaolong; Zhang, Cheng; Li, Xiaofeng; Zhan, Yaohui

2015-03-01

We focus on the light-trapping characteristics of a thin film with locally clustered nanoholes (NHs), considering that the clustering effect is usually encountered in preparing the nanostructures. Our full-wave finite-element simulation indicates that an intentionally introduced clustering effect could be employed for improving the light-trapping performance of the nanostructured thin film. For a 100 nm thick amorphous silicon film, an optimal clustering design with NH diameter of 100 nm is able to double the integrated optical absorption over the solar spectrum, compared to the planar counterpart, as well as show much improved optical performance over that of the nonclustered setup. A further insight into the underlying physics explains the outstanding light-trapping capability in terms of the increased available modes, a stronger power coupling efficiency, a higher fraction of electric field concentrated in absorbable material, and a higher density of photon states.

Clustering promotes switching dynamics in networks of noisy neurons

NASA Astrophysics Data System (ADS)

Franović, Igor; Klinshov, Vladimir

2018-02-01

Macroscopic variability is an emergent property of neural networks, typically manifested in spontaneous switching between the episodes of elevated neuronal activity and the quiescent episodes. We investigate the conditions that facilitate switching dynamics, focusing on the interplay between the different sources of noise and heterogeneity of the network topology. We consider clustered networks of rate-based neurons subjected to external and intrinsic noise and derive an effective model where the network dynamics is described by a set of coupled second-order stochastic mean-field systems representing each of the clusters. The model provides an insight into the different contributions to effective macroscopic noise and qualitatively indicates the parameter domains where switching dynamics may occur. By analyzing the mean-field model in the thermodynamic limit, we demonstrate that clustering promotes multistability, which gives rise to switching dynamics in a considerably wider parameter region compared to the case of a non-clustered network with sparse random connection topology.

Data mining with unsupervised clustering using photonic micro-ring resonators

NASA Astrophysics Data System (ADS)

McAulay, Alastair D.

2013-09-01

Data is commonly moved through optical fiber in modern data centers and may be stored optically. We propose an optical method of data mining for future data centers to enhance performance. For example, in clustering, a form of unsupervised learning, we propose that parameters corresponding to information in a database are converted from analog values to frequencies, as in the brain's neurons, where similar data will have close frequencies. We describe the Wilson-Cowan model for oscillating neurons. In optics we implement the frequencies with micro ring resonators. Due to the influence of weak coupling, a group of resonators will form clusters of similar frequencies that will indicate the desired parameters having close relations. Fewer clusters are formed as clustering proceeds, which allows the creation of a tree showing topics of importance and their relationships in the database. The tree can be used for instance to target advertising and for planning.

Detecting synchronization clusters in multivariate time series via coarse-graining of Markov chains.

PubMed

Allefeld, Carsten; Bialonski, Stephan

2007-12-01

Synchronization cluster analysis is an approach to the detection of underlying structures in data sets of multivariate time series, starting from a matrix R of bivariate synchronization indices. A previous method utilized the eigenvectors of R for cluster identification, analogous to several recent attempts at group identification using eigenvectors of the correlation matrix. All of these approaches assumed a one-to-one correspondence of dominant eigenvectors and clusters, which has however been shown to be wrong in important cases. We clarify the usefulness of eigenvalue decomposition for synchronization cluster analysis by translating the problem into the language of stochastic processes, and derive an enhanced clustering method harnessing recent insights from the coarse-graining of finite-state Markov processes. We illustrate the operation of our method using a simulated system of coupled Lorenz oscillators, and we demonstrate its superior performance over the previous approach. Finally we investigate the question of robustness of the algorithm against small sample size, which is important with regard to field applications.

Modeling of Cluster-Induced Turbulence in Particle-Laden Channel Flow

NASA Astrophysics Data System (ADS)

Baker, Michael; Capecelatro, Jesse; Kong, Bo; Fox, Rodney; Desjardins, Olivier

2017-11-01

A phenomenon often observed in gas-solid flows is the formation of mesoscale clusters of particles due to the relative motion between the solid and fluid phases that is sustained through the dampening of collisional particle motion from interphase momentum coupling inside these clusters. The formation of such sustained clusters, leading to cluster-induced turbulence (CIT), can have a significant impact in industrial processes, particularly in regards to mixing, reaction progress, and heat transfer. Both Euler-Lagrange (EL) and Euler-Euler anisotropic Gaussian (EE-AG) approaches are used in this work to perform mesoscale simulations of CIT in fully developed gas-particle channel flow. The results from these simulations are applied in the development of a two-phase Reynolds-Averaged Navier-Stokes (RANS) model to capture the wall-normal flow characteristics in a less computationally expensive manner. Parameters such as mass loading, particle size, and gas velocity are varied to examine their respective impact on cluster formation and turbulence statistics. Acknowledging support from the NSF (AN:1437865).

Dimensionality effects on magnetic properties of FexCo1-x nanoclusters on Pt(1 1 1)

NASA Astrophysics Data System (ADS)

Miranda, I. P.; Igarashi, R. N.; Klautau, A. B.; Petrilli, H. M.

2017-11-01

The behavior of local magnetic moments and exchange coupling parameters of FexCo1-x nanostructures (nanowires and compact clusters) on the fcc Pt(1 1 1) surface is here investigated using the first-principles real-space RS-LMTO-ASA method, in the framework of the DFT. Different configurations of FexCo1-x trimers and heptamers on Pt(1 1 1) are considered, varying the positions and the concentration of Fe or Co atoms. We discuss the influence of dimensionality and stoichiometry changes on the magnetic properties, specially on the orbital moments, which are very important in establishing a nanoscopic understanding of delocalized electron systems. We demonstrate the existence of a strictly decreasing nonlinear trend of the average orbital moments with the Fe concentration for the compact clusters, different from what was found for FexCo1-x nanowires on Pt(1 1 1) and also for corresponding higher-dimensional systems (FexCo1-x monolayer on Pt(1 1 1) and FexCo1-x bulk). The average spin moments, however, are invariably described by a linear function with respect to stoichiometry. In all studied cases, the nearest neighbors exchange couplings have shown to be strongly ferromagnetic.

Application of relativistic coupled-cluster theory to electron impact excitation of Mg+ in the plasma environment

NASA Astrophysics Data System (ADS)

Sharma, Lalita; Sahoo, Bijaya Kumar; Malkar, Pooja; Srivastava, Rajesh

2018-01-01

A relativistic coupled-cluster theory is implemented to study electron impact excitations of atomic species. As a test case, the electron impact excitations of the 3 s 2 S 1/2-3 p 2 P 1/2;3/2 resonance transitions are investigated in the singly charged magnesium (Mg+) ion using this theory. Accuracies of wave functions of Mg+ are justified by evaluating its attachment energies of the relevant states and compared with the experimental values. The continuum wave function of the projectile electron are obtained by solving Dirac equations assuming distortion potential as static potential of the ground state of Mg+. Comparison of the calculated electron impact excitation differential and total cross-sections with the available measurements are found to be in very good agreements at various incident electron energies. Further, calculations are carried out in the plasma environment in the Debye-Hückel model framework, which could be useful in the astrophysics. Influence of plasma strength on the cross-sections as well as linear polarization of the photon emission in the 3 p 2 P 3/2-3 s 2 S 1/2 transition is investigated for different incident electron energies.

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

Bazante, Alexandre P., E-mail: abazante@chem.ufl.edu; Bartlett, Rodney J.; Davidson, E. R.

The benzene radical anion is studied with ab initio coupled-cluster theory in large basis sets. Unlike the usual assumption, we find that, at the level of theory investigated, the minimum energy geometry is non-planar with tetrahedral distortion at two opposite carbon atoms. The anion is well known for its instability to auto-ionization which poses computational challenges to determine its properties. Despite the importance of the benzene radical anion, the considerable attention it has received in the literature so far has failed to address the details of its structure and shape-resonance character at a high level of theory. Here, we examinemore » the dynamic Jahn-Teller effect and its impact on the anion potential energy surface. We find that a minimum energy geometry of C{sub 2} symmetry is located below one D{sub 2h} stationary point on a C{sub 2h} pseudo-rotation surface. The applicability of standard wave function methods to an unbound anion is assessed with the stabilization method. The isotropic hyperfine splitting constants (A{sub iso}) are computed and compared to data obtained from experimental electron spin resonance experiments. Satisfactory agreement with experiment is obtained with coupled-cluster theory and large basis sets such as cc-pCVQZ.« less

Bidirectional Coupling between Astrocytes and Neurons Mediates Learning and Dynamic Coordination in the Brain: A Multiple Modeling Approach

PubMed Central

Wade, John J.; McDaid, Liam J.; Harkin, Jim; Crunelli, Vincenzo; Kelso, J. A. Scott

2011-01-01

In recent years research suggests that astrocyte networks, in addition to nutrient and waste processing functions, regulate both structural and synaptic plasticity. To understand the biological mechanisms that underpin such plasticity requires the development of cell level models that capture the mutual interaction between astrocytes and neurons. This paper presents a detailed model of bidirectional signaling between astrocytes and neurons (the astrocyte-neuron model or AN model) which yields new insights into the computational role of astrocyte-neuronal coupling. From a set of modeling studies we demonstrate two significant findings. Firstly, that spatial signaling via astrocytes can relay a “learning signal” to remote synaptic sites. Results show that slow inward currents cause synchronized postsynaptic activity in remote neurons and subsequently allow Spike-Timing-Dependent Plasticity based learning to occur at the associated synapses. Secondly, that bidirectional communication between neurons and astrocytes underpins dynamic coordination between neuron clusters. Although our composite AN model is presently applied to simplified neural structures and limited to coordination between localized neurons, the principle (which embodies structural, functional and dynamic complexity), and the modeling strategy may be extended to coordination among remote neuron clusters. PMID:22242121

The chemistry of the superheavy elements. II. The stability of high oxidation states in group 11 elements: Relativistic coupled cluster calculations for the di-, tetra- and hexafluoro metallates of Cu, Ag, Au, and element 111

NASA Astrophysics Data System (ADS)

Seth, Michael; Cooke, Fiona; Schwerdtfeger, Peter; Heully, Jean-Louis; Pelissier, Michel

1998-09-01

The stability of the high oxidation states +3 and +5 in Group 11 fluorides is studied by relativistic Møller-Plesset (MP) and coupled cluster methods. Higher metal oxidation states are stabilized by relativistic effects. As a result, the hexafluoro complex of the Group 11 element with nuclear charge 111 and oxidation state +5 is the most stable compared to the other congeners. The results also suggest that AgF6- is thermodynamically stable and, therefore, it might be feasable to synthesize this compound. For the copper fluorides we observe very large oscillations in the Møller-Plesset series up to the fourth order. Nonrelativistic calculations lead to the expected trend in the metal-fluorine bond distances for the MF2- compounds, CuF2-

Interplay between Oxygen and Fe–S Cluster Biogenesis: Insights from the Suf Pathway

PubMed Central

2015-01-01

Iron–sulfur (Fe–S) cluster metalloproteins conduct essential functions in nearly all contemporary forms of life. The nearly ubiquitous presence of Fe–S clusters and the fundamental requirement for Fe–S clusters in both aerobic and anaerobic Archaea, Bacteria, and Eukarya suggest that these clusters were likely integrated into central metabolic pathways early in the evolution of life prior to the widespread oxidation of Earth’s atmosphere. Intriguingly, Fe–S cluster-dependent metabolism is sensitive to disruption by oxygen because of the decreased bioavailability of ferric iron as well as direct oxidation of sulfur trafficking intermediates and Fe–S clusters by reactive oxygen species. This fact, coupled with the ubiquity of Fe–S clusters in aerobic organisms, suggests that organisms evolved with mechanisms that facilitate the biogenesis and use of these essential cofactors in the presence of oxygen, which gradually began to accumulate around 2.5 billion years ago as oxygenic photosynthesis proliferated and reduced minerals that buffered against oxidation were depleted. This review highlights the most ancient of the Fe–S cluster biogenesis pathways, the Suf system, which likely was present in early anaerobic forms of life. Herein, we use the evolution of the Suf pathway to assess the relationships between the biochemical functions and physiological roles of Suf proteins, with an emphasis on the selective pressure of oxygen toxicity. Our analysis suggests that diversification into oxygen-containing environments disrupted iron and sulfur metabolism and was a main driving force in the acquisition of accessory Suf proteins (such as SufD, SufE, and SufS) by the core SufB–SufC scaffold complex. This analysis provides a new framework for the study of Fe–S cluster biogenesis pathways and Fe–S cluster-containing metalloenzymes and their complicated patterns of divergence in response to oxygen. PMID:25153801

Evidence against the selfish operon theory.

PubMed

Pál, Csaba; Hurst, Laurence D

2004-06-01

According to the selfish operon hypothesis, the clustering of genes and their subsequent organization into operons is beneficial for the constituent genes because it enables the horizontal gene transfer of weakly selected, functionally coupled genes. The majority of these are expected to be non-essential genes. From our analysis of the Escherichia coli genome, we conclude that the selfish operon hypothesis is unlikely to provide a general explanation for clustering nor can it account for the gene composition of operons. Contrary to expectations, essential genes with related functions have an especially strong tendency to cluster, even if they are not in operons. Moreover, essential genes are particularly abundant in operons.

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.

Gravitational couplings of the inflaton in extended inflation

NASA Technical Reports Server (NTRS)

Holman, Richard; Wang, Yun; Kolb, Edward W.

1990-01-01

A new extended inflationary scenario evading the difficulties of the original model is discussed. The model can thermalize the energy in the bubble walls by the necessary epoch, and establish a Robertson-Walker frame in the bubble clusters. The essential new ingredient in the model is the observation that the coupling of the inflaton to the Jordan-Brans-Dicke field is expected to be different from that of visible matter.

Highly efficient preparation of selectively isotope cluster-labeled long chain fatty acids via two consecutive C(sp3)-C(sp3) cross-coupling reactions.

PubMed

Lethu, Sébastien; Matsuoka, Shigeru; Murata, Michio

2014-02-07

An efficient synthesis involving two copper-catalyzed alkyl-alkyl coupling reactions has been designed to easily access doubly isotope-labeled fatty acids. Such NMR- and IR-active compounds were obtained in excellent overall yields and will be further used for determining the conformation of an alkyl chain of lipidic biomolecules upon interaction with proteins.

Towards a comprehensive knowledge of the star cluster population in the Small Magellanic Cloud

NASA Astrophysics Data System (ADS)

Piatti, A. E.

2018-07-01

The Small Magellanic Cloud (SMC) has recently been found to harbour an increase of more than 200 per cent in its known cluster population. Here, we provide solid evidence that this unprecedented number of clusters could be greatly overestimated. On the one hand, the fully automatic procedure used to identify such an enormous cluster candidate sample did not recover ˜50 per cent, on average, of the known relatively bright clusters located in the SMC main body. On the other hand, the number of new cluster candidates per time unit as a function of time is noticeably different from the intrinsic SMC cluster frequency (CF), which should not be the case if these new detections were genuine physical systems. We found additionally that the SMC CF varies spatially, in such a way that it resembles an outside-in process coupled with the effects of a relatively recent interaction with the Large Magellanic Cloud. By assuming that clusters and field stars share the same formation history, we showed for the first time that the cluster dissolution rate also depends on position in the galaxy. The cluster dissolution becomes higher as the concentration of galaxy mass increases or if external tidal forces are present.

From sticky-hard-sphere to Lennard-Jones-type clusters

NASA Astrophysics Data System (ADS)

Trombach, Lukas; Hoy, Robert S.; Wales, David J.; Schwerdtfeger, Peter

2018-04-01

A relation MSHS →LJ between the set of nonisomorphic sticky-hard-sphere clusters MSHS and the sets of local energy minima ML J of the (m ,n ) -Lennard-Jones potential Vmn LJ(r ) =ɛ/n -m [m r-n-n r-m] is established. The number of nonisomorphic stable clusters depends strongly and nontrivially on both m and n and increases exponentially with increasing cluster size N for N ≳10 . While the map from MSHS→MSHS →LJ is noninjective and nonsurjective, the number of Lennard-Jones structures missing from the map is relatively small for cluster sizes up to N =13 , and most of the missing structures correspond to energetically unfavorable minima even for fairly low (m ,n ) . Furthermore, even the softest Lennard-Jones potential predicts that the coordination of 13 spheres around a central sphere is problematic (the Gregory-Newton problem). A more realistic extended Lennard-Jones potential chosen from coupled-cluster calculations for a rare gas dimer leads to a substantial increase in the number of nonisomorphic clusters, even though the potential curve is very similar to a (6,12)-Lennard-Jones potential.

Photodetachment and UV-Vis spectral properties of Cl2rad -·nHO clusters: Extrapolation to bulk

NASA Astrophysics Data System (ADS)

Pathak, A. K.; Mukherjee, T.; Maity, D. K.

2008-03-01

Vertical detachment energy (VDE) and UV-Vis spectra of Cl2rad -·nHO clusters ( n = 1-11) are reported based on first principle electronic structure calculations. VDE of the hydrated clusters are calculated following second order Moller-Plesset perturbation (MP2) as well as coupled cluster theory with 6-311++G(d,p) set of basis function. The excess electron in these hydrated clusters is mainly localized over the solute Cl atoms. A linear relationship is obtained for VDE vs. ( n + 2.6) -1/3 and bulk VDE of Cl2rad - aqueous solution is calculated as 10.61 eV at CCSD(T) level of theory. UV-Vis spectra of these hydrated clusters are calculated applying CI with single electron (CIS) excitation procedure. Simulated UV-Vis spectra of Cl2rad -·10HO cluster is noted to be in excellent agreement with the reported spectra of Cl2rad - (aq) system, λmax for Cl2rad -·11HO system is calculated to be red shifted though.

From sticky-hard-sphere to Lennard-Jones-type clusters.

PubMed

Trombach, Lukas; Hoy, Robert S; Wales, David J; Schwerdtfeger, Peter

2018-04-01

A relation M_{SHS→LJ} between the set of nonisomorphic sticky-hard-sphere clusters M_{SHS} and the sets of local energy minima M_{LJ} of the (m,n)-Lennard-Jones potential V_{mn}^{LJ}(r)=ɛ/n-m[mr^{-n}-nr^{-m}] is established. The number of nonisomorphic stable clusters depends strongly and nontrivially on both m and n and increases exponentially with increasing cluster size N for N≳10. While the map from M_{SHS}→M_{SHS→LJ} is noninjective and nonsurjective, the number of Lennard-Jones structures missing from the map is relatively small for cluster sizes up to N=13, and most of the missing structures correspond to energetically unfavorable minima even for fairly low (m,n). Furthermore, even the softest Lennard-Jones potential predicts that the coordination of 13 spheres around a central sphere is problematic (the Gregory-Newton problem). A more realistic extended Lennard-Jones potential chosen from coupled-cluster calculations for a rare gas dimer leads to a substantial increase in the number of nonisomorphic clusters, even though the potential curve is very similar to a (6,12)-Lennard-Jones potential.

Distal [FeS]-Cluster Coordination in [NiFe]-Hydrogenase Facilitates Intermolecular Electron Transfer

PubMed Central

Petrenko, Alexander; Stein, Matthias

2017-01-01

Biohydrogen is a versatile energy carrier for the generation of electric energy from renewable sources. Hydrogenases can be used in enzymatic fuel cells to oxidize dihydrogen. The rate of electron transfer (ET) at the anodic side between the [NiFe]-hydrogenase enzyme distal iron–sulfur cluster and the electrode surface can be described by the Marcus equation. All parameters for the Marcus equation are accessible from Density Functional Theory (DFT) calculations. The distal cubane FeS-cluster has a three-cysteine and one-histidine coordination [Fe4S4](His)(Cys)3 first ligation sphere. The reorganization energy (inner- and outer-sphere) is almost unchanged upon a histidine-to-cysteine substitution. Differences in rates of electron transfer between the wild-type enzyme and an all-cysteine mutant can be rationalized by a diminished electronic coupling between the donor and acceptor molecules in the [Fe4S4](Cys)4 case. The fast and efficient electron transfer from the distal iron–sulfur cluster is realized by a fine-tuned protein environment, which facilitates the flow of electrons. This study enables the design and control of electron transfer rates and pathways by protein engineering. PMID:28067774

Electron wavepacket dynamics in highly quasi-degenerate coupled electronic states: a theory for chemistry where the notion of adiabatic potential energy surface loses the sense.

PubMed

Yonehara, Takehiro; Takatsuka, Kazuo

2012-12-14

We develop a theory and the method of its application for chemical dynamics in systems, in which the adiabatic potential energy hyper-surfaces (PES) are densely quasi-degenerate to each other in a wide range of molecular geometry. Such adiabatic electronic states tend to couple each other through strong nonadiabatic interactions. Technically, therefore, it is often extremely hard to accurately single out the individual PES in those systems. Moreover, due to the mutual nonadiabatic couplings that may spread wide in space and due to the energy-time uncertainty relation, the notion of the isolated and well-defined potential energy surface should lose the sense. On the other hand, such dense electronic states should offer a very interesting molecular field in which chemical reactions to proceed in characteristic manners. However, to treat these systems, the standard theoretical framework of chemical reaction dynamics, which starts from the Born-Oppenheimer approximation and ends up with quantum nuclear wavepacket dynamics, is not very useful. We here explore this problem with our developed nonadiabatic electron wavepacket theory, which we call the phase-space averaging and natural branching (PSANB) method [T. Yonehara and K. Takatsuka, J. Chem. Phys. 129, 134109 (2008)], or branching-path representation, in which the packets are propagated in time along the non-Born-Oppenheimer branching paths. In this paper, after outlining the basic theory, we examine using a one-dimensional model how well the PSANB method works with such densely quasi-degenerate nonadiabatic systems. To do so, we compare the performance of PSANB with the full quantum mechanical results and those given by the fewest switches surface hopping (FSSH) method, which is known to be one of the most reliable and flexible methods to date. It turns out that the PSANB electron wavepacket approach actually yields very good results with far fewer initial sampling paths. Then we apply the electron wavepacket dynamics in path-branching representation and the so-called semiclassical Ehrenfest theory to a hydrogen molecule embedded in twelve membered boron cluster (B(12)) in excited states, which are densely quasi-degenerate due to the vacancy in 2p orbitals of boron atom [1s(2)2s(2)2p(1)]. Bond dissociation of the hydrogen molecule quickly takes place in the cluster and the resultant hydrogen atoms are squeezed out to the surface of the cluster. We further study collision dynamics between H(2) and B(12), which also gives interesting phenomena. The present study suggests an interesting functionality of the boron clusters.

Understanding the nucleon as a Borromean bound-state

DOE PAGES

Segovia, Jorge; Roberts, Craig D.; Schmidt, Sebastian M.

2015-08-20

Analyses of the three valence-quark bound-state problem in relativistic quantum field theory predict that the nucleon may be understood primarily as a Borromean bound-state, in which binding arises mainly from two separate effects. One originates in non-Abelian facets of QCD that are expressed in the strong running coupling and generate confined but strongly-correlated colourantitriplet diquark clusters in both the scalar-isoscalar and pseudovector-isotriplet channels. That attraction is magnified by quark exchange associated with diquark breakup and reformation. Diquark clustering is driven by the same mechanism which dynamically breaks chiral symmetry in the Standard Model. It has numerous observable consequences, the completemore » elucidation of which requires a framework that also simultaneously expresses the running of the coupling and masses in the strong interaction. Moreover, planned experiments are capable of validating this picture.« less

Range-Separated Brueckner Coupled Cluster Doubles Theory

NASA Astrophysics Data System (ADS)

Shepherd, James J.; Henderson, Thomas M.; Scuseria, Gustavo E.

2014-04-01

We introduce a range-separation approximation to coupled cluster doubles (CCD) theory that successfully overcomes limitations of regular CCD when applied to the uniform electron gas. We combine the short-range ladder channel with the long-range ring channel in the presence of a Bruckner renormalized one-body interaction and obtain ground-state energies with an accuracy of 0.001 a.u./electron across a wide range of density regimes. Our scheme is particularly useful in the low-density and strongly correlated regimes, where regular CCD has serious drawbacks. Moreover, we cure the infamous overcorrelation of approaches based on ring diagrams (i.e., the particle-hole random phase approximation). Our energies are further shown to have appropriate basis set and thermodynamic limit convergence, and overall this scheme promises energetic properties for realistic periodic and extended systems which existing methods do not possess.

The equation-of-motion coupled cluster method for triple electron attached states

NASA Astrophysics Data System (ADS)

Musiał, Monika; Olszówka, Marta; Lyakh, Dmitry I.; Bartlett, Rodney J.

2012-11-01

The initial implementation of the triple electron attachment (TEA) equation-of-motion (EOM) coupled cluster (CC) method is presented, aiming at the description of electronic states with three open shell electrons outside a suitably chosen closed shell vacuum. In particular, such an approach can be used for describing dissociation of chemical bonds predominantly formed by three valence electrons, for example, in LiC and NaC molecules. Both ground and excited states are considered while rigorously maintaining the correct spin value. The preliminary results show a correct asymptotic behavior of the dissociation curves. At the same time, we emphasize that a chemically accurate description will require an extension of the minimal TEA-EOM-CC model introduced here, analogous to those already used in the double ionization potential and double electron attachment methods.

An efficient formulation and implementation of the analytic energy gradient method to the single and double excitation coupled-cluster wave function - Application to Cl2O2

NASA Technical Reports Server (NTRS)

Rendell, Alistair P.; Lee, Timothy J.

1991-01-01

The analytic energy gradient for the single and double excitation coupled-cluster (CCSD) wave function has been reformulated and implemented in a new set of programs. The reformulated set of gradient equations have a smaller computational cost than any previously published. The iterative solution of the linear equations and the construction of the effective density matrices are fully vectorized, being based on matrix multiplications. The new method has been used to investigate the Cl2O2 molecule, which has recently been postulated as an important intermediate in the destruction of ozone in the stratosphere. In addition to reporting computational timings, the CCSD equilibrium geometries, harmonic vibrational frequencies, infrared intensities, and relative energetics of three isomers of Cl2O2 are presented.

Multiferroic and magnetoelectric nanocomposites for data processing

NASA Astrophysics Data System (ADS)

Kleemann, Wolfgang

2017-06-01

Recent progress in preparing and understanding composite magnetoelectrics is highlighted. Apart from optimized standard solutions novel methods of switching magnetism with electric fields and vice versa with focus on magnetoelectric (ME) data processing in multiferroic and magnetoelectric nanocomposites deserve particular interest. First, we report on the patented MERAM, which uses the electric field control of exchange bias in a layered composite via an epitaxial magnetoelectric Cr2O3 layer exchange coupled to a Pt/Co/Pt trilayer. It promises to crucially reduce Joule energy losses in RAM devices. Second, magnetic switching of the electric polarization by a transverse magnetic field in a composite of CoFe2O4 nanopillars embedded in a vertically poled BaTiO3 thick film produces a regular surface polarization pattern with rectangular local symmetry. Its possible use for data processing is discussed. Third, in the relaxor ferroelectric single-phase compound (BiFe0.9Co0.1O3)0.4-(Bi1/2K1/2TiO3)0.6 polar nanoregions emerging from ferrimagnetic Bi(Fe,Co)O3 regions embedded in a Bi1/2K1/2TiO3 relaxor component transform into ferroelectric clusters and simultaneously enable congruent magnetic clusters. The local polarization and magnetization couple with record-high direct and converse magnetoelectric coupling coefficients, α  ≈  1.0  ×  10-5 s m-1. These ‘multiferroic’ clusters are promising for applications in data storage or processing devices.

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

Eriksen, Janus J., E-mail: janusje@chem.au.dk; Jørgensen, Poul; Matthews, Devin A.

The accuracy at which total energies of open-shell atoms and organic radicals may be calculated is assessed for selected coupled cluster perturbative triples expansions, all of which augment the coupled cluster singles and doubles (CCSD) energy by a non-iterative correction for the effect of triple excitations. Namely, the second- through sixth-order models of the recently proposed CCSD(T–n) triples series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)] are compared to the acclaimed CCSD(T) model for both unrestricted as well as restricted open-shell Hartree-Fock (UHF/ROHF) reference determinants. By comparing UHF- and ROHF-based statistical results for a test setmore » of 18 modest-sized open-shell species with comparable RHF-based results, no behavioral differences are observed for the higher-order models of the CCSD(T–n) series in their correlated descriptions of closed- and open-shell species. In particular, we find that the convergence rate throughout the series towards the coupled cluster singles, doubles, and triples (CCSDT) solution is identical for the two cases. For the CCSD(T) model, on the other hand, not only its numerical consistency, but also its established, yet fortuitous cancellation of errors breaks down in the transition from closed- to open-shell systems. The higher-order CCSD(T–n) models (orders n > 3) thus offer a consistent and significant improvement in accuracy relative to CCSDT over the CCSD(T) model, equally for RHF, UHF, and ROHF reference determinants, albeit at an increased computational cost.« less