Madsen, Niels K; Godtliebsen, Ian H; Christiansen, Ove
2017-04-07
Vibrational coupled-cluster (VCC) theory provides an accurate method for calculating vibrational spectra and properties of small to medium-sized molecules. Obtaining these properties requires the solution of the non-linear VCC equations which can in some cases be hard to converge depending on the molecule, the basis set, and the vibrational state in question. We present and compare a range of different algorithms for solving the VCC equations ranging from a full Newton-Raphson method to approximate quasi-Newton models using an array of different convergence-acceleration schemes. The convergence properties and computational cost of the algorithms are compared for the optimization of VCC states. This includes both simple ground-state problems and difficult excited states with strong non-linearities. Furthermore, the effects of using tensor-decomposed solution vectors and residuals are investigated and discussed. The results show that for standard ground-state calculations, the conjugate residual with optimal trial vectors algorithm has the shortest time-to-solution although the full Newton-Raphson method converges in fewer macro-iterations. Using decomposed tensors does not affect the observed convergence rates in our test calculations as long as the tensors are decomposed to sufficient accuracy.
Seniority zero pair coupled cluster doubles theory.
Stein, Tamar; Henderson, Thomas M; Scuseria, Gustavo E
2014-06-07
Coupled cluster theory with single and double excitations accurately describes weak electron correlation but is known to fail in cases of strong static correlation. Fascinatingly, however, pair coupled cluster doubles (p-CCD), a simplified version of the theory limited to pair excitations that preserve the seniority of the reference determinant (i.e., the number of unpaired electrons), has mean field computational cost and is an excellent approximation to the full configuration interaction (FCI) of the paired space provided that the orbital basis defining the pairing scheme is adequately optimized. In previous work, we have shown that optimization of the pairing scheme in the seniority zero FCI leads to a very accurate description of static correlation. The same conclusion extends to p-CCD if the orbitals are optimized to make the p-CCD energy stationary. We here demonstrate these results with numerous examples. We also explore the contributions of different seniority sectors to the coupled cluster doubles (CCD) correlation energy using different orbital bases. We consider both Hartree-Fock and Brueckner orbitals, and the role of orbital localization. We show how one can pair the orbitals so that the role of the Brueckner orbitals at the CCD level is retained at the p-CCD level. Moreover, we explore ways of extending CCD to accurately describe strongly correlated systems.
Coupled cluster approach to nuclear physics
Dean, D J
2004-01-01
Using many-body perturbation theory and coupled-cluster theory, we calculate the ground-state energy of He-4 and O-16. We perform these calculations using a no-core G-matrix interaction derived from a realistic nucleon-nucleon potential. Our calculations employ up to two-particle-two-hole coupled-cluster amplitudes.
Convergence of coupled cluster perturbation theory
Eriksen, Janus Juul; Matthews, Devin A; Jørgensen, Poul; Olsen, Jeppe
2016-01-01
The convergence of a recently proposed coupled cluster (CC) family of perturbation series [Eriksen et al., J. Chem. Phys. 140, 064108 (2014)], in which the energetic difference between a parent and a target CC model is expanded in orders of the M{\\o}ller-Plesset (MP) fluctuation potential, is investigated for four prototypical closed-shell systems (Ne, singlet methylene, distorted HF, and the fluoride anion) in standard and augmented basis sets. In these investigations, energy corrections of the various series have been calculated to high orders and their convergence radii determined by probing for possible front- and back-door intruder states. In summary, we conclude how it is primarily the choice of target state, and not the choice of parent state, which ultimately governs the convergence behavior of a given series. For example, restricting the target state to, say, triple or quadruple excitations might remove intruders present in series that target the full configuration interaction (FCI) limit, such as th...
Amplitude determinant coupled cluster with pairwise doubles
Zhao, Luning
2016-01-01
Recently developed pair coupled cluster doubles (pCCD) theory successfully reproduces doubly occupied configuration interaction (DOCI) with mean field cost. However, the projective nature of pCCD makes the method non-variational and thus hard to improve systematically. As a variational alternative, we explore the idea of coupled-cluster-like expansions based on amplitude determinants and develop a specific theory similar to pCCD based on determinants of pairwise doubles. The new ansatz admits a variational treatment through Monte Carlo methods while remaining size-consistent and, crucially, polynomial cost. In the dissociations of LiH, HF, H2O and N2, the method performs very similarly to pCCD and DOCI, suggesting that coupled-cluster-like ansatzes and variational evaluation may not be mutually exclusive.
Coupled-cluster computations of atomic nuclei
Hagen, G; Hjorth-Jensen, M; Dean, D J
2013-01-01
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.
Equation-of-motion coupled cluster perturbation theory revisited
DEFF Research Database (Denmark)
Eriksen, Janus Juul; Jørgensen, Poul; Olsen, Jeppe
2014-01-01
The equation-of-motion coupled cluster (EOM-CC) framework has been used for deriving a novel series of perturbative corrections to the coupled cluster singles and doubles energy that formally con- verges towards the full configuration interaction energy limit. The series is based on a Møller-Ples......-Plesset partitioning of the Hamiltonian and thus size extensive at any order in the perturbation, thereby rem- edying the major deficiency inherent to previous perturbation series based on the EOM-CC ansatz. © 2014 AIP Publishing LLC. [http://dx.doi.org/10.1063/1.4873138]...
Equation-of-motion coupled cluster perturbation theory revisited
DEFF Research Database (Denmark)
Eriksen, Janus Juul; Jørgensen, Poul; Olsen, Jeppe;
2014-01-01
The equation-of-motion coupled cluster (EOM-CC) framework has been used for deriving a novel series of perturbative corrections to the coupled cluster singles and doubles energy that formally con- verges towards the full configuration interaction energy limit. The series is based on a Møller-Ples......-Plesset partitioning of the Hamiltonian and thus size extensive at any order in the perturbation, thereby rem- edying the major deficiency inherent to previous perturbation series based on the EOM-CC ansatz. © 2014 AIP Publishing LLC. [http://dx.doi.org/10.1063/1.4873138]...
Coupled-cluster calculations of nucleonic matter
Hagen, G; Ekström, A; Wendt, K A; Baardsen, G; Gandolfi, S; Hjorth-Jensen, M; Horowitz, C J
2014-01-01
Background: The equation of state (EoS) of nucleonic matter is central for the understanding of bulk nuclear properties, the physics of neutron star crusts, and the energy release in supernova explosions. Purpose: This work presents coupled-cluster calculations of infinite nucleonic matter using modern interactions from chiral effective field theory (EFT). It assesses the role of correlations beyond particle-particle and hole-hole ladders, and the role of three-nucleon-forces (3NFs) in nuclear matter calculations with chiral interactions. Methods: This work employs the optimized nucleon-nucleon NN potential NNLOopt at next-to-next-to leading-order, and presents coupled-cluster computations of the EoS for symmetric nuclear matter and neutron matter. The coupled-cluster method employs up to selected triples clusters and the single-particle space consists of a momentum-space lattice. We compare our results with benchmark calculations and control finite-size effects and shell oscillations via twist-averaged bound...
The polarizable embedding coupled cluster method
DEFF Research Database (Denmark)
Sneskov, Kristian; Schwabe, Tobias; Kongsted, Jacob
2011-01-01
We formulate a new combined quantum mechanics/molecular mechanics (QM/MM) method based on a self-consistent polarizable embedding (PE) scheme. For the description of the QM region, we apply the popular coupled cluster (CC) method detailing the inclusion of electrostatic and polarization effects...... all coupled to a polarizable MM environment. In the process, we identify CC densitylike intermediates that allow for a very efficient implementation retaining a computational low cost of the QM/MM terms even when the number of MM sites increases. The strengths of the new implementation are illustrated...
Communication: A simplified coupled-cluster Lagrangian for polarizable embedding
Energy Technology Data Exchange (ETDEWEB)
Krause, Katharina; Klopper, Wim, E-mail: klopper@kit.edu [Karlsruhe Institute of Technology (KIT), Institute of Physical Chemistry, Theoretical Chemistry Group, KIT Campus South, P.O. Box 6980, 76049 Karlsruhe (Germany)
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.
Coupled cluster calculations of ground and excited states of nuclei
Kowalski, K L; Hjorth-Jensen, M; Papenbrock, T; Piecuch, P
2004-01-01
The standard and renormalized coupled cluster methods with singles, doubles, and noniterative triples and their generalizations to excited states, based on the equation of motion coupled cluster approach, are applied to the He-4 and O-16 nuclei. A comparison of coupled cluster results with the results of the exact diagonalization of the Hamiltonian in the same model space shows that the quantum chemistry inspired coupled cluster approximations provide an excellent description of ground and excited states of nuclei. The bulk of the correlation effects is obtained at the coupled cluster singles and doubles level. Triples, treated noniteratively, provide the virtually exact description.
Recent advances in coupled-cluster methods
Bartlett, Rodney J
1997-01-01
Today, coupled-cluster (CC) theory has emerged as the most accurate, widely applicable approach for the correlation problem in molecules. Furthermore, the correct scaling of the energy and wavefunction with size (i.e. extensivity) recommends it for studies of polymers and crystals as well as molecules. CC methods have also paid dividends for nuclei, and for certain strongly correlated systems of interest in field theory.In order for CC methods to have achieved this distinction, it has been necessary to formulate new, theoretical approaches for the treatment of a variety of essential quantities
Ab initio Bogoliubov coupled cluster theory
Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas
2014-09-01
Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.
Coupled Cluster studies of infinite nuclear matter
Baardsen, G; Hagen, G; Hjorth-Jensen, M
2013-01-01
The aim of this work is to develop the relevant formalism for performing Coupled Cluster calculations in nuclear matter and neutron star matter, including thereby important correlations to infinite order in the interaction and testing modern nuclear forces based on chiral effective field theory. Our formalism includes the exact treatment of the so-called Pauli operator in a partial wave expansion of the equation of state. Nuclear and neutron matter calculations are done using a coupled particle-particle and hole-hole ladder approximation. The coupled ladder equations are derived as an approximation of CC theory, leaving out particle-hole and non-linear diagrams from the CC doubles amplitude equation. This study is a first step toward CC calculations for nuclear and neutron matter. We present results for both symmetric nuclear matter and pure neutron matter employing state-of-the-art nucleon-nucleon interactions based on chiral effective field theory. We employ also the newly optimized chiral interaction [A. E...
Full text clustering and relationship network analysis of biomedical publications.
Directory of Open Access Journals (Sweden)
Renchu Guan
Full Text Available Rapid developments in the biomedical sciences have increased the demand for automatic clustering of biomedical publications. In contrast to current approaches to text clustering, which focus exclusively on the contents of abstracts, a novel method is proposed for clustering and analysis of complete biomedical article texts. To reduce dimensionality, Cosine Coefficient is used on a sub-space of only two vectors, instead of computing the Euclidean distance within the space of all vectors. Then a strategy and algorithm is introduced for Semi-supervised Affinity Propagation (SSAP to improve analysis efficiency, using biomedical journal names as an evaluation background. Experimental results show that by avoiding high-dimensional sparse matrix computations, SSAP outperforms conventional k-means methods and improves upon the standard Affinity Propagation algorithm. In constructing a directed relationship network and distribution matrix for the clustering results, it can be noted that overlaps in scope and interests among BioMed publications can be easily identified, providing a valuable analytical tool for editors, authors and readers.
Coupled Cluster Theory for Large Molecules
DEFF Research Database (Denmark)
Baudin, Pablo
2017-01-01
This thesis describes the development of local approximations to coupled cluster (CC) theory for large molecules. Two different methods are presented, the divide–expand–consolidate scheme (DEC), for the calculation of ground state energies, and a local framework denoted LoFEx, for the calculation...... of electronic excitation energies and oscillator strengths. After an introduction to the relevant notions of electronic-structure theory, the principal aspects of DEC and LoFEx are summarized. For comparison, a selected review of the state-of-the-art is presented for each domain. This thesis should serve...... as an introduction to the work developed and presented in the scientific articles collected as appendices. The DEC scheme has been applied successfully to the calculation of MP2, CCSD and CCSD(T) ground state energies. The intrinsic structure of DEC allows for a linear-scaling (with system size) and massively...
Range Separated Brueckner Coupled Cluster Doubles Theory
Shepherd, James J; Scuseria, Gustavo E
2013-01-01
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.
Structural factors of solar system cluster ground coupled storage rationalization
Directory of Open Access Journals (Sweden)
Viktor V. Wysochin
2015-12-01
Full Text Available The computational investigations of unsteady heat transfer in seasonal solar heat storage system were conducted. This storage system consists of nine ground heat exchangers. The investigations were made for periodical diurnal cycle charging during summer season. The heat exchanger is presented as vertical probe with concentric tubes arrangement. Aim: The aim of the work is the optimization of cluster ground coupled storage – the probes quantity in cluster, their lengths and interval – using high precision mathematical model. Materials and Methods: The mathematical model of conjugate solar system functioning and ground coupled storage involves differential equations describing the incoming and conversion of solar energy in solar collector. Also it includes the heat exchange in ground heat exchangers and three-dimensional soil mass. Results: The need of mutual influence accounting of the solar collector and the ground heat exchanger size ranges is shown. One more thing – capability of effectiveness improvement of the collector based on reasonable step size selection for cluster and selection of active heat exchangers quantity in requisite construction. Conclusions: The recommendations for organization of heat exchangers of the collector work are offered. The five-probe structure is the most effective one for cluster arrangement of seasonal heat storage. The recommended interval between probes is 4 meters.
Full vector complex coupled mode theory for tilted fiber gratings.
Lu, Yu-Chun; Huang, Wei-Ping; Jian, Shui-Sheng
2010-01-18
A full vector complex coupled mode theory (CMT) for the analysis of tilted fiber gratings is presented. With the combination of the perfectly matched layer (PML) and the perfectly reflecting boundary (PRB), the continuous radiation modes are well represented by a set of discrete complex modes. Simulation of coupling to radiation modes is greatly simplified and may be treated in the same fashion as guided modes. Numerical results of the tilted fiber Bragg gratings (TFBGs) with outer-cladding index equal, lower and higher than that of the inner-cladding indicate that the complex coupled mode approach is highly effective in the simulation of couplings to cladding and radiation modes in tilted fiber gratings. The reflective TFBGs are investigated by the proposed approach in detail.
The coupled cluster method and entanglement in three fermion systems
Lévay, Péter; Nagy, Szilvia; Pipek, János; Sárosi, Gábor
2017-01-01
The Coupled Cluster (CC) and full CI expansions are studied for three fermions with six and seven modes. Surprisingly the CC expansion is tailor made to characterize the usual stochastic local operations and classical communication (SLOCC) entanglement classes. It means that the notion of a SLOCC transformation shows up quite naturally as a one relating the CC and CI expansions, and going from the CI expansion to the CC one is equivalent to obtaining a form for the state where the structure of the entanglement classes is transparent. In this picture, entanglement is characterized by the parameters of the cluster operators describing transitions from occupied states to singles, doubles, and triples of non-occupied ones. Using the CC parametrization of states in the seven-mode case, we give a simple formula for the unique SLOCC invariant J . Then we consider a perturbation problem featuring a state from the unique SLOCC class characterized by J ≠ 0 . For this state with entanglement generated by doubles, we investigate the phenomenon of changing the entanglement type due to the perturbing effect of triples. We show that there are states with real amplitudes such that their entanglement encoded into configurations of clusters of doubles is protected from errors generated by triples. Finally we put forward a proposal to use the parameters of the cluster operator describing transitions to doubles for entanglement characterization. Compared to the usual SLOCC classes, this provides a coarse grained approach to fermionic entanglement.
Coupled Two-Way Clustering Analysis of Gene Microarray Data
Getz, G; Domany, E
2000-01-01
We present a novel coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant partitions emerge. The search for such subsets is a computationally complex task: we present an algorithm, based on iterative clustering, which performs such a search. This analysis is especially suitable for gene microarray data, where the contributions of a variety of biological mechanisms to the gene expression levels are entangled in a large body of experimental data. The method was applied to two gene microarray data sets, on colon cancer and leukemia. By identifying relevant subsets of the data and focusing on them we were able to discover partitions and correlations that were masked and hidden when the full dataset was used in the analysis. Some of these partitions have clear biological interpretation; others can serve to identify possible directions for future research.
Coupled two-way clustering analysis of gene microarray data
Getz, Gad; Levine, Erel; Domany, Eytan
2000-10-01
We present a coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant partitions emerge. The search for such subsets is a computationally complex task. We present an algorithm, based on iterative clustering, that performs such a search. This analysis is especially suitable for gene microarray data, where the contributions of a variety of biological mechanisms to the gene expression levels are entangled in a large body of experimental data. The method was applied to two gene microarray data sets, on colon cancer and leukemia. By identifying relevant subsets of the data and focusing on them we were able to discover partitions and correlations that were masked and hidden when the full dataset was used in the analysis. Some of these partitions have clear biological interpretation; others can serve to identify possible directions for future research.
Cluster synchronization modes in an ensemble of coupled chaotic oscillators
Belykh, Vladimir N.; Belykh, Igor V.; Mosekilde, Erik
2001-01-01
Considering systems of diffusively coupled identical chaotic oscillators, an effective method to determine the possible states of cluster synchronization and ensure their stability is presented. The method, which may find applications in communication engineering and other fields of science and technology, is illustrated through concrete examples of coupled biological cell models.
Cluster synchronization modes in an ensemble of coupled chaotic oscillators
DEFF Research Database (Denmark)
Belykh, Vladimir N.; Belykh, Igor V.; Mosekilde, Erik
2001-01-01
Considering systems of diffusively coupled identical chaotic oscillators, an effective method to determine the possible states of cluster synchronization and ensure their stability is presented. The method, which may find applications in communication engineering and other fields of science and t...... and technology, is illustrated through concrete examples of coupled biological cell models....
Application of Bibliographic Coupling versus Cited Titles Words in Patent Fuzzy Clustering
Directory of Open Access Journals (Sweden)
Anahita Kermani
2013-03-01
Full Text Available Attribute selection is one of the steps before patent clustering. Various attributes can be used for clustering. In this study, the effect of using citation and citation title words, respectively, in form of bibliographic coupling and citation title words sharing, were measured and compared with each other, as patent attributes. This study was done in an experimental method, on a collection of 717 US Patent cited in the patents belong to 977/774 subclass of US Patent Classification. Fuzzy C-means was used for patent clustering and extended BCubed precision and extended BCubed recall were used as evaluation measure. The results showed that the clustering produced by bibliographic coupling had better performance than clustering used citation title words and existence of cluster structure were in a wider range of exhaustivity than citation title words.
Full-time working couples and their life course : An analysis of leaving full-time employment
Gils, W. van; Kraaykamp, G.; Lippe, T. van der
2009-01-01
In the initial phase of family formation a majority of all spouses works full-time. As a result most couples start off as full-time working couples. We used complete career reports of 2.014 couples from the Netherlands to answer the question of which life-course events and individual social resource
Full-time working couples and their life course: An analysis of leaving full-time employment
Kraaykamp, G.L.M.; Gils, W.S. van; Lippe, A.G. van der
2009-01-01
In the initial phase of family formation a majority of all spouses works full-time. As a result most couples start off as full-time working couples. We used complete career reports of 2.014 couples from the Netherlands to answer the question of which life-course events and individual social resource
Report of a Workshop on Parallelization of Coupled Cluster Methods
Energy Technology Data Exchange (ETDEWEB)
Rodney J. Bartlett Erik Deumens
2008-05-08
The benchmark, ab initio quantum mechanical methods for molecular structure and spectra are now recognized to be coupled-cluster theory. To benefit from the transiiton to tera- and petascale computers, such coupled-cluster methods must be created to run in a scalable fashion. This Workshop, held as a aprt of the 48th annual Sanibel meeting, at St. Simns, Island, GA, addressed that issue. Representatives of all the principal scientific groups who are addressing this topic were in attendance, to exchange information about the problem and to identify what needs to be done in the future. This report summarized the conclusions of the workshop.
Cluster synchrony in systems of coupled phase oscillators with higher-order coupling.
Skardal, Per Sebastian; Ott, Edward; Restrepo, Juan G
2011-09-01
We study the phenomenon of cluster synchrony that occurs in ensembles of coupled phase oscillators when higher-order modes dominate the coupling between oscillators. For the first time, we develop a complete analytic description of the dynamics in the limit of a large number of oscillators and use it to quantify the degree of cluster synchrony, cluster asymmetry, and switching. We use a variation of the recent dimensionality-reduction technique of Ott and Antonsen [Chaos 18, 037113 (2008)] and find an analytic description of the degree of cluster synchrony valid on a globally attracting manifold. Shaped by this manifold, there is an infinite family of steady-state distributions of oscillators, resulting in a high degree of multistability in the cluster asymmetry. We also show how through external forcing the degree of asymmetry can be controlled, and suggest that systems displaying cluster synchrony can be used to encode and store data.
Cluster Synchrony in Systems of Coupled Phase Oscillators with Higher-Order Coupling
Skardal, Per Sebastian; Restrepo, Juan G
2011-01-01
We study the phenomenon of cluster synchrony that occurs in ensembles of coupled phase oscillators when higher-order modes dominate the coupling between oscillators. For the first time, we develop a complete analytic description of the dynamics in the limit of a large number of oscillators and use it to quantify the degree of cluster synchrony, cluster asymmetry, and switching. We use a variation of the recent dimensionality-reduction technique of Ott and Antonsen \\cite{OA1} and find an analytic description of the degree of cluster synchrony valid on a globally attracting manifold. Shaped by this manifold, there is an infinite family of steady-state distributions of oscillators, resulting in a high degree of multi-stability in the cluster asymmetry. We also show how through external forcing the degree of asymmetry can be controlled, and suggest that systems displaying cluster synchrony can be used to encode and store data.
Translationally-invariant coupled-cluster method for finite systems
Guardiola, R; Navarro, J; Portesi, M
1998-01-01
The translational invariant formulation of the coupled-cluster method is presented here at the complete SUB(2) level for a system of nucleons treated as bosons. The correlation amplitudes are solution of a non-linear coupled system of equations. These equations have been solved for light and medium systems, considering the central but still semi-realistic nucleon-nucleon S3 interaction.
Banik, Subrata; Pal, Sourav; Prasad, M Durga
2008-10-07
Vibrational excited state energies have been calculated using vibrational coupled cluster linear response theory (CCLRT). The method has been implemented on formaldehyde and water molecule. Convergence studies have been shown with varying the cluster operator from S(4) to S(6) as well as the excitation operator from four bosons to six bosons. A good agreement with full configuration interaction results has been observed with S(6) truncation at coupled-cluster method level and six bosonic excitations at CCLRT level.
Computation of expectation values from vibrational coupled-cluster at the two-mode coupling level
DEFF Research Database (Denmark)
Zoccante, Alberto; Seidler, Peter; Christiansen, Ove
2011-01-01
In this work we show how the vibrational coupled-cluster method at the two-mode coupling level can be used to calculate zero-point vibrational averages of properties. A technique is presented, where any expectation value can be calculated using a single set of Lagrangian multipliers computed...
Computation of expectation values from vibrational coupled-cluster at the two-mode coupling level
DEFF Research Database (Denmark)
Zoccante, Alberto; Seidler, Peter; Christiansen, Ove
2011-01-01
In this work we show how the vibrational coupled-cluster method at the two-mode coupling level can be used to calculate zero-point vibrational averages of properties. A technique is presented, where any expectation value can be calculated using a single set of Lagrangian multipliers computed...
Mode couplings and resonance instabilities in dust clusters.
Qiao, Ke; Kong, Jie; Oeveren, Eric Van; Matthews, Lorin S; Hyde, Truell W
2013-10-01
The normal modes for three to seven particle two-dimensional (2D) dust clusters in a complex plasma are investigated using an N-body simulation. The ion wakefield downstream of each particle is shown to induce coupling between horizontal and vertical modes. The rules of mode coupling are investigated by classifying the mode eigenvectors employing the Bessel and trigonometric functions indexed by order integers (m, n). It is shown that coupling only occurs between two modes with the same m and that horizontal modes having a higher shear contribution exhibit weaker coupling. Three types of resonances are shown to occur when two coupled modes have the same frequency. Discrete instabilities caused by both the first and third type of resonances are verified and instabilities caused by the third type of resonance are found to induce melting. The melting procedure is observed to go through a two-step process with the solid-liquid transition closely obeying the Lindemann criterion.
Event-based cluster synchronization of coupled genetic regulatory networks
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.
On the Use of Connected Moments Expansion with Coupled Cluster Reference
Directory of Open Access Journals (Sweden)
PÃƒÂ©ter R. SurjÃƒÂ¡n
2002-05-01
Full Text Available Abstract: We examine the possibility of introducing a new class of so called noniterative corrections to coupled cluster energies, based on the connected moments expansion (CMX. Approximate Coupled Cluster (CC wave functions are used as reference states and then the Ã¢Â€Âœimproved energiesÃ¢Â€Â can be formally obtained either by CMX in terms of the moments of CC similarity transformed Hamiltonian, or in CMX of the usual Hamiltonian. Numerical results are given for some model systems that show the superiority of the latter approach.
Spencer, James S
2015-01-01
We describe further details of the Stochastic Coupled Cluster method and a diagnostic of such calculations, the shoulder height, akin to the plateau found in Full Configuration Interaction Quantum Monte Carlo. We describe an initiator modification to Stochastic Coupled Cluster Theory and show that initiator calculations can be extrapolated to the unbiased limit. We apply this method to the 3D 14-electron uniform electron gas and present complete basis set limit values of the CCSD and previously unattainable CCSDT correlation energies for up to rs = 2, showing a requirement to include triple excitations to accurately calculate energies at high densities.
Energy Technology Data Exchange (ETDEWEB)
Brabec, Jiri; Banik, Subrata; Kowalski, Karol; Pittner, Jiří
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.
Directory of Open Access Journals (Sweden)
M. Durga Prasad
2002-05-01
Full Text Available Abstract: A time dependent coupled cluster approach to the calculation of Resonance Raman excitation profiles on general anharmonic surfaces is presented. The vibrational wave functions on the ground electronic surface are obtained by the coupled cluster method (CCM. It is shown that the propagation of the vibrational ground state on the upper surface is equivalent to propagation of the vacuum state by an effective hamiltonian generated by the similarity transformation of the vibrational hamiltonian of that surface by the CCM wave operator of the lower surface up to a normalization constant. This time propagation is carried out by the time-dependent coupled cluster method in a time dependent frame. Numerical studies are presented to asses the validity of the approach.
Ab initio quantum dynamics using coupled-cluster.
Kvaal, Simen
2012-05-21
The curse of dimensionality (COD) limits the current state-of-the-art ab initio propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schrödinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster, and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given.
Ab initio quantum dynamics using coupled-cluster
Kvaal, Simen
2012-01-01
The curse of dimensionality (COD) limits the current state-of-the-art {\\it ab initio} propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schr\\"odinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster (OATDCC), and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given.
Coupled Cluster Channels in the Homogeneous Electron Gas
Shepherd, James J; Scuseria, Gustavo E
2013-01-01
We discuss diagrammatic modifications to the coupled cluster doubles (CCD) equations, wherein different groups of terms out of rings, ladders, crossed-rings and mosaics can be removed to form approximations to the coupled cluster method, of interest due to their similarity with various types of random phase approximations. The finite uniform electron gas is benchmarked for 14- and 54-electron systems at the complete basis set limit over a wide density range and performance of different flavours of CCD are determined. These results confirm that rings generally overcorrelate and ladders generally undercorrelate; mosaics-only CCD yields a result surprisingly close to CCD. We use a recently developed numerical analysis [J. J. Shepherd and A. Gr\\"uneis, Phys. Rev. Lett. 110, 226401 (2013)] to study the behaviours of these methods in the thermodynamic limit. We determine that the mosaics, on forming the Brueckner Hamltonian, open a gap in the effective one-particle eigenvalues at the Fermi energy. Numerical evidenc...
Analytic evaluation of Raman intensities in coupled-cluster theory
Gauss, Jürgen; Kallay, Mihaly; O'Neill, Darragh P.
2008-01-01
Abstract We present the first implementation for the analytic calculation of polarizability derivatives using coupled-cluster theory. These derivatives are related to the intensity of bands seen in Raman spectroscopy, and are therefore important quantities which can also be measured experimentally. The required theory of analytic third derivatives is discussed and also connected to response theory to allow the calculation of frequency-dependent quantities. This work includes the...
Energetics of H$_2$ clusters from density functional and coupled cluster theories
Trail, J R; Needs, R J
2016-01-01
We use coupled-cluster quantum chemical methods to calculate the energetics of molecular clusters cut out of periodic molecular hydrogen structures that model observed phases of solid hydrogen. The hydrogen structures are obtained from Kohn-Sham density functional theory (DFT) calculations at pressures of 150, 250 and 350 GPa, which are within the pressure range in which phases II, III and IV are found to be stable. The calculated deviations in the DFT energies from the coupled-cluster data are reported for different functionals, and optimized functionals are generated which provide reduced errors. We give recommendations for semi-local and hybrid density functionals that are expected to accurately describe hydrogen at high pressures.
Energetics of H2 clusters from density functional and coupled cluster theories
Trail, J. R.; López Ríos, P.; Needs, R. J.
2017-03-01
We use coupled-cluster quantum chemical methods to calculate the energetics of molecular clusters cut out of periodic molecular hydrogen structures that model observed phases of solid hydrogen. The hydrogen structures are obtained from Kohn-Sham density functional theory (DFT) calculations at pressures of 150, 250, and 350 GPa, which are within the pressure range in which phases II, III, and IV are found to be stable. The calculated deviations in the DFT energies from the coupled-cluster data are reported for different functionals, and optimized functionals are generated which provide reduced errors. We give recommendations for semilocal and hybrid density functionals that are expected to provide an accurate description of hydrogen at high pressures.
A Coupled User Clustering Algorithm Based on Mixed Data for Web-Based Learning Systems
Directory of Open Access Journals (Sweden)
Ke Niu
2015-01-01
Full Text Available In traditional Web-based learning systems, due to insufficient learning behaviors analysis and personalized study guides, a few user clustering algorithms are introduced. While analyzing the behaviors with these algorithms, researchers generally focus on continuous data but easily neglect discrete data, each of which is generated from online learning actions. Moreover, there are implicit coupled interactions among the data but are frequently ignored in the introduced algorithms. Therefore, a mass of significant information which can positively affect clustering accuracy is neglected. To solve the above issues, we proposed a coupled user clustering algorithm for Wed-based learning systems by taking into account both discrete and continuous data, as well as intracoupled and intercoupled interactions of the data. The experiment result in this paper demonstrates the outperformance of the proposed algorithm.
Constraining ALP-photon coupling using galaxy clusters
Schlederer, Martin
2015-01-01
In this study, we propose a new approach to constrain the coupling of axion-like particles (ALPs) to photons. One intriguing property of these ALPs is their mixing with photons within magnetic fields. This mixing allows photons propagating in magnetic fields to convert into ALPs and \\textit{vice versa}. Plasma effects can lead to resonant conversion, further enhancing the conversion probability. For suitable ALP masses, this resonant conversion can occur for cosmic microwave background photons transversing galaxy clusters which would distort the CMB spectrum in the direction of galaxy clusters. We compare the predicted distortion with recent measurements of the thermal Sunyaev-Zeldovich Compton parameter to obtain upper limits on the coupling between photons and ALPs. The constraints apply to the mass range of approximately $2\\cdot 10^{-14}$ eV $ \\lesssim m_\\phi \\lesssim 3\\cdot 10^{-12}$ eV in which resonant photon-ALP conversions can occur. Using simple galaxy cluster models, we obtain new limits for this ma...
Directory of Open Access Journals (Sweden)
Ze Tang
2013-01-01
Full Text Available We focus on the cluster synchronization problem for a kind of general networks with nondelayed and delayed coupling. Based on the pinning control scheme, a small fraction of the nodes in each cluster are pinned for successful control, and the states of the whole dynamical networks can be globally forced to the objective cluster states. Sufficient conditions are derived to guarantee the realization of the cluster synchronization pattern for all initial values by means of the Lyapunov stability theorem and linear matrix inequalities (LMIs. By using the adaptive update law, relative smaller control gains are obtained, and hence the control cost can be substantially lower. Numerical simulations are also exploited to demonstrate the effectiveness and validity of the main result.
Time-dependent coupled-cluster method for atomic nuclei
Pigg, D A; Nam, H; Papenbrock, T
2012-01-01
We study time-dependent coupled-cluster theory in the framework of nuclear physics. Based on Kvaal's bi-variational formulation of this method [S. Kvaal, arXiv:1201.5548], we explicitly demonstrate that observables that commute with the Hamiltonian are conserved under time evolution. We explore the role of the energy and of the similarity-transformed Hamiltonian under real and imaginary time evolution and relate the latter to similarity renormalization group transformations. Proof-of-principle computations of He-4 and O-16 in small model spaces, and computations of the Lipkin model illustrate the capabilities of the method.
Multiple Ionic-Covalent Couplings in Molecules and Clusters
Institute of Scientific and Technical Information of China (English)
GwangHi Jeung
2009-01-01
The electronic states of molecules made of electropositive and electronegative components result from the interfcrence between the covalent configurations and the ionic configurations.This work shows complex aspects of these ionic-covalent couplings in small molecules such as Li2H, Li2F, and Li4F. The extension of this type of analysis to the adsorption of the electrophilic molecules on the metal clusters or on the metal surfaces is supposed to lead to a radically new interpretation of the observed physical and chemical properties.
Automatic derivation and evaluation of vibrational coupled cluster theory equations
Seidler, Peter; Christiansen, Ove
2009-12-01
A scheme for automatic derivation and evaluation of the expressions occurring in vibrational coupled cluster theory is introduced. The method is based on a Baker-Campbell-Hausdorff expansion of the similarity transformed Hamiltonian and is general both with respect to the excitation level in the parameter space and the mode coupling level in the Hamiltonian. In addition to deriving general expressions, intermediates that lower the computational scaling are automatically detected. The final equations are then evaluated. Due to the commutator based nature of the algorithm, it is also applicable to the evaluation of quantities needed for response theory. Different aspects of the theory and implementation are illustrated by calculations on model systems. Furthermore, all fundamental excitation energies of ethylene oxide are calculated.
The Integral- and Intermediate-Screened Coupled-Cluster Method
Sørensen, L K
2016-01-01
We present the formulation and implementation of the integral- and intermediate-screened coupled-cluster method (ISSCC). The IISCC method gives a simple and rigorous integral and intermediate screening (IIS) of the coupled-cluster method and will significantly reduces the scaling for all orders of the CC hierarchy exactly like seen for the integral-screened configuration-interaction method (ISCI). The rigorous IIS in the IISCC gives a robust and adjustable error control which should allow for the possibility of converging the energy without any loss of accuracy while retaining low or linear scaling at the same time. The derivation of the IISCC is performed in a similar fashion as in the ISCI where we show that the tensor contractions for the nested commutators are separable up to an overall sign and that this separability can lead to a rigorous IIS. In the nested commutators the integrals are screened in the first tensor contraction and the intermediates are screened in all successive tensor contractions. The...
Energy Technology Data Exchange (ETDEWEB)
Lara-Castells, M. P. de, E-mail: delara@iff.csic.es; Aguirre, N. F., E-mail: delara@iff.csic.es; Delgado-Barrio, G., E-mail: delara@iff.csic.es; Villarreal, P., E-mail: delara@iff.csic.es [Instituto de Física Fundamental (CSIC), Serrano 123, 28006 Madrid (Spain); Mitrushchenkov, A. O. [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France)
2015-01-22
An efficient full-configuration-interaction 'nuclear orbital' treatment was developed as a benchmark quantum-chemistry-like method to calculate, ground and excited, fermionic 'solvent' wave-functions and applied to {sup 3}He{sub N} clusters with atomic or molecular impurities [J. Chem. Phys. (Communication) 125, 221101 (2006)]. The main difficulty in handling doped {sup 3}He{sub N} clusters lies in the Fermi-Dirac nuclear statistics, the wide amplitudes of the He-dopant and He-He motions, and the hard-core He-He interaction at short distances. This paper overviews the theoretical approach and its recent applications to energetic, structural and spectroscopic aspects of different dopant-{sup 3}He{sub N} clusters. Preliminary results by using the latest version of the FCI-NO computational implementation, to bosonic Cl{sub 2}(X)-({sup 4}He){sub N} clusters, are also shown.
Mapping the Generator Coordinate Method to the Coupled Cluster Approach
Stuber, Jason L
2015-01-01
The generator coordinate method (GCM) casts the wavefunction as an integral over a weighted set of non-orthogonal single determinantal states. In principle this representation can be used like the configuration interaction (CI) or shell model to systematically improve the approximate wavefunction towards an exact solution. In practice applications have generally been limited to systems with less than three degrees of freedom. This bottleneck is directly linked to the exponential computational expense associated with the numerical projection of broken symmetry Hartree-Fock (HF) or Hartree-Fock-Bogoliubov (HFB) wavefunctions and to the use of a variational rather than a bi-variational expression for the energy. We circumvent these issues by choosing a hole-particle representation for the generator and applying algebraic symmetry projection, via the use of tensor operators and the invariant mean (operator average). The resulting GCM formulation can be mapped directly to the coupled cluster (CC) approach, leading...
Heat Transport in Confined Strongly Coupled 2D Dust Clusters
Kudelis, Giedrius; Bonitz, Michael
2013-01-01
Dusty plasmas are a model system for studying strong correlation. The dust grains' size of a few micro-meters and their characteristic oscillation frequency of a few hertz allows for an investigation of many particle effects on an atomic level. In this article, we model the heat transport through an axially confined 2D dust cluster from the center to the outside. The system behaves particularly interesting since heat is not only conducted within the dust component but also transfered to the neutral gas. Fitting the analytical solution to the obtained radial temperature profiles allows to determine the heat conductivity $\\kheat$. The heat conductivity is found to be constant over a wide range of coupling strengths even including the phase transition from solid to liquid here, as it was also found in extended systems by V. Nosenko et al. in 2008 \\cite{PhysRevLett.100.025003}
Relativistic extended coupled cluster method for magnetic hyperfine structure constant
Sasmal, Sudip; Nayak, Malaya K; Vaval, Nayana; Pal, Sourav
2015-01-01
This article deals with the general implementation of 4-component spinor relativistic extended coupled cluster (ECC) method to calculate first order property of atoms and molecules in their open-shell ground state configuration. The implemented relativistic ECC is employed to calculate hyperfine structure (HFS) constant of alkali metals (Li, Na, K, Rb and Cs), singly charged alkaline earth metal atoms (Be+, Mg+, Ca+ and Sr+) and molecules (BeH, MgF and CaH). We have compared our ECC results with the calculations based on restricted active space configuration interaction (RAS-CI) method. Our results are in better agreement with the available experimental values than those of the RAS-CI values.
Coupled cluster calculations of neutron-rich nuclei
Hagen, Gaute
2016-09-01
In this talk I will present recent highlights from ab initio computations of atomic nuclei using coupled-cluster methods with state-of-the-art interactions from chiral effective field theory (EFT). The recent progress in computing nuclei from scratch is based on new optimizations of interactions from chiral EFT, and ab initio methods with a polynomial computational cost together with available super computing resources. The physics advancements I will discuss include: (i) accurate nuclear binding energies and radii of light and medium-mass nuclei, (ii) the neutron distribution and electric dipole polarizability of the nucleus 48Ca, (iii) and the structure of the rare nucleus 78Ni from first principles. All these quantities are currently targeted by precision measurements worldwide.
Constraining ALP-photon coupling using galaxy clusters
Energy Technology Data Exchange (ETDEWEB)
Schlederer, Martin; Sigl, Günter [II. Institut für theoretische Physik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany)
2016-01-21
We study photon-ALP conversion by resonance effects in the magnetized plasma of galaxy clusters and compare the predicted distortion of the cosmic microwave background spectrum in the direction of such objects to measurements of the thermal Sunyaev-Zeldovich effect. Using galaxy cluster models based on current knowledge, we obtain upper limits on the photon-ALP coupling constant g of ≲O(10{sup −11} GeV{sup −1}). The constraints apply to the mass range of 2⋅10{sup −14} eV ≲m{sub ALP}≲3⋅10{sup −12} eV in which resonant photon-ALP conversions can occur. These limits are slightly stronger than current limits, and furthermore provide an independent constraint. We find that a next generation PRISM-like experiment would allow limits down to g≈O(10{sup −14} GeV{sup −1}), two orders of magnitude stronger than the currently strongest limits in this mass range.
Scuseria, Gustavo E; Henderson, Thomas M; Bulik, Ireneusz W
2013-09-14
We establish a formal connection between the particle-particle (pp) random phase approximation (RPA) and the ladder channel of the coupled cluster doubles (CCD) equations. The relationship between RPA and CCD is best understood within a Bogoliubov quasiparticle (qp) RPA formalism. This work is a follow-up to our previous formal proof on the connection between particle-hole (ph) RPA and ring-CCD. Whereas RPA is a quasibosonic approximation, CC theory is a "correct bosonization" in the sense that the wavefunction and Hilbert space are exactly fermionic, yet the amplitude equations can be interpreted as adding different quasibosonic RPA channels together. Coupled cluster theory achieves this goal by interacting the ph (ring) and pp (ladder) diagrams via a third channel that we here call "crossed-ring" whose presence allows for full fermionic antisymmetry. Additionally, coupled cluster incorporates what we call "mosaic" terms which can be absorbed into defining a new effective one-body Hamiltonian. The inclusion of these mosaic terms seems to be quite important. The pp-RPA and qp-RPA equations are textbook material in nuclear structure physics but are largely unknown in quantum chemistry, where particle number fluctuations and Bogoliubov determinants are rarely used. We believe that the ideas and connections discussed in this paper may help design improved ways of incorporating RPA correlation into density functionals based on a CC perspective.
Scuseria, Gustavo E; Bulik, Ireneusz W
2013-01-01
We establish a formal connection between the particle-particle (pp) random phase approximation (RPA) and the ladder channel of the coupled cluster doubles (CCD) equations. The relationship between RPA and CCD is best understood within a Bogoliubov quasiparticle (qp) RPA formalism. This work is a follow-up to our previous formal proof on the connection between particle-hole (ph) RPA and ring-CCD. Whereas RPA is a quasibosonic approximation, CC theory is a correct bosonization in the sense that the wavefunction and Hilbert space are exactly fermionic. Coupled cluster theory achieves this goal by interacting the ph (ring) and pp (ladder) diagrams via a third channel that we here call "crossed-ring" whose presence allows for full fermionic antisymmetry. Additionally, coupled cluster incorporates what we call "mosaic" terms which can be absorbed into defining a new effective one-body Hamiltonian. The inclusion of these mosaic terms seems to be quite important. The pp-RPA an d qp-RPA equations are textbook material...
Towards an unbiased, full-sky clustering search with IceCube in real time
Energy Technology Data Exchange (ETDEWEB)
Bernardini, Elisa; Franckowiak, Anna; Kintscher, Thomas; Kowalski, Marek; Stasik, Alexander [DESY, Zeuthen (Germany); Collaboration: IceCube-Collaboration
2016-07-01
The IceCube neutrino observatory is a 1 km{sup 3} detector for Cherenkov light in the ice at the South Pole. Having observed the presence of a diffuse astrophysical neutrino flux, static point source searches have come up empty handed. Thus, transient and variable objects emerge as promising, detectable source candidates. An unbiased, full-sky clustering search - run in real time - can find neutrino events with close temporal and spatial proximity. The most significant of these clusters serve as alerts to third-party observatories in order to obtain a complete picture of cosmic accelerators. The talk showcases the status and prospects of this project.
Coupled-cluster singles and doubles for extended systems
Hirata, So; Podeszwa, Rafał; Tobita, Motoi; Bartlett, Rodney J.
2004-02-01
Coupled-cluster theory with connected single and double excitation operators (CCSD) and related approximations, such as linearized CCSD, quadratic configuration interaction with single and double excitation operators, coupled-cluster with connected double excitation operator (CCD), linearized CCD, approximate CCD, and second- and third-order many-body perturbation theories, are formulated and implemented for infinitely extended one-dimensional systems (polymers), on the basis of the periodic boundary conditions and distance-based screening of integrals, density matrix elements, and excitation amplitudes. The variation of correlation energies with the truncation radii of short- and long-range lattice sums and with the number of wave vector sampling points in the first Brillouin zone is examined for polyethylene, polyacetylene, and polyyne, and is shown to be a function of the degree of π-electron conjugation or the fundamental band gaps. The t2 and t1 amplitudes in the atomic orbital (AO) basis are obtained by first computing the t amplitudes in the Bloch-orbital basis and subsequently back-transforming them into the AO basis. The plot of these AO-based t amplitudes as a function of unit cells also indicates that the t2 amplitudes of polyacetylene and polyyne exhibit appreciably slower decay than those of polyethylene, although the asymptotic decay behavior is invariably 1/r3. The AO-based t1 amplitudes appear to correlate strongly with the electronic structure, and they decay seemingly exponentially for polyethylene whereas they stay at a constant magnitude across the seventh nearest neighbors of polyacetylene and polyyne, which attests to far reaching effects of nondynamical electron correlation mediated by orbital rotation. Nonetheless, the unit cell contributions to the correlation energies taper below 10-6 hartree after 15 Å for all three polymers. The basis set dependence of the decay behavior of t2 amplitudes is also examined for linear hydrogen fluoride
Coupled Two-Way Clustering Analysis of Breast Cancer and Colon Cancer Gene Expression Data
Getz, G; Kela, I; Domany, E; Notterman, D A; Getz, Gad; Gal, Hilah; Kela, Itai; Domany, Eytan; Notterman, Dan A.
2003-01-01
We present and review Coupled Two Way Clustering, a method designed to mine gene expression data. The method identifies submatrices of the total expression matrix, whose clustering analysis reveals partitions of samples (and genes) into biologically relevant classes. We demonstrate, on data from colon and breast cancer, that we are able to identify partitions that elude standard clustering analysis.
Coupled-cluster methods for core-hole dynamics
Picon, Antonio; Cheng, Lan; Hammond, Jeff R.; Stanton, John F.; Southworth, Stephen H.
2014-05-01
Coupled cluster (CC) is a powerful numerical method used in quantum chemistry in order to take into account electron correlation with high accuracy and size consistency. In the CC framework, excited, ionized, and electron-attached states can be described by the equation of motion (EOM) CC technique. However, bringing CC methods to describe molecular dynamics induced by x rays is challenging. X rays have the special feature of interacting with core-shell electrons that are close to the nucleus. Core-shell electrons can be ionized or excited to a valence shell, leaving a core-hole that will decay very fast (e.g. 2.4 fs for K-shell of Ne) by emitting photons (fluorescence process) or electrons (Auger process). Both processes are a clear manifestation of a many-body effect, involving electrons in the continuum in the case of Auger processes. We review our progress of developing EOM-CC methods for core-hole dynamics. Results of the calculations will be compared with measurements on core-hole decays in atomic Xe and molecular XeF2. This work is funded by the Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy, under Contract No. DE-AC02-06CH11357.
Efficiency of a Multi-Reference Coupled Cluster method
Giner, Emmanuel; Scemama, Anthony; Malrieu, Jean Paul
2015-01-01
The multi-reference Coupled Cluster method first proposed by Meller et al (J. Chem. Phys. 1996) has been implemented and tested. Guess values of the amplitudes of the single and double excitations (the ${\\hat T}$ operator) on the top of the references are extracted from the knowledge of the coefficients of the Multi Reference Singles and Doubles Configuration Interaction (MRSDCI) matrix. The multiple parentage problem is solved by scaling these amplitudes on the interaction between the references and the Singles and Doubles. Then one proceeds to a dressing of the MRSDCI matrix under the effect of the Triples and Quadruples, the coefficients of which are estimated from the action of ${\\hat T}^2$. This dressing follows the logics of the intermediate effective Hamiltonian formalism. The dressed MRSDCI matrix is diagonalized and the process is iterated to convergence. The method is tested on a series of benchmark systems from Complete Active Spaces (CAS) involving 2 or 4 active electrons up to bond breakings. The...
Coupled-cluster based basis sets for valence correlation calculations
Claudino, Daniel; Gargano, Ricardo; Bartlett, Rodney J.
2016-03-01
Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These new sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via (-3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within "chemical accuracy" of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.
Banik, Subrata; Pal, Sourav; Prasad, M Durga
2010-10-12
An effective operator approach based on the coupled cluster method is described and applied to calculate vibrational expectation values and absolute transition matrix elements. Coupled cluster linear response theory (CCLRT) is used to calculate excited states. The convergence pattern of these properties with the rank of the excitation operator is studied. The method is applied to a water molecule. Arponen-type double similarity transformation in extended coupled cluster (ECCM) framework is also used to generate an effective operator, and the convergence pattern of these properties is compared to the normal coupled cluster (NCCM) approach. It is found that the coupled cluster method provides an accurate description of these quantities for low lying vibrational excited states. The ECCM provides a significant improvement for the calculation of the transition matrix elements.
Approximating electronically excited states with equation-of-motion linear coupled-cluster theory
Byrd, Jason N.; Rishi, Varun; Perera, Ajith; Bartlett, Rodney J.
2015-10-01
A new perturbative approach to canonical equation-of-motion coupled-cluster theory is presented using coupled-cluster perturbation theory. A second-order Møller-Plesset partitioning of the Hamiltonian is used to obtain the well known equation-of-motion many-body perturbation theory equations and two new equation-of-motion methods based on the linear coupled-cluster doubles and linear coupled-cluster singles and doubles wavefunctions. These new methods are benchmarked against very accurate theoretical and experimental spectra from 25 small organic molecules. It is found that the proposed methods have excellent agreement with canonical equation-of-motion coupled-cluster singles and doubles state for state orderings and relative excited state energies as well as acceptable quantitative agreement for absolute excitation energies compared with the best estimate theory and experimental spectra.
Ivanov, Vladimir V.; Zakharov, Anton B.; Adamowicz, Ludwik
2013-12-01
A new semi-empirical π-electron local coupled cluster theory has been developed to calculate static dipole polarisabilities and hyperpolarisabilities of extended π-conjugated systems. The key idea of the approach is the use of the ethylene molecular orbitals as the orbital basis set for π-conjugated compounds (the method is termed the Covalent Unbonded Molecules of Ethylene method, cue). Test calculations of some small model organic conjugated compounds demonstrate high accuracy of the version of the cue local coupled cluster theory developed in this work in comparison with the π-electron full configuration interaction (FCI) method. Calculations of different conjugated carbon-based oligomer chains (polyenes, polyynes, polyacenes, polybenzocyclobutadiene, etc.) demonstrate fast convergence (per π-electron) of the polarisability and hyperpolarisability values in the calculations when more classes of orbital excitations are included in the coupled cluster single and double (CCSD) excitation operator. The results show qualitatively correct dependence on the system size.
The DSUBm approximation scheme for the coupled cluster method and applications to quantum magnets
Directory of Open Access Journals (Sweden)
R.F. Bishop
2009-01-01
Full Text Available A new approximate scheme, DSUBm, is described for the coupled cluster method. We apply it to two well-studied (spin-1/2 Heisenberg antiferromagnet spin-lattice models, namely: the XXZ and the XY models on the square lattice in two dimensions. Results are obtained in each case for the ground-state energy, the sublattice magnetization and the quantum critical point. They are in good agreement with those from such alternative methods as spin-wave theory, series expansions, exact diagonalization techniques, quantum Monte Carlo methods and those from the CCM using the LSUBm scheme.
Directory of Open Access Journals (Sweden)
Tapan Kumar Jain
2014-01-01
Full Text Available The research work proposes a cluster head selection algorithm for a wireless sensor network. A node can be a cluster head if it is connected to at least one unique neighbor node where the unique neighbor is the one that is not connected to any other node. If there is no connected unique node then the CH is selected on the basis of residual energy and the number of neighbor nodes. With the increase in number of clusters, the processing energy of the network increases; hence, this algorithm proposes minimum number of clusters which further leads to increased network lifetime. The major novel contribution of the proposed work is an algorithm that ensures a completely connected network with minimum number of isolated nodes. An isolated node will remain only if it is not within the transmission range of any other node. With the maximum connectivity, the coverage of the network is automatically maximized. The superiority of the proposed design is verified by simulation results done in MATLAB, where it clearly depicts that the total numbers of rounds before the network dies out are maximum compared to other existing protocols.
Full hamiltonian structure for a parametric coupled Korteweg-de Vries system
Restuccia, A
2014-01-01
We obtain the full hamiltonian structure for a parametric coupled KdV system. The coupled system arises from four different real basic lagrangians. The associated hamiltonian functionals and the corresponding Poisson structures follow from the geometry of a constrained phase space by using the Dirac approach for constrained systems. The overall algebraic structure for the system is given in terms of two pencils of Poisson structures with associated hamiltonians depending on the parameter of the Poisson pencils. The algebraic construction we present admits the most general space of observables related to the coupled system.
Directory of Open Access Journals (Sweden)
Ian S.O. Pimienta
2002-05-01
Full Text Available Abstract: A new approach to the many-electron correlation problem, termed the method of moments of coupled-cluster equations (MMCC, is further developed and tested. The main idea of the MMCC theory is that of the noniterative energy corrections which, when added to the energies obtained in the standard coupled-cluster calculations, recover the exact (full configuration interaction energy. The MMCC approximations require that a guess is provided for the electronic wave function of interest. The idea of using simple estimates of the wave function, provided by the inexpensive configuration interaction (CI methods employing small sets of active orbitals to define higherÃ¢Â€Â“thanÃ¢Â€Â“double excitations, is tested in this work. The CI-corrected MMCC methods are used to study the single bond breaking in HF and the simultaneous breaking of both OÃ¢Â€Â“H bonds in H2O.
Clustering in Globally Coupled Oscillators Near a Hopf Bifurcation: Theory and Experiments
Kori, Hiroshi; Jain, Swati; Kiss, István Z; Hudson, John
2014-01-01
A theoretical analysis is presented to show the general occurrence of phase clusters in weakly, globally coupled oscillators close to a Hopf bifurcation. Through a reductive perturbation method, we derive the amplitude equation with a higher order correction term valid near a Hopf bifurcation point. This amplitude equation allows us to calculate analytically the phase coupling function from given limit-cycle oscillator models. Moreover, using the phase coupling function, the stability of phase clusters can be analyzed. We demonstrate our theory with the Brusselator model. Experiments are carried out to confirm the presence of phase clusters close to Hopf bifurcations with electrochemical oscillators.
Clustering and Synchronization in an Array of Repulsively Coupled Phase Oscillators
Institute of Scientific and Technical Information of China (English)
LI Juan; WU Liang; ZHU Shi-Qun
2007-01-01
Clustering and synchronization in an array of repulsively coupled phase oscillators are numerically investigated. It is found that oscillators are divided into several clusters according to the symmetry in the structure.Synchronization occurs between oscillators in each cluster, while those oscillators belonging to different clusters remain asynchronous. Such synchronization may collapse for all clusters when the dynamics of only one oscillator is altered properly. The synchronous state may return back after a short period of transient process. This is determined by the strength of the oscillator altered. Its application in the communication of one-to-several is suggested.
Energy Technology Data Exchange (ETDEWEB)
Feller, David, E-mail: dfeller@owt.com; Peterson, Kirk A. [Department of Chemistry, Washington State University, Pullman, Washington 99164-4630 (United States); Davidson, Ernest R. [Department of Chemistry, University of Washington, Seattle, Washington 98195-1700 (United States)
2014-09-14
A systematic sequence of configuration interaction and coupled cluster calculations were used to describe selected low-lying singlet and triplet vertically excited states of ethylene with the goal of approaching the all electron, full configuration interaction/complete basis set limit. Included among these is the notoriously difficult, mixed valence/Rydberg {sup 1}B{sub 1u} V state. Techniques included complete active space and iterative natural orbital configuration interaction with large reference spaces which led to variational spaces of 1.8 × 10{sup 9} parameters. Care was taken to avoid unintentionally biasing the results due to the widely recognized sensitivity of the V state to the details of the calculation. The lowest vertical and adiabatic ionization potentials to the {sup 2}B{sub 3u} and {sup 2}B{sub 3} states were also determined. In addition, the heat of formation of twisted ethylene {sup 3}A{sub 1} was obtained from large basis set coupled cluster theory calculations including corrections for core/valence, scalar relativistic and higher order correlation recovery.
Wang, Yi-Siang; Chao, Sheng D
2011-03-10
We have calculated the structural and energetic properties of neutral and ionic (singly charged anionic and cationic) semiconductor binary silicon-germanium clusters Si(m)Ge(n) for s = m + n ≤ 12 using the density functional theory (DFT-B3LYP) and coupled cluster [CCSD(T)] methods with Pople's 6-311++G(3df, 3pd) basis set. Neutral and anionic clusters share similar ground state structures for s = 3-7, independent of the stoichiometry and atom locations, but start to deviate at s = 8. The relative energetic stability of the calculated ground state structures among possible isomers has been analyzed through a bond strength propensity model where the pair interactions of Si-Si, Si-Ge, and Ge-Ge are competing. Electron affinities, ionization potentials, energy gaps between the highest and lowest occupied molecular orbitals (HOMO-LUMO gaps), and cluster mixing energies were calculated and analyzed. Overall, for a fixed s, the vertical ionization potential increases as the number of silicon atoms m increases, while the vertical electron affinity shows a dip at m = 2. As s increases, the ionization potentials increase from s = 2 to s = 3 and then decrease slowly to s = 8. The mixing energies for neutral and ionic clusters are all negative, indicating that the binary clusters are more stable than pure elemental clusters. Except for s = 4 and 8, cationic clusters are more stable than anionic ones and, thus, are more likely to be observed in experiments.
Lai, Yi Ming
2013-07-09
We study ensembles of globally coupled, nonidentical phase oscillators subject to correlated noise, and we identify several important factors that cause noise and coupling to synchronize or desynchronize a system. By introducing noise in various ways, we find an estimate for the onset of synchrony of a system in terms of the coupling strength, noise strength, and width of the frequency distribution of its natural oscillations. We also demonstrate that noise alone can be sufficient to synchronize nonidentical oscillators. However, this synchrony depends on the first Fourier mode of a phase-sensitivity function, through which we introduce common noise into the system. We show that higher Fourier modes can cause desynchronization due to clustering effects, and that this can reinforce clustering caused by different forms of coupling. Finally, we discuss the effects of noise on an ensemble in which antiferromagnetic coupling causes oscillators to form two clusters in the absence of noise. © 2013 American Physical Society.
Landau, Arie
2013-07-07
This paper presents a new method for calculating spectroscopic properties in the framework of response theory utilizing a sequence of similarity transformations (STs). The STs are preformed using the coupled cluster (CC) and Fock-space coupled cluster operators. The linear and quadratic response functions of the new similarity transformed CC response (ST-CCR) method are derived. The poles of the linear response yield excitation-energy (EE) expressions identical to the ones in the similarity transformed equation-of-motion coupled cluster (STEOM-CC) approach. ST-CCR and STEOM-CC complement each other, in analogy to the complementarity of CC response (CCR) and equation-of-motion coupled cluster (EOM-CC). ST-CCR/STEOM-CC and CCR/EOM-CC yield size-extensive and size-intensive EEs, respectively. Other electronic-properties, e.g., transition dipole strengths, are also size-extensive within ST-CCR, in contrast to STEOM-CC. Moreover, analysis suggests that in comparison with CCR, the ST-CCR expressions may be confined to a smaller subspace, however, the precise scope of the truncation can only be determined numerically. In addition, reformulation of the time-independent STEOM-CC using the same parameterization as in ST-CCR, as well as an efficient truncation scheme, is presented. The shown convergence of the time-dependent and time-independent expressions displays the completeness of the presented formalism.
Liu, Ji; Guo, Ji-Tao; Li, Yong-Guo; Johnston, Randal N; Liu, Gui-Rong; Liu, Shu-Lin
2013-07-01
Type VI secretion system (T6SS) has increasingly been believed to participate in the infection process for many bacterial pathogens, but its role in the virulence of Salmonella typhimurium remains unclear. To look into this, we deleted the T6SS cluster from the genome of S. typhimurium 14028s and analyzed the phenotype of the resulting T6SS knockout mutant (T6SSKO mutant) in vitro and in vivo. We found that the T6SSKO mutant exhibited reduced capability in colonizing the spleen and liver in an in vivo colonization competition model in BALB/c mice infected by the oral route. Additionally, infection via intraperitoneal administration also showed that the T6SSKO mutant was less capable of colonizing the mouse spleen and liver than the wild-type strain. We did not detect significant differences between the T6SSKO and wild-type strains in epithelial cell invasion tests. However, in the macrophage RAW264.7 cell line, the T6SSKO mutant survived and proliferated significantly more poorly than the wild-type strain. These findings indicate that T6SS gene cluster is required for full virulence of S. typhimurium 14028s in BALB/c mice, possibly due to its roles in bacterial survival and proliferation in macrophages.
openPC : a toolkit for public cluster with full ownership
Akbar, Z; Hermanto, B; Handoko, L T
2010-01-01
The openPC is a set of open source tools that realizes a parallel machine and distributed computing environment divisible into several independent blocks of nodes, and each of them is remotely but fully in any means accessible for users with a full ownership policy. The openPC components address fundamental issues relating to security, resource access, resource allocation, compatibilities with heterogeneous middlewares, user-friendly and integrated web-based interfaces, hardware control and monitoring systems. These components have been deployed successfully to the LIPI Public Cluster which is open for public use. In this paper, the unique characteristics of openPC due to its rare requirements are introduced, its components and a brief performance analysis are discussed.
Nonparametric Bayesian Clustering of Structural Whole Brain Connectivity in Full Image Resolution
DEFF Research Database (Denmark)
Ambrosen, Karen Marie Sandø; Albers, Kristoffer Jon; Dyrby, Tim B.
2014-01-01
Diffusion magnetic resonance imaging enables measuring the structural connectivity of the human brain at a high spatial resolution. Local noisy connectivity estimates can be derived using tractography approaches and statistical models are necessary to quantify the brain’s salient structural...... organization. However, statistically modeling these massive structural connectivity datasets is a computational challenging task. We develop a high-performance inference procedure for the infinite relational model (a prominent non-parametric Bayesian model for clustering networks into structurally similar...... groups) that defines structural units at the resolution of statistical support. We apply the model to a network of structural brain connectivity in full image resolution with more than one hundred thousand regions (voxels in the gray-white matter boundary) and around one hundred million connections...
A Coupled Hidden Markov Random Field Model for Simultaneous Face Clustering and Tracking in Videos
Wu, Baoyuan
2016-10-25
Face clustering and face tracking are two areas of active research in automatic facial video processing. They, however, have long been studied separately, despite the inherent link between them. In this paper, we propose to perform simultaneous face clustering and face tracking from real world videos. The motivation for the proposed research is that face clustering and face tracking can provide useful information and constraints to each other, thus can bootstrap and improve the performances of each other. To this end, we introduce a Coupled Hidden Markov Random Field (CHMRF) to simultaneously model face clustering, face tracking, and their interactions. We provide an effective algorithm based on constrained clustering and optimal tracking for the joint optimization of cluster labels and face tracking. We demonstrate significant improvements over state-of-the-art results in face clustering and tracking on several videos.
Full-coupled channel approach to S=-2 s-shell hypernuclear systems
Energy Technology Data Exchange (ETDEWEB)
Nemura, H. [Institute of Particle and Nuclear Studies, KEK, Tsukuba 305-0801 (Japan)]. E-mail: hidekatsu.nemura@kek.jp; Shinmura, S. [Department of Information Science, Gifu University, Gifu 501-1193 (Japan); Akaishi, Y. [College of Science and Technology, Nihon University, Funabashi 274-8501 (Japan); Myint, Khin Swe [Department of Physics, Mandalay University, Mandalay (Myanmar)
2005-05-30
We describe full-coupled-channel ab initio calculations among the octet baryons for S=-2 s-shell hypernuclei, {sup 4}{sub {lambda}}{sub {lambda}}H, {sup 5}{sub {lambda}}{sub {lambda}}H and {sup 6}{sub {lambda}}{sub {lambda}}He. The wave function includes {lambda}{lambda}, {lambda}{sigma}, N{xi} and {sigma}{sigma} channels. Minnesota NN, D2' YN and Nijmegen model D simulated YY interactions are used. This is the first attempt to explore the few-body problem of the full-coupled channel scheme for A=4-6, S=-2 multistrangeness hypernuclear systems. Bound state solutions of the {lambda}{lambda} hypernuclei, {sup 4}{sub {lambda}}{sub {lambda}}H, {sup 5}{sub {lambda}}{sub {lambda}}H and {sup 6}{sub {lambda}}{sub {lambda}}He, are obtained.
Pinning cluster synchronization in an array of coupled neural networks under event-based mechanism.
Li, Lulu; Ho, Daniel W C; Cao, Jinde; Lu, Jianquan
2016-04-01
Cluster synchronization is a typical collective behavior in coupled dynamical systems, where the synchronization occurs within one group, while there is no synchronization among different groups. In this paper, under event-based mechanism, pinning cluster synchronization in an array of coupled neural networks is studied. A new event-triggered sampled-data transmission strategy, where only local and event-triggering states are utilized to update the broadcasting state of each agent, is proposed to realize cluster synchronization of the coupled neural networks. Furthermore, a self-triggered pinning cluster synchronization algorithm is proposed, and a set of iterative procedures is given to compute the event-triggered time instants. Hence, this will reduce the computational load significantly. Finally, an example is given to demonstrate the effectiveness of the theoretical results.
Phase correlation and clustering of a nearest neighbour coupled oscillators system
Ei-Nashar, H F
2002-01-01
We investigated the phases in a system of nearest neighbour coupled oscillators before complete synchronization in frequency occurs. We found that when oscillators under the influence of coupling form a cluster of the same time-average frequency, their phases start to correlate. An order parameter, which measures this correlation, starts to grow at this stage until it reaches maximum. This means that a time-average phase locked state is reached between the oscillators inside the cluster of the same time- average frequency. At this strength the cluster attracts individual oscillators or a cluster to join in. We also observe that clustering in averaged frequencies orders the phases of the oscillators. This behavior is found at all the transition points studied.
Directory of Open Access Journals (Sweden)
Rajat K. Chaudhuri
2003-12-01
Full Text Available Abstract: The coupled cluster based linear response theory which is applicable to the direct calculation of atomic and molecular properties are presented and applied to compute the ionization potentials and excitation energies of light and moderately heavy atoms. The eÃ‚Â®ect of electron correlation on the ground and excited states is studied using Hartree-Fock, Dirac-Fock and approximate two-component relativistic spinors.
Precise and full extraction of the coupling-of-mode parameters with periodic Green's function
Institute of Scientific and Technical Information of China (English)
林基明; 吴浩东; 王宁; 仇洪冰; 水永安
2003-01-01
Precise extraction of coupling-of-mode (COM) parameters plays a key role in the design for modern high performance surface acoustic wave (SAW) filters. An accurate and efficient analysis of characteristics for SAW propagating under periodic metal gratings has been developed based on the concept of harmonic admittance and periodic Green's function. Some further improvement is made on the numerical algorithm, such as isolation of the logarithmic singularity, asymptotic simplification of periodic Green's function, and utilization of Chebyshev polynomials as basis functions of the charge distribution. The most important point is extraction of the phase of coupling reflection coefficient by the characteris- tics of standing wave on the edges of stopband. This approach leads to a fast, precise and full extraction of COM parameters. The results and discussions for several materials have been presented.
Panel/full-span free-wake coupled method for unsteady aerodynamics of helicopter rotor blade
Institute of Scientific and Technical Information of China (English)
Tan Jianfeng; Wang Haowen
2013-01-01
A full-span free-wake method is coupled with an unsteady panel method to accurately predict the unsteady aerodynamics of helicopter rotor blades in hover and forward flight.The unsteady potential-based panel method is used to consider aerodynamics of finite thickness multi-bladed rotors,and the full-span free-wake method is applied to simulating dynamics of rotor wake.These methods are tightly coupled through trailing-edge Kutta condition and by converting doublet-wake panels to full-span vortex filaments.A velocity-field integration technique is also adopted to overcome singularity problem during the interaction between the rotor wake and blades.Helicopter rotors including Caradonna-Tung,UH-60A,and AH-1G rotors,are simulated in hover and forward flight to validate the accuracy of this approach.The predicted aerodynamic loads of rotor blades agree well with available measured data and computational fluid dynamics (CFD) results,and the unsteady dynamics of rotor wake is also well simulated.Compared to CFD,the present method obtains accurate results more efficiently and is suitable to rotorcraft aeroelastic analysis.
Eliav, Ephraim; Vilkas, Marius J; Ishikawa, Yasuyuki; Kaldor, Uzi
2005-06-08
The intermediate Hamiltonian (IH) coupled-cluster method makes possible the use of very large model spaces in coupled-cluster calculations without running into intruder states. This is achieved at the cost of approximating some of the IH matrix elements, which are not taken at their rigorous effective Hamiltonian (EH) value. The extrapolated intermediate Hamiltonian (XIH) approach proposed here uses a parametrized IH and extrapolates it to the full EH, with model spaces larger by several orders of magnitude than those possible in EH coupled-cluster methods. The flexibility and resistance to intruders of the IH approach are thus combined with the accuracy of full EH. Various extrapolation schemes are described. A pilot application to the electron affinities (EAs) of alkali atoms is presented, where converged EH results are obtained by XIH for model spaces of approximately 20,000 determinants; direct EH calculations converge only for a one-dimensional model space. Including quantum electrodynamic effects, the average XIH error for the EAs is 0.6 meV and the largest error is 1.6 meV. A new reference estimate for the EA of Fr is proposed at 486+/-2 meV.
Quantum Implementation of Unitary Coupled Cluster for Simulating Molecular Electronic Structure
Shen, Yangchao; Zhang, Shuaining; Zhang, Jing-Ning; Yung, Man-Hong; Kim, Kihwan
2015-01-01
Quantum simulation represents an efficient solution to a certain classically intractable problem in various research area including quantum chemistry. The central problem of quantum chemistry is to determine the electronic structure and the ground-state energy of atoms and molecules. The exact classical calculation of the problem is demanding even for molecules with moderate size due to the "exponential catastrophe." To deal with such quantum chemistry problem, the coupled-cluster methods have been successfully developed, which are considered to be the current "gold standard" in classical computational chemistry. However, the coupled-cluster ansatz is built with non-unitary operation, which leads to drawbacks such as lacking variational bound of ground-state energy. The unitary version of the coupled-cluster methods would perfectly address the problem, whereas it is classically inefficient without proper truncation of the infinite series expansion. It has been a long-standing challenge to build an efficient c...
Wahlen-Strothman, Jacob M; Hermes, Matthew R; Degroote, Matthias; Qiu, Yiheng; Zhao, Jinmo; Dukelsky, Jorge; Scuseria, Gustavo E
2016-01-01
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. 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...
Potential Functions of Al2 by the Relativistic Fock-Space Coupled Cluster Method
Directory of Open Access Journals (Sweden)
Uzi Kaldor
2002-05-01
Full Text Available Abstract: Potential functions of the ground and low excited states of Al2 are calculated by the relativistic Fock-space coupled cluster method in the framework of the projected Dirac-Coulomb Hamiltonian. A moderate-size basis [16s11p3d3f/6s6p3d2f] is used. 3ÃŽÂ u is confirmed as the ground state of the system. Its spin orbit splittings are reproduced well, with the ÃŽÂ› = 1, 2 states lying 32.5 and 66.1 cmÃ¢ÂˆÂ’1, respectively, above the ÃŽÂ› = 0 minimum (experimental values are 30.4 and 63.4 cmÃ¢ÂˆÂ’1. The bond is somewhat too weak, with De 0.14 eV below experiment, Re too high by 0.08 Ã‹ÂšA, and ÃÂ‰e 21 cmÃ¢ÂˆÂ’1 too low. It is speculated that the better agreement obtained in earlier calculations may be due to neglect of basis set superposition errors. The description of bonding in the molecule may be improved by the use of a better basis and the inclusion of more correlation by the intermediate Hamiltonian coupled cluster method, which makes it possible to handle larger P spaces and extend the potential functions to the whole range of internuclear separations.
Shee, Avijit; Visscher, Lucas; Saue, Trond
2016-11-01
We present a formulation and implementation of the calculation of (orbital-unrelaxed) expectation values at the 4-component relativistic coupled cluster level with spin-orbit coupling included from the start. The Lagrangian-based analytical energy derivative technique constitutes the basic theoretical framework of this work. The key algorithms for single reference relativistic coupled cluster have been implemented using routines for general tensor contractions of up to rank-2 tensors in which the direct product decomposition scheme is employed to benefit from double group symmetry. As a sample application, we study the electric field gradient at the bismuth nucleus in the BiX (X = N, P) series of molecules, where the effect of spin-orbit coupling is substantial. Our results clearly indicate that the current reference value for the nuclear quadrupole moment of 209Bi needs revision. We also have applied our method to the calculation of the parity violating energy shift of chiral molecules. The latter property is strictly zero in the absence of spin-orbit coupling. For the H2X2 (X = O,S,Se,Te) series of molecules the effect of correlation is found to be quite small.
Coupled-cluster computations of unbound states in neutron rich calcium isotopes
Hagen, Gaute
2014-09-01
In this talk I will present microscopic coupled-cluster computations of weakly bound and unbound states in the neutron rich calcium region. Starting from state-of-the-art nucleon-nucleon and schematic three-nucleon forces, the role of continuum on ordering of states close to and above the threshold is discussed. In particular several new level orderings are predicted that contrast the naïve shell-model ordering of states. We also discuss the possibility for Efimov physics around the very neutron rich calcium-62 by merging input from coupled-cluster calculations with halo effective-field-theory.
Coupled-cluster calculations of properties of Boron atom as a monovalent system
Gharibnejad, H
2015-01-01
We present relativistic coupled-cluster (CC) calculations of energies, magnetic-dipole hyperfine constants, and electric-dipole transition amplitudes for low-lying states of atomic boron. The trivalent boron atom is computationally treated as a monovalent system. We explore performance of the CC method at various approximations. Our most complete treatment involves singles, doubles and the leading valence triples. The calculations are done using several approximations in the coupled-cluster (CC) method. The results are within 0.2-0.4% of the energy benchmarks. The hyperfine constants are reproduced with 1-2% accuracy.
Communication: Finite size correction in periodic coupled cluster theory calculations of solids
Liao, Ke; Grüneis, Andreas
2016-10-01
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.
Byrd, Jason N; Jin, Yifan; Ranasinghe, Duminda S; Montgomery, John A; Perera, Ajith; Duan, Xiaofeng F; Burggraf, Larry W; Sanders, Beverly A; Bartlett, Rodney J
2016-01-01
The accurate determination of the preferred ${\\rm Si}_{12}{\\rm C}_{12}$ 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 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$_3$ to ${\\rm Si}_{12}{\\rm C}_{12}$. It is found that post-MBPT(2) correlation energy plays a significant role 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 CCSD extrapolation wit...
Clostridium cluster I and their pathogenic members in a full-scale operating biogas plant.
Dohrmann, Anja B; Walz, Meike; Löwen, Achim; Tebbe, Christoph C
2015-04-01
A biogas production plant operating with main and secondary digesters (MD, SD) was analysed for the diversity of bacteria from Clostridium cluster I and its pathogenic members. The plant was run in two parallel lines, both receiving silages, and one, in addition, cattle manure (CM). Quantitative PCR of 16S rRNA genes from directly extracted DNA indicated that cluster I represented 0.2 to 5.6 % of the total bacterial communities. Its prevalence was particularly low in CM and also in SD compared to MD, indicating its decline during fermentation. In contrast, another highly abundant clostridial group, i.e. the "faecal" cluster XIVa, remained quantitatively unaffected during fermentation. A total of 85.1 % of 581,934 rRNA gene sequences gathered by group-specific PCR from the silages, CM and digesters could be assigned to cluster I. All remaining sequences fell into other clostridial groups. The three most dominant operational taxonomic units (OTUs) introduced with CM were from cluster I, and they declined during fermentation. Fermentation with CM significantly increased OTUs of clostridia outside of cluster I but not within. The only OTUs related to pathogens were detected for Clostridium botulinum with 0.18 % of all cluster I sequences in maize silage and less than 0.01 % in the other substrates and digester materials. These OTUs could be assigned to all four established C. botulinum groups, thus, potentially covering all seven neurotoxins. Mouse lethality tests of samples with suspected presence of C. botulinum, however, indicated no toxigenic potential and, thus, no risk associated with the rare occurrence of these OTUs.
Canola, Sofia; Pecoraro, Claudia; Negri, Fabrizia
2016-10-01
Hole transport properties are modeled for two polymorphs of pentacene: the single crystal polymorph and the thin film polymorph relevant for organic thin-film transistor applications. Electronic couplings are evaluated in the standard dimer approach but also considering a cluster approach in which the central molecule is surrounded by a large number of molecules quantum-chemically described. The effective electronic couplings suitable for the parametrization of a tight-binding model are derived either from the orthogonalization scheme limited to HOMO orbitals and from the orthogonalization of the full basis of molecular orbitals. The angular dependent mobilities estimated for the two polymorphs using the predicted pattern of couplings display different anisotropy characteristics as suggested from experimental investigations.
Improved Particle Identification Using Cluster Counting in a Full-Length Drift Chamber Prototype
Caron, Jean-François; Lu, Philip; So, Rocky; Cheaib, Racha; Martin, Jean-Pierre; Faszer, Wayne; Beaulieu, Alexandre; de Jong, Samuel; Roney, Michael; de Sangro, Riccardo; Felici, Giulietto; Finocchiaro, Giuseppe; Piccolo, Marcello
2014-01-01
Single-cell prototype drift chambers were built at TRIUMF and tested with a $\\sim\\unit[210]{MeV/c}$ beam of positrons, muons, and pions. A cluster-counting technique is implemented which improves the ability to distinguish muons and pions when combined with a traditional truncated-mean charge measurement. Several cluster-counting algorithms and equipment variations are tested, all showing significant improvement when combined with the traditional method. The results show that cluster counting is a feasible option for any particle physics experiment using drift chambers for particle identification. The technique does not require electronics with an overly high sampling rate. Optimal results are found with a signal smoothing time of $\\sim\\unit[5]{ns}$ corresponding to a $\\sim\\unit[100]{MHz}$ Nyquist frequency.
KKR-DCA Thermodynamics for Cluster Short-Range Order with Full Charge Self-Consistency
Biava, Dominic A.; Johnson, Duane D.
The Dynamical Cluster Approximation (DCA) implemented in the Korringa-Kohn-Rostoker (KKR) electronic-structure method gives a systematically exact, course-grained theory of the electronic states of substitutionally disordered alloys, including the effects of chemical short-ranged order (SRO). We implement the KKR-DCA within density functional theory (DFT) to calculate directly the charge self-consistent electronic contributions to the alloy grand potential. The KKR-DCA is combined with the chemical entropy from the Cluster Variation Method (CVM), which when minimized predicts the SRO directly. The calculated SRO has been tested in several metallic systems with agreement to measured values. For very large clusters, the KKR-DCA can be sampled, as done within Quantum Monte Carlo, and provides the charge self-consistent thermodynamic grand potential in complex alloys with SRO at finite temperature, at the same level as done for perfect ordered alloys in other electronic-structure methods at zero Kelvin.
Approximating electronically excited states with equation-of-motion linear coupled-cluster theory
Byrd, Jason N; Perera, Ajith; Bartlett, Rodney J
2015-01-01
A new perturbative approach to canonical equation-of-motion coupled-cluster theory is presented using coupled-cluster perturbation theory. A second-order M{\\o}ller-Plesset partitioning of the Hamiltonian is used to obtain the well known equation-of-motion many-body perturbation theory (EOM-MBPT(2)) equations and two new equation-of-motion methods based on the linear coupled-cluster doubles (EOM-LCCD) and linear coupled-cluster singles and doubles (EOM-LCCSD) wavefunctions. This is achieved by performing a short-circuiting procedure on the MBPT(2) similarity transformed Hamiltonian. These new methods are benchmarked against very accurate theoretical and experimental spectra from 25 small organic molecules. It is found that the proposed methods have excellent agreement with canonical EOM-CCSD state for state orderings and relative excited state energies as well as acceptable quantitative agreement for absolute excitation energies compared with the best estimate theory and experimental spectra.
Tang, Ze; Park, Ju H.; Lee, Tae H.
2016-10-01
This paper is devoted to the cluster synchronization issue of nonlinearly coupled Lur'e networks under the distributed adaptive pinning control strategy. The time-varying delayed networks consisted of identical and nonidentical Lur'e systems are discussed respectively by applying the edge-based pinning control scheme. In each cluster, the edges belonging to the spanning tree are pinned. In view of the nonlinearly couplings of the networks, for the first time, an efficient distributed nonlinearly adaptive update law based on the local information of the dynamical behaviors of node is proposed. Sufficient criteria for the achievement of cluster synchronization are derived based on S-procedure, Kronecker product and Lyapunov stability theory. Additionally, some illustrative examples are provided to demonstrate the effectiveness of the theoretical results.
Experimental observation of chimera and cluster states in a minimal globally coupled network
Energy Technology Data Exchange (ETDEWEB)
Hart, Joseph D. [Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, Maryland 20742 (United States); Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Bansal, Kanika [Department of Mathematics, University at Buffalo, SUNY Buffalo, New York 14260 (United States); US Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States); Murphy, Thomas E. [Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, Maryland 20742 (United States); Department of Electrical and Computer Engineering, University of Maryland, College Park, Maryland 20742 (United States); Roy, Rajarshi [Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, Maryland 20742 (United States); Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742 (United States)
2016-09-15
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.
Subharmonic phase clusters in the complex Ginzburg-Landau equation with nonlinear global coupling.
García-Morales, Vladimir; Orlov, Alexander; Krischer, Katharina
2010-12-01
A wide variety of subharmonic n -phase cluster patterns was observed in experiments with spatially extended chemical and electrochemical oscillators. These patterns cannot be captured with a phase model. We demonstrate that the introduction of a nonlinear global coupling (NGC) in the complex Ginzburg-Landau equation has subharmonic cluster pattern solutions in wide parameter ranges. The NGC introduces a conservation law for the oscillatory state of the homogeneous mode, which describes the strong oscillations of the mean field in the experiments. We show that the NGC causes a pronounced 2:1 self-resonance on any spatial inhomogeneity, leading to two-phase subharmonic clustering, as well as additional higher resonances. Nonequilibrium Ising-Bloch transitions occur as the coupling strength is varied.
Spin-Orbit Coupling Effects in AumPtn Clusters (m + n = 4).
Moreno, Norberto; Ferraro, Franklin; Flórez, Elizabeth; Hadad, C Z; Restrepo, Albeiro
2016-03-17
A study of AumPtn(m + n = 4) clusters with and without spin-orbit (SO) coupling using scalar relativistic (SR) and two component methods with the ZORA Hamiltonian was carried out. We employed the PW91 functional in conjunction with the all-electron TZ2P basis set. This paper offers a detailed analysis of the SO effects on the cluster geometries, on the LUMO-HOMO gap, on the charge distribution, and on the relative energies for each relativistic method. In general, SO coupling led to an energetic rearrangement of the species, to changes in geometries and structural preferences, to changes in the structural identity of the global minimum for the Au3Pt, AuPt3 and Pt4 cases, and to a reduction of relative energies among the clusters, an effect that appears stronger as the amount of Pt increases.
Liu, Xiaoming; Mei, Ming; Liu, Jun; Hu, Wei
2015-12-01
Clustered microcalcifications (MCs) in mammograms are an important early sign of breast cancer in women. Their accurate detection is important in computer-aided detection (CADe). In this paper, we integrated the possibilistic fuzzy c-means (PFCM) clustering algorithm and weighted support vector machine (WSVM) for the detection of MC clusters in full-field digital mammograms (FFDM). For each image, suspicious MC regions are extracted with region growing and active contour segmentation. Then geometry and texture features are extracted for each suspicious MC, a mutual information-based supervised criterion is used to select important features, and PFCM is applied to cluster the samples into two clusters. Weights of the samples are calculated based on possibilities and typicality values from the PFCM, and the ground truth labels. A weighted nonlinear SVM is trained. During the test process, when an unknown image is presented, suspicious regions are located with the segmentation step, selected features are extracted, and the suspicious MC regions are classified as containing MC or not by the trained weighted nonlinear SVM. Finally, the MC regions are analyzed with spatial information to locate MC clusters. The proposed method is evaluated using a database of 410 clinical mammograms and compared with a standard unweighted support vector machine (SVM) classifier. The detection performance is evaluated using response receiver operating (ROC) curves and free-response receiver operating characteristic (FROC) curves. The proposed method obtained an area under the ROC curve of 0.8676, while the standard SVM obtained an area of 0.8268 for MC detection. For MC cluster detection, the proposed method obtained a high sensitivity of 92 % with a false-positive rate of 2.3 clusters/image, and it is also better than standard SVM with 4.7 false-positive clusters/image at the same sensitivity.
Tensor-decomposed vibrational coupled-cluster theory
DEFF Research Database (Denmark)
Madsen, Niels Kristian; Godtliebsen, Ian Heide; Christiansen, Ove
can be reduced by decomposing the VCC amplitudes and error vectors to the CANDECOMP/PARAFAC (CP) tensor format. Using the CP format allows us to automatically adapt the size of the parameter space as well as the computational effort to the strength of the physical interactions in the molecule while...... maintaining the same accuracy as the standard VCC method. We have implemented our VCC algorithms and equation solvers such that the VCC equations can be solved without constructing any tensors in full dimension. The tensors are automatically recompressed during the summation of the many terms in the VCC...
Cao, Zhanli; Wang, Fan; Yang, Mingli
2016-10-01
Various approximate approaches to calculate cluster amplitudes in equation-of-motion coupled-cluster (EOM-CC) approaches for ionization potentials (IP) and electron affinities (EA) with spin-orbit coupling (SOC) included in post self-consistent field (SCF) calculations are proposed to reduce computational effort. Our results indicate that EOM-CC based on cluster amplitudes from the approximate method CCSD-1, where the singles equation is the same as that in CCSD and the doubles amplitudes are approximated with MP2, is able to provide reasonable IPs and EAs when SOC is not present compared with CCSD results. It is an economical approach for calculating IPs and EAs and is not as sensitive to strong correlation as CC2. When SOC is included, the approximate method CCSD-3, where the same singles equation as that in SOC-CCSD is used and the doubles equation of scalar-relativistic CCSD is employed, gives rise to IPs and EAs that are in closest agreement with those of CCSD. However, SO splitting with EOM-CC from CC2 generally agrees best with that with CCSD, while that of CCSD-1 and CCSD-3 is less accurate. This indicates that a balanced treatment of SOC effects on both single and double excitation amplitudes is required to achieve reliable SO splitting.
Query Recommendation by Coupling Personalization with Clustering for Search Engine
Directory of Open Access Journals (Sweden)
Dhiliphanrajkumar.Thambidurai
2016-11-01
Full Text Available In the present world internet and web search engines have become an important part in one’s day-today life. For a user query, more than few thousand web pages are retrieved but most of them are irrelevant. A major problem in search engine is that the user queries are usually short and ambiguous, and they are not sufficient to satisfy the precise user needs. Also listing more number of results according to user make them worry about searching the desired results and it takes large amount of time to search from the huge list of results. To overcome all the problems, an effective approach is developed by capturing the users’ click through and bookmarking data to provide personalized query recommendation. For retrieving the results, Google API is used. Experimental results show that the proposed method is providing better query recommendation results than the existing query suggestion methods.
An Efficient Full-Wave Electromagnetic Analysis for Capacitive Body-Coupled Communication
Directory of Open Access Journals (Sweden)
Muhammad Irfan Kazim
2015-01-01
Full Text Available Measured propagation loss for capacitive body-coupled communication (BCC channel (1 MHz to 60 MHz is limitedly available in the literature for distances longer than 50 cm. This is either because of experimental complexity to isolate the earth-ground or design complexity in realizing a reliable communication link to assess the performance limitations of capacitive BCC channel. Therefore, an alternate efficient full-wave electromagnetic (EM simulation approach is presented to realistically analyze capacitive BCC, that is, the interaction of capacitive coupler, the human body, and the environment all together. The presented simulation approach is first evaluated for numerical/human body variation uncertainties and then validated with measurement results from literature, followed by the analysis of capacitive BCC channel for twenty different scenarios. The simulation results show that the vertical coupler configuration is less susceptible to physiological variations of underlying tissues compared to the horizontal coupler configuration. The propagation loss is less for arm positions when they are not touching the torso region irrespective of the communication distance. The propagation loss has also been explained for complex scenarios formed by the ground-plane and the material structures (metals or dielectrics with the human body. The estimated propagation loss has been used to investigate the link-budget requirement for designing capacitive BCC system in CMOS sub-micron technologies.
Yue, Tongtao; Zhang, Xianren
2012-01-01
One key question in signal transduction is how the signal is relayed from the outer leaflet of a cellular membrane to the inner leaflet. Using a simulation model, a mechanism for the mediation of signal transduction is proposed here in which the coupling between membrane proteins in different leaflets can be achieved by the clustering of anchored proteins, without recruiting transmembrane proteins. Depending on the hydrophobic length of the anchored proteins, three coupling patterns, including face-to-face clustering, interdigitated clustering, and weak-coupled clustering, are observed in this work. This observation provides a possible explanation of how a particular downstream signaling pathway is selected.
Full extremal process, cluster law and freezing for two-dimensional discrete Gaussian Free Field
Biskup, Marek; Louidor, Oren
2016-01-01
We study the extremal process associated with the Discrete Gaussian Free Field (DGFF) in scaled-up (square-)lattice versions of bounded open planar domains subject to mild regularity conditions on the boundary. We prove that, in the scaling limit, this process tends to a Cox process decorated by independent, correlated clusters whose distribution is completely characterized. As an application, we control the scaling limit of the discrete supercritical Liouville measure, extract a Poisson-Diri...
Scalable fault tolerant algorithms for linear-scaling coupled-cluster electronic structure methods.
Energy Technology Data Exchange (ETDEWEB)
Leininger, Matthew L.; Nielsen, Ida Marie B.; Janssen, Curtis L.
2004-10-01
By means of coupled-cluster theory, molecular properties can be computed with an accuracy often exceeding that of experiment. The high-degree polynomial scaling of the coupled-cluster method, however, remains a major obstacle in the accurate theoretical treatment of mainstream chemical problems, despite tremendous progress in computer architectures. Although it has long been recognized that this super-linear scaling is non-physical, the development of efficient reduced-scaling algorithms for massively parallel computers has not been realized. We here present a locally correlated, reduced-scaling, massively parallel coupled-cluster algorithm. A sparse data representation for handling distributed, sparse multidimensional arrays has been implemented along with a set of generalized contraction routines capable of handling such arrays. The parallel implementation entails a coarse-grained parallelization, reducing interprocessor communication and distributing the largest data arrays but replicating as many arrays as possible without introducing memory bottlenecks. The performance of the algorithm is illustrated by several series of runs for glycine chains using a Linux cluster with an InfiniBand interconnect.
Byrd, Jason N.; Lutz, Jesse J.; Jin, Yifan; Ranasinghe, Duminda S.; Montgomery, John A.; Perera, Ajith; Duan, Xiaofeng F.; Burggraf, Larry W.; Sanders, Beverly A.; Bartlett, Rodney J.
2016-07-01
The accurate determination of the preferred Si12C12 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 SiC3 to Si12C12. It is found that post-MBPT(2) correlation energy plays a significant role 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 Si12C12 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.
The Application of High-Level Iterative Coupled-Cluster Methods to the Cytosine Molecule
Energy Technology Data Exchange (ETDEWEB)
Kowalski, Karol; Valiev, Marat
2008-06-19
The need for inclusion higher-order correlation effects for adequate description of the excitation energies of the DNA bases became clear in the last few years. In particular, we demonstrated that there is a sizable effect of triply excited configurations estimated in a non-iterative manner on the coupled-cluster excitation energies of the cytosine molecule in DNA environment. In this paper we discuss the accuracies of the non-iterative methods for biologically relevant systems in realistic environment in comparison with interative formulations that explicitly include the effect of triply excited clusters.
Brabec, Jiri; Banik, Subrata; Kowalski, Karol; Pittner, Jiří
2016-10-01
In this work, we report an extension of our previous development of the universal state-selective (USS) multireference coupled-cluster (MRCC) formalism. It was shown [Brabec et al., J. Chem. Phys. 136, 124102 (2012)] and [Banik et al., J. Chem. Phys. 142, 114106 (2015)] that the USS(2) approach significantly improves the accuracy of Brillouin-Wigner and Mukherjee MRCC formulations, however, the numerical and storage costs associated with calculating highly excited intermediates pose a significant challenge, which can restrict the applicability of the USS(2) method. Therefore, we introduce a perturbative variant of the USS(2) approach (USS(pt)), which substantially reduces numerical overhead of the full USS(2) correction while preserving its accuracy. Since the new USS(pt) implementation calculates the triple and quadruple projections in on-the-fly manner, the memory bottleneck associated with the need of storing expensive recursive intermediates is entirely eliminated. On the example of several benchmark systems, we demonstrate accuracies of USS(pt) and USS(2) approaches and their efficiency in describing quasidegenerate electronic states. It is also shown that the USS(pt) method significantly alleviates problems associated with the lack of invariance of MRCC theories upon the rotation of active orbitals.
Full-Eulerian fluid-structure coupling simulation of hyperelastic channel flow
Nagano, Naohiro; Sugiyama, Kazuyasu; Takeuchi, Shintaro; Satoshi, II; Takagi, Shu; Matsumoto, Yoichiro
2010-11-01
A full-Eulerian simulation for coupling a Newtonian fluid and hyperelastic material is conducted. The system involves an interaction problem between the fluid and hyperelastic walls and is driven by pressure difference, mimicking a blood flow in a blood vessel. A single set of the governing equations for the fluid and solid is employed, and a volume-of-fluid idea is employed to describe a multi-component geometry. The solid stress is defined in Eulerian frame by using a left Cauchy-Green deformation tensor, and the temporal change in the solid deformation is described by updating the tensor. The method employs a uniform fixed grid system for both fluid and solid and it does not require any mesh generation or reconstruction, aiming at facilitating the practical bio-mechanical fluid-structure analysis based on a medical image. The validity of the simulation results is established through comparison with a theoretical prediction. As an application of the present method, pulsating flows are simulated to demonstrate a nonlinear behavior of the flow rate on the pulsating amplitude, and an effect of employing an anisotropic hyperelastic material is discussed.
Hot Zero and Full Power Validation of PHISICS RELAP-5 Coupling
Energy Technology Data Exchange (ETDEWEB)
F. Lodi; C. Rabiti; A. Alfonsi; A. Epiney; M. Sumini
2013-06-01
PHISICS is a reactor analysis toolkit developed in the last 3 years at the Idaho National Laboratory that has been also coupled with the thermo-hydraulic plant simulator RELAP5-3D. PHISICS is aimed to provide an optimal trade off between needed computational resources and accuracy in the range of 10~100 cores. In fact this range has been identified as the next 5 to 10 years average computational capability available to nuclear engineer designing and optimizing nuclear reactor cores. Different publication has been already presented [1] showing test of the single modules composing the PHISICS package. Lately the Idaho National Laboratory had the opportunity to access to plant data for the first cycle of a PWR including Hot Zero Power (HZP) and Hot Full Power (HFP). This data provided the opportunity to validate the transport solver, the interpolation capability for mixed macro and micro cross section and the criticality search option of the PHISICS package. In the following we will firstly recall briefly the structure of the different PHISICS modules and then we will illustrate the modeling process and some preliminary results.
Directory of Open Access Journals (Sweden)
Bo Jarneving
2007-01-01
Full Text Available In this study a novel method of science mapping is presented which combines bibliographic coupling, as a measure of document-document similarity, with an agglomerative hierarchical cluster method. The focus in this study is on the mapping of so called ‘core documents’, a concept presented first in 1995 by Glänzel and Czerwon. The term ‘core document’ denote documents that have a central position in the research front in terms of many and strong bibliographic coupling links. The identification and mapping of core documents usually requires a large multidisciplinary research setting and in this study the 2003 volume of the Science Citation Index was applied. From this database, a sub-set of core documents reporting on the outbreak of SARS in 2002 was chosen for the demonstration of the application of this mapping method. It was demonstrated that the method, in this case, successfully identified interpretable research themes and that iterative clustering on two subsequent levels of cluster agglomeration may provide with useful and current information.
Bertolami, Orfeu; Páramos, Jorge
2011-01-01
In this work, one shows that a specific non-minimal coupling between the scalar curvature and matter can mimic the dark matter component of relaxed galaxy clusters. For this purpose, one assesses the Abell Cluster A586, a massive strong-lensing nearby relaxed cluster of galaxies in virial equilibrium, where direct mass estimates are possible. The total density, which generally follows a cusped profile and reveals a very small baryonic component, can be effectively described within this framework.
Energy Technology Data Exchange (ETDEWEB)
Wang, Z.M. [Institute of Theoretical Physics and Department of Physics, Shanxi University, Taiyuan 030006 (China); Xue, H.B. [College of Physics and Optoelectronics, Taiyuan University of Technology, Taiyuan 030024 (China); Xue, N.T. [Institute of Theoretical Physics and Department of Physics, Shanxi University, Taiyuan 030006 (China); Liang, J.-Q., E-mail: jqliang@sxu.edu.cn [Institute of Theoretical Physics and Department of Physics, Shanxi University, Taiyuan 030006 (China)
2015-02-15
We study the full counting statistics of transport electrons through a semiconductor two-level quantum dot with Rashba spin–orbit (SO) coupling, which acts as a nonabelian gauge field and thus induces the electron transition between two levels along with the spin flip. By means of the quantum master equation approach, shot noise and skewness are obtained at finite temperature with two-body Coulomb interaction. We particularly demonstrate the crucial effect of SO coupling on the super-Poissonian fluctuation of transport electrons, in terms of which the SO coupling can be probed by the zero-frequency cumulants. While the charge currents are not sensitive to the SO coupling.
Nonequilibrium dynamics of polariton entanglement in a cluster of coupled traps
Energy Technology Data Exchange (ETDEWEB)
Quiroga, L [Departamento de Fisica, Universidad de Los Andes, A.A.4976, Bogota D.C. (Colombia); Tejedor, C, E-mail: lquiroga@uniandes.edu.c [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, Cantoblanco, E-28049, Madrid (Spain)
2009-05-01
We study in detail the generation and relaxation of quantum coherences (entanglement) in a system of coupled polariton traps. By exploiting a Lie algebraic based super-operator technique we provide an analytical exact solution for the Markovian dissipative dynamics (Master equation) of such system which is valid for arbitrary cluster size, polariton-polariton interaction strength, temperature and initial state. Based on the exact solution of the Master equation at T = OK, we discuss how dissipation affects the quantum entanglement dynamics of coupled polariton systems.
Sizeable Kane-Mele-like spin orbit coupling in graphene decorated with iridium clusters
Qin, Yuyuan; Wang, Siqi; Wang, Rui; Bu, Haijun; Wang, Xuefeng; Wang, Xinran; Song, Fengqi; Wang, Baigeng; Wang, Guanghou
2016-05-01
The spin-orbit coupling strength of graphene can be enhanced by depositing iridium nanoclusters. Weak localization is intensely suppressed near zero fields after the cluster deposition, rather than changing to weak anti-localization. Fitting the magnetoresistance gives the spin relaxation time, which increases by two orders with the application of a back gate. The spin relaxation time is found to be proportional to the electronic elastic scattering time, demonstrating the Elliot-Yafet spin relaxation mechanism. A sizeable Kane-Mele-like coupling strength of over 5.5 meV is determined by extrapolating the temperature dependence to zero.
Symmetry broken and restored coupled-cluster theory: II. Global gauge symmetry and particle number
Duguet, T.; Signoracci, A.
2017-01-01
We have recently extended many-body perturbation theory (MBPT) and coupled-cluster theory performed on top of a Slater determinant breaking rotational symmetry to allow for the restoration of the angular momentum at any truncation order (Duguet 2015 J. Phys. G: Nucl. Part. Phys. 42 025107). Following a similar route, we presently extend Bogoliubov MBPT and Bogoliubov coupled cluster theory performed on top of a Bogoliubov reference state breaking global gauge symmetry to allow for the restoration of the particle number at any truncation order. Eventually, formalisms can be merged to handle SU(2) and U(1) symmetries at the same time. The long-term goal relates to the ab initio description of near-degenerate finite quantum systems with an open-shell character.
Orbital spaces in the divide-expand-consolidate coupled cluster method
Ettenhuber, Patrick; Baudin, Pablo; Kjærgaard, Thomas; Jørgensen, Poul; Kristensen, Kasper
2016-04-01
The theoretical foundation for solving coupled cluster singles and doubles (CCSD) amplitude equations to a desired precision in terms of independent fragment calculations using restricted local orbital spaces is reinvestigated with focus on the individual error sources. Four different error sources are identified theoretically and numerically and it is demonstrated that, for practical purposes, local orbital spaces for CCSD calculations can be identified from calculations at the MP2 level. The development establishes a solid theoretical foundation for local CCSD calculations for the independent fragments, and thus for divide-expand-consolidate coupled cluster calculations for large molecular systems with rigorous error control. Based on this theoretical foundation, we have developed an algorithm for determining the orbital spaces needed for obtaining the single fragment energies to a requested precision and numerically demonstrated the robustness and precision of this algorithm.
NOx Catalyzed Pathway of Stratospheric Ozone Depletion: A Coupled Cluster Investigation.
Dutta, Achintya Kumar; Vaval, Nayana; Pal, Sourav
2012-06-12
We report a theoretical investigation on the NOx catalyzed pathways of stratospheric ozone depletion using highly accurate coupled cluster methods. These catalytic reactions represent a great challenge to state-of-the-art ab initio methods, while their mechanisms remain unclear to both experimentalists and theoreticians. In this work, we have used the so-called "gold standard of quantum chemistry," the CCSD(T) method, to identify the saddle points on NOx-based reaction pathways of ozone hole formation. Energies of the saddle points are calculated using the multireference variants of coupled cluster methods. The calculated activation energies and rate constants show good agreement with available experimental results. Tropospheric precursors to stratospheric NOx radicals have been identified, and their potential importance in stratospheric chemistry has been discussed. Our calculations resolve previous conflicts between ab initio and experimental results for a trans nitro peroxide intermediate, in the NOx catalyzed pathway of ozone depletion.
Emergent organization of oscillator clusters in coupled self-regulatory chaotic maps
Indian Academy of Sciences (India)
Hiroyasu Ando; Sudeshna Sinha; Kazuyuki Aihara
2008-06-01
Here we introduce a model of parametrically coupled chaotic maps on a one-dimensional lattice. In this model, each element has its internal self-regulatory dynamics, whereby at fixed intervals of time the nonlinearity parameter at each site is adjusted by feedback from its past evolution. Additionally, the maps are coupled sequentially and unidirectionally, to their nearest neighbor, through the difference of their parametric variations. Interestingly we find that this model asymptotically yields clusters of superstable oscillators with different periods. We observe that the sizes of these oscillator clusters have a power-law distribution. Moreover, we find that the transient dynamics gives rise to a 1/ power spectrum. All these characteristics indicate self-organization and emergent scaling behavior in this system. We also interpret the power-law characteristics of the proposed system from an ecological point of view.
Linear scaling coupled cluster and perturbation theories in the atomic orbital basis
Scuseria, Gustavo E.; Ayala, Philippe Y.
1999-11-01
We present a reformulation of the coupled cluster equations in the atomic orbital (AO) basis that leads to a linear scaling algorithm for large molecules. Neglecting excitation amplitudes in a screening process designed to achieve a target energy accuracy, we obtain an AO coupled cluster method which is competitive in terms of number of amplitudes with the traditional molecular orbital (MO) solution, even for small molecules. For large molecules, the decay properties of integrals and excitation amplitudes becomes evident and our AO method yields a linear scaling algorithm with respect to molecular size. We present benchmark calculations to demonstrate that our AO reformulation of the many-body electron correlation problem defeats the "exponential scaling wall" that has characterized high-level MO quantum chemistry calculations for many years.
Energy Technology Data Exchange (ETDEWEB)
Peng, Bo; Govind, Niranjan; Aprà, Edoardo; Klemm, Michael; Hammond, Jeff R.; Kowalski, Karol
2017-02-03
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 of 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.
Quantum implementation of the unitary coupled cluster for simulating molecular electronic structure
Shen, Yangchao; Zhang, Xiang; Zhang, Shuaining; Zhang, Jing-Ning; Yung, Man-Hong; Kim, Kihwan
2017-02-01
In classical computational chemistry, the coupled-cluster ansatz is one of the most commonly used ab initio methods, which is critically limited by its nonunitary nature. The unitary modification as an ideal solution to the problem is, however, extremely inefficient in classical conventional computation. Here, we provide experimental evidence that indeed the unitary version of the coupled-cluster ansatz can be reliably performed in a physical quantum system, a trapped-ion system. We perform a simulation on the electronic structure of a molecular ion (HeH+), where the ground-state energy surface curve is probed, the energies of the excited states are studied, and bond dissociation is simulated nonperturbatively. Our simulation takes advantages from quantum computation to overcome the intrinsic limitations in classical computation, and our experimental results indicate that the method is promising for preparing molecular ground states for quantum simulations.
Analytic evaluation of the dipole Hessian matrix in coupled-cluster theory
Jagau, Thomas-C.; Gauss, Jürgen; Ruud, Kenneth
2013-10-01
The general theory required for the calculation of analytic third energy derivatives at the coupled-cluster level of theory is presented and connected to preceding special formulations for hyperpolarizabilities and polarizability gradients. Based on our theory, we have implemented a scheme for calculating the dipole Hessian matrix in a fully analytical manner within the coupled-cluster singles and doubles approximation. The dipole Hessian matrix is the second geometrical derivative of the dipole moment and thus a third derivative of the energy. It plays a crucial role in IR spectroscopy when taking into account anharmonic effects and is also essential for computing vibrational corrections to dipole moments. The superior accuracy of the analytic evaluation of third energy derivatives as compared to numerical differentiation schemes is demonstrated in some pilot calculations.
Bhaskaran-Nair, Kiran; Kowalski, Karol
2013-05-28
The universal state selective (USS) multireference approach is used to construct new energy functionals which offer a 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 employing a MRCC trial wavefunction. Special cases of the USS formulations, which utilize single reference state specific CC [V. V. Ivanov, D. I. Lyakh, and L. Adamowicz, Phys. Chem. Chem. Phys. 11, 2355 (2009)] and tailored CC [T. Kinoshita, O. Hino, and R. J. Bartlett, J. Chem. Phys. 123, 074106 (2005)] expansions are also discussed.
Energy Technology Data Exchange (ETDEWEB)
Ku, Wai Lim; Girvan, Michelle; Ott, Edward [Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, Maryland 20742 (United States)
2015-12-15
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.
Communication: Coupled-cluster interpretation of the photoelectron spectrum of Au{sub 3}{sup −}
Energy Technology Data Exchange (ETDEWEB)
Bauman, Nicholas P.; Piecuch, Piotr, E-mail: piecuch@chemistry.msu.edu [Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 (United States); Hansen, Jared A. [Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 (United States); Institute for Molecular Science and Research Center for Computational Science, Okazaki 444-8585 (Japan); Ehara, Masahiro, E-mail: ehara@ims.ac.jp [Institute for Molecular Science and Research Center for Computational Science, Okazaki 444-8585 (Japan); Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8245 (Japan)
2014-09-14
We use the scalar relativistic ionized equation-of-motion coupled-cluster approaches, correlating valence and semi-core electrons and including up to 3-hole-2-particle terms in the ionizing operator, to investigate the photoelectron spectrum of Au{sub 3}{sup −}. We provide an accurate assignment of peaks and shoulders in the experimental photoelectron spectrum of Au{sub 3}{sup −} for the first time.
Critical slowing down of cluster algorithms for Ising models coupled to 2-d gravity
Bowick, Mark; Falcioni, Marco; Harris, Geoffrey; Marinari, Enzo
1994-02-01
We simulate single and multiple Ising models coupled to 2-d gravity using both the Swendsen-Wang and Wolff algorithms to update the spins. We study the integrated autocorrelation time and find that there is considerable critical slowing down, particularly in the magnetization. We argue that this is primarily due to the local nature of the dynamical triangulation algorithm and to the generation of a distribution of baby universes which inhibits cluster growth.
Critical Slowing Down of Cluster Algorithms for Ising Models Coupled to 2-d Gravity
Bowick, M; Harris, G; Marinari, E
1994-01-01
We simulate single and multiple Ising models coupled to 2-d gravity using both the Swendsen-Wang and Wolff algorithms to update the spins. We study the integrated autocorrelation time and find that there is considerable critical slowing down, particularly in the magnetization. We argue that this is primarily due to the local nature of the dynamical triangulation algorithm and to the generation of a distribution of baby universes which inhibits cluster growth.
Sharma, Sandeep; Alavi, Ali
2015-01-01
We propose a multireference linearized coupled cluster theory using matrix product states (MPS-LCC) which provides remarkably accurate ground-state energies, at a computational cost that has the same scaling as multireference configuration interaction singles and doubles (MRCISD), for a wide variety of electronic Hamiltonians. These range from first-row dimers at equilibrium and stretched geometries, to highly multireference systems such as the chromium dimer and lattice models such as period...
Transition properties from the Hermitian formulation of the coupled cluster polarization propagator
Energy Technology Data Exchange (ETDEWEB)
Tucholska, Aleksandra M., E-mail: tuchol@tiger.chem.uw.edu.pl; Modrzejewski, Marcin; Moszynski, Robert [Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw (Poland)
2014-09-28
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.
Itagaki, N.; Matsuno, H.; Suhara, T.
2016-09-01
The antisymmetrized quasi-cluster model (AQCM) is a method to describe transitions from the α cluster wave functions to jj-coupling shell model wave functions. In this model, the cluster-shell transition is characterized by only two parameters: R representing the distance between α clusters and Λ describing the breaking of α clusters. The contribution of the spin-orbit interaction, very important in the jj-coupling shell model, can be taken into account starting with the α cluster model wave function. In this article we show the generality of AQCM by extending the application to heavier regions: various 4N nuclei from 4He to 100Sn. The characteristic magic numbers of the jj-coupling shell model, 28 and 50, are described starting with the α cluster model. The competition of two different configurations is discussed in 20Ne (16O + one quasi-cluster and 12C + two quasi-clusters) and 28Si (pentagon shape of five quasi-clusters and 12C + 16O). Also, we compare the energy curves for the α + 40Ca cluster configuration calculated with and without the α breaking effect in 44Ti.
Dynamically coupling the full Stokes equations and the SIA - the ISCAL method
Ahlkrona, Josefin; Lötstedt, Per; Zwinger, Thomas
2016-04-01
The ISCAL (Ice Sheet Coupled Approximation Level) is a new method for computing ice sheet flow, implemented in the community ice-sheet model Elmer/Ice. ISCAL combines the exact Stokes equations with the set of equations obained applying the Shallow Ice Approximation (SIA), confining the computationally cheap SIA to only those areas where it is accurate enough. The coupling is done dynamically and is based on SIA error estimates. In this way, the simulation times are significantly reduced, while the user has control over the error introduced by the approximations applied. Accuracy and efficiency is demonstrated using synthetic set-ups as well as for the Greenland Ice Sheet.
Tucholska, Aleksandra; Moszynski, Robert
2016-01-01
We introduce a new method for the computation of the transition moments between the excited electronic states based on the expectation value formalism of the coupled cluster theory [B. Jeziorski and R. Moszynski, Int. J. Quant. Chem. 48, 161 (1993)]. The working expressions of the new method solely employ the coupled cluster amplitudes. In the approximation adopted in the present paper the cluster expansion is limited to single, double, and linear triple excitations. The computed dipole transition probabilities for the singlet-singlet and triplet-triplet transitions in alkali earth atoms agree well with the available theoretical and experimental data. In contrast to the existing coupled cluster response theory, the matrix elements obtained by using our approach satisfy the Hermitian symmetry even if the excitations in the cluster operator are truncated. As a part of the numerical evidence for the new method, we report calculations of the transition moments between the excited triplet states which have not yet...
Full scale ambient water flow tests of a 10-inch emergency release coupling for LNG transfer
Putte, L.J. van der; Webber, T.; Bokhorst, E. van; Revell, C.
2016-01-01
For LNG transfer in ship-to-ship and ship-to-shore configurations emergency release couplings (F.RC) in combination with loading arms and multi-composite hoses are applied In view of a demand for increasing transfer flow rates in offshore LNG applications a 10-inch ERC has been developed intended fo
Full-time working couples in the Netherlands : causes and consequences
Gils, Wouter Sebastiaan van
2007-01-01
The past decades have shown a dramatic increase in women's labour force participation in the Netherlands. Not only did this change the traditional division of labour within Dutch families, it also instigated the emergence of dual-earner couples. Households with two working spouses raised significant
Zhang, Yifan
2016-08-18
For face naming in TV series or movies, a typical way is using subtitles/script alignment to get the time stamps of the names, and tagging them to the faces. We study the problem of face naming in videos when subtitles are not available. To this end, we divide the problem into two tasks: face clustering which groups the faces depicting a certain person into a cluster, and name assignment which associates a name to each face. Each task is formulated as a structured prediction problem and modeled by a hidden conditional random field (HCRF) model. We argue that the two tasks are correlated problems whose outputs can provide prior knowledge of the target prediction for each other. The two HCRFs are coupled in a unified graphical model called coupled HCRF where the joint dependence of the cluster labels and face name association is naturally embedded in the correlation between the two HCRFs. We provide an effective algorithm to optimize the two HCRFs iteratively and the performance of the two tasks on real-world data set can be both improved.
Revisiting the bound on axion-photon coupling from globular clusters.
Ayala, Adrian; Domínguez, Inma; Giannotti, Maurizio; Mirizzi, Alessandro; Straniero, Oscar
2014-11-07
We derive a strong bound on the axion-photon coupling g(aγ) from the analysis of a sample of 39 Galactic Globular Clusters. As recognized long ago, the R parameter, i.e., the number ratio of stars in horizontal over red giant branch of old stellar clusters, would be reduced by the axion production from photon conversions occurring in stellar cores. In this regard, we have compared the measured R with state-of-the-art stellar models obtained under different assumptions for g(aγ). We show that the estimated value of g(aγ) substantially depends on the adopted He mass fraction Y, an effect often neglected in previous investigations. Taking as a benchmark for our study the most recent determinations of the He abundance in H ii regions with O/H in the same range of the Galactic Globular Clusters, we obtain an upper bound g(aγ)axion-photon coupling in a wide mass range.
CLASH: MASS DISTRIBUTION IN AND AROUND MACS J1206.2-0847 FROM A FULL CLUSTER LENSING ANALYSIS
Energy Technology Data Exchange (ETDEWEB)
Umetsu, Keiichi; Koch, Patrick M.; Lin, Kai-Yang [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 10617, Taiwan (China); Medezinski, Elinor [Department of Physics and Astronomy, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Nonino, Mario [INAF/Osservatorio Astronomico di Trieste, via G. B. Tiepolo 11, 34143 Trieste (Italy); Merten, Julian; Mroczkowski, Tony [Jet Propulsion Laboratory, California Institute of Technology, MS 169-327, Pasadena, CA 91109 (United States); Zitrin, Adi [Institut fuer Theoretische Astrophysik, ZAH, Heidelberg (Germany); Molino, Alberto [Instituto de Astrofisica de Andalucia (CSIC), Granada (Spain); Grillo, Claudio [Dark Cosmology Centre, Niels Bohr Institute, University of Copenhagen, Juliane Mariesvej 30, DK-2100 Copenhagen (Denmark); Carrasco, Mauricio [Centro de Astro-Ingenieria, Departamento de Astronomia y Astrofisica, Pontificia Universidad Catolica de Chile, V. Mackenna 4860, Santiago (Chile); Donahue, Megan [Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824 (United States); Mahdavi, Andisheh [Department of Physics and Astronomy, San Francisco State University, Thornton Hall 527, CA (United States); Coe, Dan; Postman, Marc; Koekemoer, Anton [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21208 (United States); Czakon, Nicole; Sayers, Jack; Golwala, Sunil [Division of Physics, Math, and Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Molnar, Sandor M., E-mail: keiichi@asiaa.sinica.edu.tw [LeCosPA Center, National Taiwan University, Taipei 10617, Taiwan (China); and others
2012-08-10
We derive an accurate mass distribution of the galaxy cluster MACS J1206.2-0847 (z = 0.439) from a combined weak-lensing distortion, magnification, and strong-lensing analysis of wide-field Subaru BVR{sub c} I{sub c} z' imaging and our recent 16-band Hubble Space Telescope observations taken as part of the Cluster Lensing And Supernova survey with Hubble program. We find good agreement in the regions of overlap between several weak- and strong-lensing mass reconstructions using a wide variety of modeling methods, ensuring consistency. The Subaru data reveal the presence of a surrounding large-scale structure with the major axis running approximately northwest-southeast (NW-SE), aligned with the cluster and its brightest galaxy shapes, showing elongation with a {approx}2: 1 axis ratio in the plane of the sky. Our full-lensing mass profile exhibits a shallow profile slope dln {Sigma}/dln R {approx} -1 at cluster outskirts (R {approx}> 1 Mpc h{sup -1}), whereas the mass distribution excluding the NW-SE excess regions steepens farther out, well described by the Navarro-Frenk-White form. Assuming a spherical halo, we obtain a virial mass M{sub vir} = (1.1 {+-} 0.2 {+-} 0.1) Multiplication-Sign 10{sup 15} M{sub Sun} h{sup -1} and a halo concentration c{sub vir} = 6.9 {+-} 1.0 {+-} 1.2 (c{sub vir} {approx} 5.7 when the central 50 kpc h{sup -1} is excluded), which falls in the range 4 {approx}< (c) {approx}< 7 of average c(M, z) predictions for relaxed clusters from recent {Lambda} cold dark matter simulations. Our full-lensing results are found to be in agreement with X-ray mass measurements where the data overlap, and when combined with Chandra gas mass measurements, they yield a cumulative gas mass fraction of 13.7{sup +4.5}{sub -3.0}% at 0.7 Mpc h{sup -1}( Almost-Equal-To 1.7 r{sub 2500}), a typical value observed for high-mass clusters.
Jaros, Jiri; Treeby, Bradley E
2014-01-01
Model-based treatment planning and exposimetry for high-intensity focused ultrasound (HIFU) requires the numerical simulation of nonlinear ultrasound propagation through heterogeneous and absorbing media. This is a computationally demanding problem due to the large distances travelled by the ultrasound waves relative to the wavelength of the highest frequency harmonic. Here, the k-space pseudospectral method is used to solve a set of coupled partial differential equations equivalent to a generalised Westervelt equation. The model is implemented in C++ and parallelised using the message passing interface (MPI) for solving large-scale problems on distributed clusters. The domain is partitioned using a 1D slab decomposition, and global communication is performed using a sparse communication pattern. Operations in the spatial frequency domain are performed in transposed space to reduce the communication burden imposed by the 3D fast Fourier transform. The performance of the model is evaluated using grid sizes up ...
Solution behaviors in coupled Schrödinger equations with full-modulated nonlinearities
Pınar, Zehra; Deliktaş, Ekin
2017-02-01
The nonlinear partial differential equations have an important role in real life problems. To obtain the exact solutions of the nonlinear partial differential equations, a number of approximate methods are known in the literature. In this work, a time- space modulated nonlinearities of coupled Schrödinger equations are considered. We provide a large class of Jacobi-elliptic solutions via the auxiliary equation method with sixth order nonlinearity and the Chebyshev approximation.
Cluster synchronization in networks of identical oscillators with α -function pulse coupling
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.
DEFF Research Database (Denmark)
List, Nanna Holmgaard; Coriani, Sonia; Kongsted, Jacob
2014-01-01
We present an extension of a previously reported implementation of a Lanczos-driven coupled-cluster (CC) damped linear response approach to molecules in condensed phases, where the effects of a surrounding environment are incorporated by means of the polarizable embedding formalism. We...... are specifically motivated by a twofold aim: (i) computation of core excitations in realistic surroundings and (ii) examination of the effect of the differential response of the environment upon excitation solely related to the CC multipliers (herein denoted the J matrix) in computations of excitation energies...
Coupled-cluster interpretation of the photoelectron spectrum of Ag3 (.).
Bauman, Nicholas P; Hansen, Jared A; Piecuch, Piotr
2016-08-28
We use the scalar relativistic ionized equation-of-motion coupled-cluster (IP-EOMCC) approaches to investigate the photoelectron spectrum of Ag3 (-), examining the effects of basis set, number of correlated electrons, level of applied theory including up to 3-hole-2-particle terms, and geometry relaxation. By employing an IP-EOMCC-based extrapolation scheme, we are able to provide an accurate interpretation and complete assignment of peaks and other key features in the experimentally observed spectra, including electron binding energies as high as about 6.5 eV.
Momose, Takamasa; Yamaguchi, Makoto; Shida, Tadamasa
1990-11-01
Following the previous work on the isotropic hyperfine coupling constants (HFCCs) of polyatomic radicals the symmetry adapted cluster expansion-configuration interaction (SAC-CI) theory is applied to calculate anisotropic HFCCs also. The results are compared with available experimental data from diatomic to polyatomic radicals such as the vinoxy. For radicals consisting of only the first row atoms Dunning's double zeta (DZ) basis set is shown to be adequate, but for those containing the second row atoms inclusion of polarization functions is required. Compared with the isotropic HFCC the calculation of the anisotropic HFCC is less formidable. However, ignorance of electron correlation causes serious disagreements with experimental data.
Coupled-cluster theory of a gas of strongly-interacting electrons in the dilute limit
Energy Technology Data Exchange (ETDEWEB)
Mihaila, Bodgan [Los Alamos National Laboratory; Cardenas, Andres L [Los Alamos National Laboratory
2008-01-01
We study the ground-state properties of a dilute gas of strongly-interacting fermions in the framework of the coupled-cluster expansion (CCE). We demonstrate that properties such as universality, opening of a gap in the excitation spectrum and applicability of s-wave approximations appear naturally in the CCE approach. In the zero-density limit, we show that the ground-state energy density depends on only one parameter which in turn may depend at most on the spatial dimensionality of the system.
Singlet-triplet gaps in substituted carbenes predicted from block-correlated coupled cluster method
Institute of Scientific and Technical Information of China (English)
2008-01-01
The block correlated coupled cluster (BCCC) method, with the complete active-space self-consistent-field (CASSCF) reference function, has been applied to investigating the singlet-triplet gaps in several substituted carbenes including four halocarbenes (CHCl, CF2, CCl2, and CBr2) and two hydroxycar-benes (CHOH and C(OH)2). A comparison of our results with the experimental data and other theoretical estimates shows that the present approach can provide quantitative descriptions for all the studied carbenes. It is demonstrated that the CAS-BCCC method is a promising theoretical tool for calculating the electronic structures of diradicals.
Bhowmik, Anal; Roy, Sourav; Majumder, Sonjoy
2016-01-01
This work presents precise calculations of important electromagnetic transition amplitudes along with detail of their many-body correlations using relativistic coupled cluster method. Studies of hyperfine interaction constants, useful for plasma diagnostic, with this correlation exhaustive many-body approach are another important area of this work. The calculated oscillator strengths of allowed transitions, amplitudes of forbidden transitions and lifetimes are compared with the other theoretical results wherever available and they show a good agreement. Hyperfine constants of ?different isotopes of W VI, presented in this paper will be helpful to get accurate picture of abundances of this element in different astronomical bodies.
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.
Real or artifactual symmetry breaking in the BNB radical: A multireference coupled cluster viewpoint
Li, Xiangzhu; Paldus, Josef
2007-06-01
The ground state of the linear BNB radical has been examined via the recently developed reduced multireference coupled cluster method with singles and doubles that is perturbatively corrected for triples [RMR CCSD(T)] using the correlation consistent basis sets (cc-pVXZ, X =D, T, and Q). Similar to earlier results that were based on the single reference CCSD(T) and BD(T) approaches, the RMR CCSD(T) method also predicts an asymmetric structure with two BN bonds of unequal length, even though the MR effects significantly reduce the barrier height. The computed frequencies for the symmetric and antisymmetric stretching modes agree reasonably well with the experimental data.
Chattopadhyay, S; Angom, D
2014-01-01
The perturbed relativistic coupled-cluster (PRCC) theory is applied to calculate the electric dipole polarizabilities of alkaline Earth metal atoms. The Dirac-Coulomb-Breit atomic Hamiltonian is used and we include the triple excitations in the relativistic coupled-cluster (RCC) theory. The theoretical issues related to the triple excitation cluster operators are described in detail and we also provide details on the computational implementation. The PRCC theory results are in good agreement with the experimental and previous theoretical results. We, then, highlight the importance of considering the Breit interaction for alkaline Earth metal atoms.
Full-wave model of D-region upward VLF coupling to whistlers in the plasmasphere
Jacobson, A. R.; Shao, X.; Lay, E. H.
2012-12-01
Atmospheric-lightning-to-plasmasphere VLF coupling via whistlers is key to understanding the problem of radiation-belt losses and the slot region. In the lowermost ionosphere, the "D-region" (roughly 60 - 100 km altitude), the coupling occurs between the VLF incident from the "vacuum" below, to the electron whistler capable of transiting upward through the E- and F-regions above. We have modified our successful and data-validated D-region VLF downward-reflection model to predict upward-coupled whistler waveforms recorded on topside satellites. The model has been run in production mode for predicting downward-reflected waveforms recorded at ground stations, but the model's internal calculation also fully describes the "penetrating" solution that merges into the oblique electron whistler. We have begun to test the model against VLF, three-dimensional electric-field recordings from the Vector Electric Field Instrument (VEFI) [Pfaff et al., 2010] on the C/NOFS satellite. VEFI's broadband recording and large on-board memory serendipitously provide an excellent platform for studying lightning whistlers in the plasmasphere. We have already demonstrated [Jacobson et al., 2011] that VEFI is superbly suited for testing transionospheric propagation, in conjunction with the World Wide Lightning Location Network (WWLLN; see www.wwlln.net) to provide groundtruth location/time of the lightning strokes. This poster will describe latest results. Jacobson, A. R., R. H. Holzworth, R. F. Pfaff, and M. P. McCarthy (2011), Study of oblique whistlers in the low-latitude ionosphere, jointly with the C/NOFS satellite and the World-Wide Lightning Location Network, Annales Geophysicae, 29, 851-863. Pfaff, R., D. Rowland, H. Freudenreich, K. Bromund, K. Le, M. Acuna, J. Klenzing, C. Liebrecht, S. Martin, W. J. Burke, N. C. Maynard, D. E. Hunton, P. A. Roddy, J. O. Ballenthin, and G. R. Wilson (2010), Observations of DC electric fields in the low-latitude ionosphere and their variations with
Directory of Open Access Journals (Sweden)
Zhao Tang
2016-04-01
Full Text Available The crashworthiness of a railway vehicle relates to its passive safety performance. Due to mesh distortion and difficulty in controlling the hourglass energy, conventional finite element methods face great challenges in crashworthiness simulation of large-scale complex railway vehicle models. Meshfree methods such as element-free Galerkin method offer an alternative approach to overcome those limitations but have proved time-consuming. In this article, a coupled finite element/meshfree method is proposed to study the crashworthiness of railway vehicles. A representative scenario, in which the leading vehicle of a high-speed train impacts to a rigid wall, is simulated with the coupled finite element/element-free Galerkin method in LS-DYNA. We have compared the conventional finite element method and the coupled finite element/element-free Galerkin method with the simulation results of different levels of discretization. Our work showed that coupled finite element/element-free Galerkin method is a suitable alternative of finite element method to handle the nonlinear deformation in full-size railway vehicle crashworthiness simulation. The coupled method can reduce the hourglass energy in finite element simulation, to produce robust simulation.
CLUSTER: A high-frequency H-mode coupled cavity linac for low and medium energies
Energy Technology Data Exchange (ETDEWEB)
Amaldi, Ugo [TERA Foundation, Via Puccini 11, 28100 Novara (Italy); University of Milano Bicocca, Milan (Italy)], E-mail: Ugo.Amaldi@cern.ch; Citterio, Alessandro; Crescenti, Massimo; Giuliacci, Arianna; Tronci, Cesare; Zennaro, Riccardo [TERA Foundation, Via Puccini 11, 28100 Novara (Italy)
2007-09-11
An innovative linear accelerating structure is proposed which is particularly suited for low-current hadrontherapy applications but can also conveniently substitute the conventional proton linacs at present considered for Accelerator Driven Systems and neutrino and muon factories. Its two main features are compactness and good power efficiency at low-medium beam velocities (0.05{<=}{beta}{<=}0.5). The first is achieved through a high working frequency and a consequent high accelerating gradient, the second is obtained by coupling several H-mode cavities together. The structure was dubbed CLUSTER for 'Coupled-cavity Linac USing Transverse Electric Radial field'. To compare the performance of this structure with other hadrontherapy linac designs involving high frequencies, a conceptual study has been performed for an operating frequency of 3 GHz. Moreover, a proof of principle has been obtained through RF measurements on a prototype operating at 1 GHz. An accelerator complex using a CLUSTER linac is also considered for protontherapy purposes. This total accelerator complex, called 'cyclinac', uses a commercial cyclotron as an injector to a high-frequency and high-gradient linac.
Energy Technology Data Exchange (ETDEWEB)
Datta, Dipayan, E-mail: datta.dipayan@gmail.com; Gauss, Jürgen, E-mail: gauss@uni-mainz.de [Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz (Germany)
2015-07-07
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 the 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.
Ab initio Bogoliubov coupled cluster theory for open-shell nuclei
Signoracci, A.; Duguet, T.; Hagen, G.; Jansen, G. R.
2015-06-01
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 within 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 Nmax=6 spherical harmonic oscillator basis for O,1816 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
Local Correlation Calculations Using Standard and Renormalized Coupled-Cluster Methods
Piecuch, Piotr; Li, Wei; Gour, Jeffrey
2009-03-01
Local correlation variants of the coupled-cluster (CC) theory with singles and doubles (CCSD) and CC methods with singles, doubles, and non-iterative triples, including CCSD(T) and the completely renormalized CR-CC(2,3) approach, are developed. The main idea of the resulting CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) methods is the realization of the fact that the total correlation energy of a large system can be obtained as a sum of contributions from the occupied orthonormal localized molecular orbitals and their respective occupied and unoccupied orbital domains. The CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) algorithms are characterized by the linear scaling of the total CPU time with the system size and embarrassing parallelism. By comparing the results of the canonical and CIM-CC calculations for normal alkanes and water clusters, it is demonstrated that the CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) approaches recover the corresponding canonical CC correlation energies to within 0.1 % or so, while offering savings in the computer effort by orders of magnitude. By examining the dissociation of dodecane into C11H23 and CH3 and several lowest-energy structures of the (H2O)n clusters, it is shown that the CIM-CC methods accurately reproduce the relative energetics of the corresponding canonical CC calculations.
Ab initio Bogoliubov coupled cluster theory for open-shell nuclei
Signoracci, Angelo; Hagen, Gaute; Jansen, Gustav
2014-01-01
Ab initio many-body methods address closed-shell nuclei up to mass A ~ 130 on the basis of realistic two- and three-nucleon interactions. Several routes to address open-shell nuclei are currently under investigation, including ideas which exploit spontaneous symmetry breaking. Singly open-shell nuclei can be efficiently described via the sole breaking of $U(1)$ gauge symmetry associated with particle number conservation, to account for their superfluid character. The present work formulates and applies Bogoliubov coupled cluster (BCC) theory, which consists of representing the exact ground-state wavefunction 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 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, wh...
Pak, Youngshang; Woods, R. Claude; Peterson, Kirk A.
1995-12-01
Three-dimensional near-equilibrium potential energy surfaces and dipole moment functions have been calculated for the X 1Σ+ ground states of NCS- and CNS-, using the coupled cluster method with single and double substitutions augmented by a perturbative estimate of triple excitations [CCSD(T)] with a set of 154 contracted Gaussian-type orbitals. The corresponding equilibrium bond lengths at their linear geometries are re(NC)=1.1788 Å and re(CS)=1.6737 Å for NCS-, and re(CN)=1.1805 Å and re(NS)=1.6874 Å for CNS-. The predicted equilibrium rotational constants Be of NCS- and CNS- are 5918.2 and 6282.7 MHz, respectively. The former agrees very well with the known experimental value (5919.0 MHz). Full three-dimensional variational calculations have also been carried out using the CCSD(T) potential energy and dipole moment functions to determine the rovibrational energy levels and dipole moment matrix elements for both NCS- and CNS-. The corresponding fundamental band origins (cm-1) ν1, ν2, and ν3 and their absolute intensities (km/mol) at the CCSD(T) level are 2060.9/306.1, 451.5/2.2, and 707.5/12.8, respectively, for NCS- and 2011.4/6.6, 343.7/2.3, and 624.9/0.2 for CNS-. The calculated ν1 (CN stretching) value for NCS- is in very good agreement with the experimental result, 2065.9 cm-1. The calculated dipole moments of NCS- and CNS- in their ground vibrational states are 1.427 and 1.347 D, respectively. The transition state geometry (saddle point) for the isomerization of NCS-→CNS- is predicted at the CCSD(T) level to be r(NC)=1.2044 Å, R(CS)=1.9411 Å and θ(∠NCS)=86.8°. Its calculated energy is 62.6 and 26.5 kcal/mol above the minima of NCS- and CNS-, respectively, including zero-point energy corrections. The structure of the NCS radical was also optimized at the same level of theory, yielding ion to neutral bond length shifts in excellent agreement with those derived from recent photoelectron spectroscopy experiments.
Full Core TREAT Kinetics Demonstration Using Rattlesnake/BISON Coupling Within MAMMOTH
Energy Technology Data Exchange (ETDEWEB)
Ortensi, Javier [Idaho National Lab. (INL), Idaho Falls, ID (United States); DeHart, Mark D. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Gleicher, Frederick N. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wang, Yaqi [Idaho National Lab. (INL), Idaho Falls, ID (United States); Alberti, Anthony L. [Oregon State Univ., Corvallis, OR (United States); Palmer, Todd S. [Oregon State Univ., Corvallis, OR (United States)
2015-08-01
This report summarizes key aspects of research in evaluation of modeling needs for TREAT transient simulation. Using a measured TREAT critical measurement and a transient for a small, experimentally simplified core, Rattlesnake and MAMMOTH simulations are performed building from simple infinite media to a full core model. Cross sections processing methods are evaluated, various homogenization approaches are assessed and the neutronic behavior of the core studied to determine key modeling aspects. The simulation of the minimum critical core with the diffusion solver shows very good agreement with the reference Monte Carlo simulation and the experiment. The full core transient simulation with thermal feedback shows a significantly lower power peak compared to the documented experimental measurement, which is not unexpected in the early stages of model development.
Coupled Models and Parallel Simulations for Three-Dimensional Full-Stokes Ice Sheet Modeling
Energy Technology Data Exchange (ETDEWEB)
Zhang, Huai; Ju, Lili
2011-01-01
A three-dimensional full-Stokes computational model is considered for determining the dynamics, temperature, and thickness of ice sheets. The governing thermomechanical equations consist of the three-dimensional full-Stokes system with nonlinear rheology for the momentum, an advective-diffusion energy equation for temperature evolution, and a mass conservation equation for icethickness changes. Here, we discuss the variable resolution meshes, the finite element discretizations, and the parallel algorithms employed by the model components. The solvers are integrated through a well-designed coupler for the exchange of parametric data between components. The discretization utilizes high-quality, variable-resolution centroidal Voronoi Delaunay triangulation meshing and existing parallel solvers. We demonstrate the gridding technology, discretization schemes, and the efficiency and scalability of the parallel solvers through computational experiments using both simplified geometries arising from benchmark test problems and a realistic Greenland ice sheet geometry.
Directory of Open Access Journals (Sweden)
Cheng-Tao Tsai
2013-01-01
Full Text Available This paper presents comparison between phase-shift full-bridge converters with noncoupled and coupled current-doubler rectifier. In high current capability and high step-down voltage conversion, a phase-shift full-bridge converter with a conventional current-doubler rectifier has the common limitations of extremely low duty ratio and high component stresses. To overcome these limitations, a phase-shift full-bridge converter with a noncoupled current-doubler rectifier (NCDR or a coupled current-doubler rectifier (CCDR is, respectively, proposed and implemented. In this study, performance analysis and efficiency obtained from a 500 W phase-shift full-bridge converter with two improved current-doubler rectifiers are presented and compared. From their prototypes, experimental results have verified that the phase-shift full-bridge converter with NCDR has optimal duty ratio, lower component stresses, and output current ripple. In component count and efficiency comparison, CCDR has fewer components and higher efficiency at full load condition. For small size and high efficiency requirements, CCDR is relatively suitable for high step-down voltage and high efficiency applications.
Tucholska, Aleksandra M; Lesiuk, Michał; Moszynski, Robert
2017-01-21
We introduce a new method for the computation of the transition moments between the excited electronic states based on the expectation value formalism of the coupled cluster theory [B. Jeziorski and R. Moszynski, Int. J. Quantum Chem. 48, 161 (1993)]. The working expressions of the new method solely employ the coupled cluster operator T and an auxiliary operator S that is expressed as a finite commutator expansion in terms of T and T(†). In the approximation adopted in the present paper, the cluster expansion is limited to single, double, and linear triple excitations. The computed dipole transition probabilities for the singlet-singlet and triplet-triplet transitions in alkali earth atoms agree well with the available theoretical and experimental data. In contrast to the existing coupled cluster response theory, the matrix elements obtained by using our approach satisfy the Hermitian symmetry even if the excitations in the cluster operator are truncated, but the operator S is exact. The Hermitian symmetry is slightly broken if the commutator series for the operator S are truncated. As a part of the numerical evidence for the new method, we report calculations of the transition moments between the excited triplet states which have not yet been reported in the literature within the coupled cluster theory. Slater-type basis sets constructed according to the correlation-consistency principle are used in our calculations.
Tucholska, Aleksandra M.; Lesiuk, Michał; Moszynski, Robert
2017-01-01
We introduce a new method for the computation of the transition moments between the excited electronic states based on the expectation value formalism of the coupled cluster theory [B. Jeziorski and R. Moszynski, Int. J. Quantum Chem. 48, 161 (1993)]. The working expressions of the new method solely employ the coupled cluster operator T and an auxiliary operator S that is expressed as a finite commutator expansion in terms of T and T†. In the approximation adopted in the present paper, the cluster expansion is limited to single, double, and linear triple excitations. The computed dipole transition probabilities for the singlet-singlet and triplet-triplet transitions in alkali earth atoms agree well with the available theoretical and experimental data. In contrast to the existing coupled cluster response theory, the matrix elements obtained by using our approach satisfy the Hermitian symmetry even if the excitations in the cluster operator are truncated, but the operator S is exact. The Hermitian symmetry is slightly broken if the commutator series for the operator S are truncated. As a part of the numerical evidence for the new method, we report calculations of the transition moments between the excited triplet states which have not yet been reported in the literature within the coupled cluster theory. Slater-type basis sets constructed according to the correlation-consistency principle are used in our calculations.
Hellman, Kristofer; Ronczka, Mathias; Günther, Thomas; Wennermark, Marcus; Rücker, Carsten; Dahlin, Torleif
2017-08-01
Electrical resistivity tomography (ERT) and refraction seismics are among the most frequently used geophysical methods for site-investigations and the combined results can be very helpful to fill in the gaps between the point measurements made by traditional geotechnical methods such as Cone Penetration Test (CPT), core-drilling and geophysical borehole logging. The interpretation of the results from a geophysical investigation constituting a single method often yields ambiguous results. Hence, an approach utilizing multiple techniques is often necessary. To facilitate interpretation of such a combined dataset, we propose a more controlled and objective approach and present a method for a structurally coupled inversion of 2D electrical resistivity and refraction seismic data using unstructured meshes. Mean shift clustering is used to combine the two images and to compare the separate and coupled inversion methodologies. Two synthetic examples are used to demonstrate the method, and a field-data example is included as a proof of concept. In all cases a significant improvement by the coupling is visible. The methodology can be used as a tool for improved data interpretation and for obtaining a more comprehensive and complete picture of the subsurface by combining geophysical methods.
Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S
2015-09-01
The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods.
Garza, Alejandro J; Scuseria, Gustavo E
2015-01-01
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 $f^0$ actinyl series (UO$_2^{2+}$, NpO$_2^{2+}$, PuO$_2^{2+}$), the isoelectronic NUN, and Thorium (ThO, ThO$^{2+}$) and Nobelium (NoO, NoO$_2$) oxides are studied.
Ellis, Benjamin H; Chakraborty, Arindam
2015-01-01
Multicomponent systems are defined as chemical systems that require a quantum mechanical description of two or more different types of particles. Non-Born-Oppenheimer electron-nuclear interactions in molecules, electron-hole interactions in electronically excited nanoparticles, and electron-positron interactions are examples of physical systems that require a multicomponent quantum mechanical formalism. The central challenge in the theoretical treatment of multicomponent systems is capturing the many-body correlation effects that exist not only between particles of identical types (electron-electron) but also between particles of different types (electron-nuclear and electron-hole). In this work, the development and implementation of multicomponent coupled-cluster (mcCC) theory for treating particle-particle correlation in multicomponent systems is presented. This method provides a balanced treatment of many-particle correlation in a general multicomponent system while maintaining a size-consistent and size-e...
Veis, Libor; Neese, Frank; Legeza, Örs; Pittner, Jiří
2016-01-01
We present an alternative method for accurate treatment of strongly correlated systems which combines the coupled cluster (CC) theory with the density matrix renormalization group method (DMRG). The connection is done in the spirit of the tailored CC method [T. Kinoshita, O. Hino, and R. J. Bartlett, \\textit{J. Chem. Phys.} {\\bf 123} (2005) 074106]. In the first step, the configuration interaction (CI) coefficients corresponding to single and double excitations within the DMRG active space are computed by contraction of the matrix product state (MPS) matrices. These coefficients are subsequently transformed into CC amplitudes. In the second step, the CC amplitudes are used to define a "tailored" single reference CCSD wavefunction. As a result, the DMRG method is responsible for the proper description of non-dynamic correlation, whereas the dynamic correlation is incorporated through the framework of the CC theory. We illustrate the potential of this method on prominent multireference model systems like N$_2$ ...
Singlet-triplet gaps in substituted carbenes predicted from block-correlated coupled cluster method
Institute of Scientific and Technical Information of China (English)
SHEN Jun; FANG Tao; LI Shuhua
2008-01-01
Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, ChinaThe block correlated coupled cluster (BCCC) method, with the complete active-space self-consistent-field (CASSCF) reference function, has been applied to investigating the singlet-triplet gaps in several substituted carbenes including four halocarbenes (CHCl, CF2, CCl2, and CBr2) and two hydroxycar-bones (CHOH and C(OH)2). A comparison of our results with the experimental data and other theoretical estimates shows that the present approach can provide quantitative descriptions for all the studied carbenes. It is demonstrated that the CAS-BCCC method is a promising theoretical tool for calculating the electronic structures of diradicals.
Energy Technology Data Exchange (ETDEWEB)
Bhaskaran-Nair, Kiran; Kowalski, Karol; Jarrell, Mark; Moreno, Juana; Shelton, William A.
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 of 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.
Low rank factorization of the Coulomb integrals for periodic coupled cluster theory
Hummel, Felix; Grüneis, Andreas
2016-01-01
We study the decomposition of the Coulomb integrals of periodic systems into a tensor 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.
Johansson, Mikael P; Sundholm, Dage
2004-02-15
We recently performed detailed analyses of the electronic structure of low-spin iron porphyrins using density-functional theory (DFT). Both the spin-density distributions of the oxidized, ferric forms, as well as the changes in total charge density upon reduction to the ferrous forms have been explored. Here, we compare the DFT results with wave-function theory, more specifically, with the approximate singles and doubles coupled-cluster method (CC2). Different spin states are considered by studying representative models of low spin, intermediate spin, and high spin species. The CC2 calculations corroborate the DFT results; the spin density exhibits the same amount of molecular spin polarization, and the charge delocalization is of comparable magnitude. Slight differences in the descriptions are noted and discussed.
Noniterative Multireference Coupled Cluster Methods on Heterogeneous CPU-GPU Systems.
Bhaskaran-Nair, Kiran; Ma, Wenjing; Krishnamoorthy, Sriram; Villa, Oreste; van Dam, Hubertus J J; Aprà, Edoardo; Kowalski, Karol
2013-04-09
A novel parallel algorithm for noniterative multireference coupled cluster (MRCC) theories, which merges recently introduced reference-level parallelism (RLP) [Bhaskaran-Nair, K.; Brabec, J.; Aprà, E.; van Dam, H. J. J.; Pittner, J.; Kowalski, K. J. Chem. Phys.2012, 137, 094112] with the possibility of accelerating numerical calculations using graphics processing units (GPUs) is presented. We discuss the performance of this approach applied to 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 effective Hamiltonian matrix. The performance of the combined RLP/GPU algorithm is illustrated on the example of the Brillouin-Wigner (BW) and Mukherjee (Mk) state-specific MRCCSD(T) formulations.
Roy, Sourav; Majumder, Sonjoy
2014-01-01
Hyperfine constants and anomalies of ground as well as few low lying excited states of $^{113,115,117}$In III are studied with highly correlated relativistic coupled-cluster theory. The ground state hyperfine splitting of $^{115}$In III is estimated to be 106.8 GHz. A shift of almost 1.9 GHz of the above frequency has been calculated due to modified nuclear dipole moment. This splitting result shows its applicability as communication band and frequency standards at $10^{-11}$ sec. Correlations study of hyperfine constants indicates a few distinct features of many-body effects in the wave-functions in and near the nuclear region of this ion. Astrophysically important forbidden transition amplitudes are estimated for the first time in the literature to our knowledge. The calculated oscillator strengths of few allowed transitions are compared with recent experimental and theoretical results wherever available.
Equation-of-motion coupled cluster method for the description of the high spin excited states
Musiał, Monika; Lupa, Łukasz; Kucharski, Stanisław A.
2016-04-01
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 R1 and R2 singlet equations in the case of quintets, only R2 operator survives with 5 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 C2 molecule and quintet states of C and Si atoms.
Connected triple excitations in coupled-cluster calculations of hyperpolarizabilities: Neon
Rice, Julia E.; Scuseria, Gustavo E.; Lee, Timothy J.; Taylor, Peter R.; Almloef, Jan
1992-01-01
We have calculated the second hyperpolarizability gamma of neon using the CCSD(T) method. The accuracy of the CCSD(T) approach has been established by explicit comparison with the single, double and triple excitation coupled-cluster (CCSDT) method using extended basis sets that are known to be adequate for the description of gamma. Our best estimate for gamma(sub 0) of 110 +/- 3 a.u. is in good agreement with other recent theoretical values and with Shelton's recent experimental estimate of 108 +/- 2 a.u. Comparison of the MP2 and CCSD(T) hyperpolarizability values indicates that MP2 gives a very good description of the electron correlation contribution to gamma(sub 0). We have combined MP2 frequency-dependent corrections with the CCSD(T) gamma(sub 0) to yield values of gamma(-2 omega;omega,omega,0) and gamma(exp K)(-omega;omega,0,0).
Coupled cluster investigation of Sternheimer shieldings and electric field gradient polarizabilities
Coriani, Sonia; Halkier, Asger; Jørgensen, Poul; Gauss, Jürgen; Christiansen, Ove; Rizzo, Antonio
2000-08-01
A coupled cluster (CC) investigation is presented for the (generalized) Sternheimer shieldings and the electric field gradient (EFG) polarizabilities which describe the effect of external electric fields and field gradients on the electric field gradient at the nuclei. Calculations are performed for the linear molecules N2, CO, HF, C2H2, HCl, HCN, and HNC. Correlation effects are monitored by employing a hierarchy of CC models consisting of CCS, CC2, CCSD, and CC3. The effect of tight basis functions and core correlation is investigated by carrying out CCSD calculations with core-valence basis sets. Accurate theoretical estimates for EFGs, Sternheimer shieldings, and EFG polarizabilities are given and the effects of vibrational corrections are discussed. Our final estimates for the considered EFG properties can be used, for example, in simulations of electric field effects on the EFG at the nuclei in interacting molecules.
An efficient and near linear scaling pair natural orbital based local coupled cluster method
Riplinger, Christoph; Neese, Frank
2013-01-01
In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009), 10.1063/1.3173827]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 105-106 relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below 8800 basis functions and >450 atoms. In all larger test calculations done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calculation, provided no approximations have been introduced in the latter. Thus, based on the present development reliable CCSD calculations on large molecules with unprecedented efficiency and accuracy are realized.
Granato, Gian Luigi; Dominguez-Tenreiro, Rosa; Obreja, Aura; Borgani, Stefano; De Lucia, Gabriella; Murante, Giuseppe
2014-01-01
We compute and study the infrared and sub-mm properties of high redshift (z>1) simulated clusters and proto-clusters, by coupling the results of a large set of hydro-dynamical zoom-in simulations including active galactic nuclei (AGN) feedback (Ragone-Figueroa et al. 2013), with the recently developed radiative transfer code GRASIL3D (Dominguez-Tenreiro et al. 2014), which accounts for the effect of dust reprocessing in an arbitrary geometry, and we customized for the present purpose. While this field is in its infancy from the observational point of view, a rapid development is expected in the near future, thanks to observations performed in the far IR and sub-mm bands. Notably, we find that in this spectral regime our prediction are little affected by the assumption required by this post-processing, and the emission is mostly powered by star formation rather than accretion onto super massive black hole (SMBH). The comparison with the little observational information available so far, highlights that the sim...
Gaussian-Based Coupled-Cluster Theory for the Ground-State and Band Structure of Solids.
McClain, James; Sun, Qiming; Chan, Garnet Kin-Lic; Berkelbach, Timothy C
2017-03-14
We present the results of Gaussian-based ground-state and excited-state equation-of-motion coupled-cluster theory with single and double excitations for three-dimensional solids. We focus on diamond and silicon, which are paradigmatic covalent semiconductors. In addition to ground-state properties (the lattice constant, bulk modulus, and cohesive energy), we compute the quasiparticle band structure and band gap. We sample the Brillouin zone with up to 64 k-points using norm-conserving pseudopotentials and polarized double- and triple-ζ basis sets, leading to canonical coupled-cluster calculations with as many as 256 electrons in 2176 orbitals.
Indian Academy of Sciences (India)
SUDIP SASMAL; KAUSHIK TALUKDAR; MALAYA K NAYAK; NAYANA VAVAL; SOURAV PAL
2016-10-01
The Z-vector method in the relativistic coupled-cluster framework is employed to calculate the parallel and perpendicular components of the magnetic hyperfine structure constant of a few small alkaline earth hydrides (BeH, MgH, and CaH) and fluorides (MgF and CaF). We have compared our Z-vector results with the values calculated by the extended coupled-cluster (ECC) method reported in Phys. Rev. A 91 022512 (2015). All these results are compared with the available experimental values. The Z-vector results are found to be in better agreement with the experimental values than those of the ECC values.
Matrix elements in the coupled-cluster approach - With application to low-lying states in Li
Martensson-Pendrill, Ann-Marie; Ynnerman, Anders
1990-01-01
A procedure is suggested for evaluating matrix elements of an operator between wavefunctions in the coupled-cluster form. The use of the exponential ansatz leads to compact exponential expressions also for matrix elements. Algorithms are developed for summing all effects of one-particle clusters and certain chains of two-particle clusters (containing the well-known random-phase approximation as a subset). The treatment of one-particle perturbations in single valence states is investigated in detail. As examples the oscillator strength for the 2s-2p transition in Li as well as the hyperfine structure for the two states are studied and compared to earlier work.
Wang, Farrah Qiuyun; Khairallah, George N.; O'Hair, Richard A. J.
2009-06-01
Previous studies have demonstrated that the silver hydride cluster cation Ag4H+ promotes CC bond coupling of allylbromide [G.N. Khairallah, R.A.J. O'Hair, Angewandte Chemie International Edition 44 (2005) 728]. Here the influence of both the nature and the size of the silver cluster cation and the substrate on CC bond coupling are examined. Thus each of the cations Ag2H+, Ag4H+, Ag3+, and Ag5+ were allowed to react with three different halides: allyl chloride, allyl bromide and allyl iodide. No CC bond coupling is observed in the reactions of the cluster cations with allyl chloride. There are four main reaction sequences that result in CC bond coupling for allyl bromide and allyl iodide mediated by Agn+ and Agn-1H+ clusters: (i) A sequence involving the reactions of silver cluster cations with two molecules of C3H5X: Agn+ --> Agn(C3H5X)+ --> AgnX2+. This only occurs in the cases of: n = 3 and X = I; n = 5 and X = Br. (ii) A sequence involving the reactions of silver cluster cations with two molecules of C3H5X via an organometallic intermediate: Agn+ --> Agn-1(C3H5)+ --> Agn-1X+. This only occurs in the cases of: n = 5 and X = Br and I. (iii) A sequence involving the reactions of silver hydride cluster cations with three molecules of C3H5X: Agn-1H+ --> Agn-1X+ --> Agn-1X(C3H5X)+ --> Ag(C3H5)2+ and Agn-1X3+. This only occurs in the cases of: n = 5 and X = Br and I. (iv) A sequence involving the reactions of silver hydride cluster cations with three molecules of C3H5X via an organometallic intermediate: Agn-1H+ --> Agn-1X+ --> Agn-3(C3H5)+ --> Ag(C3H5)2+ and Agn-3X+. This only occurs in the cases of: n = 5 and X = I.
Energy Technology Data Exchange (ETDEWEB)
Heiser, J.H. [Brookhaven National Lab., Upton, NY (United States). Environmental and Waste Technology Center; Dwyer, B. [Sandia National Lab., Albuquerque, NM (United States)
1997-09-01
The primary objective of this project was to develop and demonstrate the installation and measure the performance of a close-coupled barrier for the containment of subsurface waste or contaminant migration. A close-coupled barrier is produced by first installing a conventional, low-cost, cement-grout containment barrier followed by a thin lining of a polymer grout. The resultant barrier is a cement-polymer composite that has economic benefits derived from the cement and performance benefits from the durable and resistant polymer layer. The technology has matured from a regulatory investigation of the issues concerning the use of polymers to laboratory compatibility and performance measurements of various polymer systems to a pilot-scale, single column injection at Sandia to full-scale demonstration. The feasibility of the close-coupled barrier concept was proven in a full-scale cold demonstration at Hanford, Washington and then moved to the final stage with a full-scale demonstration at an actual remediation site at Brookhaven National Laboratory (BNL). At the Hanford demonstration the composite barrier was emplaced around and beneath a 20,000 liter tank. The secondary cement layer was constructed using conventional jet grouting techniques. Drilling was completed at a 45{degree} angle to the ground, forming a cone-shaped barrier. The primary barrier was placed by panel jet-grouting with a dual-wall drill stem using a two part polymer grout. The polymer chosen was a high molecular weight acrylic. At the BNL demonstration a V-trough barrier was installed using a conventional cement grout for the secondary layer and an acrylic-gel polymer for the primary layer. Construction techniques were identical to the Hanford installation. This report summarizes the technology development from pilot- to full-scale demonstrations and presents some of the performance and quality achievements attained.
Upadhyay, Apoorva; Komatireddy, Navatha; Ghirri, Alberto; Tuna, Floriana; Langley, Stuart K; Srivastava, Anant K; Sañudo, E Carolina; Moubaraki, Boujemaa; Murray, Keith S; McInnes, Eric J L; Affronte, Marco; Shanmugam, Maheswaran
2014-01-07
A linear trimeric cluster of molecular formula [Ni2Gd(L(-))6](NO3) (1) (L(-) = (C14H12NO2) has been isolated with its structure determined via single crystal X-ray diffraction. Magnetic susceptibility measurements of 1 show that the nickel and gadolinium ions are coupled ferromagnetically, with a ground total spin state (S) of 11/2. Best fit spin Hamiltonian parameters obtained for 1 are J(1(Ni-Gd)) = +0.54 cm(-1), g = 2.01. EPR measurements confirm a low magnetic anisotropy (D = -0.135 cm(-1)) for 1. Heat capacity determination of the magnetocaloric effect (MCE) parameters for 1 shows that the change in magnetic entropy (-ΔS(m)) achieves a maximum of 13.74 J kg(-1) K(-1) at 4.0 K, with the ferromagnetic coupling giving a rapid change in low applied fields, confirming the potential of Gd molecular derivatives as coolants at liquid helium temperature.
Coupled-cluster singles, doubles and triples (CCSDT) calculations of atomization energies
DEFF Research Database (Denmark)
Bak, KL; Jorgensen, P; Olsen, Jeppe
2000-01-01
Atomization energies have been calculated for CO, H2O, F-2, HF, N-2 and CH2 (the (1)A(1) state) using the coupled-duster singles, doubles and triples (CCSDT) model as well as the coupled-cluster singles and doubles model with a perturbative correction for triples [CCSD(T)]. TheCCSD(T) model...... provides an excellent approximation to the CCSDT model; at the cc-pV5Z basis set level, the CCSDT valence triples contribution is underestimated by 9.1% (0.8 kJ/mol) for CH, and overestimated for the remaining molecules by as little as 4.3%(1.3 kJ/mol) for F-2,and as much as 8.4% (3.0 kJ/mol) for N-2....... At the CCSDT level, the agreement with experiment is not improved, suggesting that some cancellation of error occurs between the missing triples contributions at the CCSD(T) level and the contributions from the connected quadruples. (C) 2000 Elsevier Science B.V, All rights reserved....
DEFF Research Database (Denmark)
Paidarová, Ivana; Sauer, Stephan P. A.
2012-01-01
We have compared the performance of density functional theory (DFT) using five different exchange-correlation functionals with four coupled cluster theory based wave function methods in the calculation of geometrical derivatives of the polarizability tensor of methane. The polarizability gradient...
Cremer, Dieter; Kraka, Elfi; Filatov, Michael
2008-01-01
Bond dissociation energies (BDEs) of neutral HgX and cationic HgX(+) molecules range from less than a kcal mol(-1) to as much as 60 kcal mol(-1). Using NESCICCCSD(T) [normalized elimination of the small component and coupled-cluster theory with all single and double excitations and a perturbative tr
Cremer, Dieter; Kraka, Elfi; Filatov, Michael
2008-01-01
Bond dissociation energies (BDEs) of neutral HgX and cationic HgX(+) molecules range from less than a kcal mol(-1) to as much as 60 kcal mol(-1). Using NESCICCCSD(T) [normalized elimination of the small component and coupled-cluster theory with all single and double excitations and a perturbative
Sen, Sangita; Shee, Avijit; Mukherjee, Debashis
2012-08-21
The traditional state universal multi-reference coupled cluster (SUMRCC) theory uses the Jeziorski-Monkhorst (JM) based Ansatz of the wave operator: Ω = Σ(μ)Ω(μ)|φ(μ)>function φ(μ). In the first formulations, φ(μ)s were chosen to be single determinants and T(μ)s were defined in terms of spinorbitals. This leads to spin-contamination for the non-singlet cases. In this paper, we propose and implement an explicitly spin-free realization of the SUMRCC theory. This method uses spin-free unitary generators in defining the cluster operators, {T(μ)}, which even at singles-doubles truncation, generates non-commuting cluster operators. We propose the use of normal-ordered exponential parameterization for Ω:Σ(μ){exp(T(μ))}|φ(μ)>functions {φ(μ)} as unitary group adapted (UGA) Gel'fand states which is why we call our theory UGA-SUMRCC. In the spirit of the original SUMRCC, we choose exactly the right number of linearly independent cluster operators in {T(μ)} such that no redundancies in the virtual functions {χ(μ)(l)} are involved. Using example applications for electron detached/attached and h-p excited states relative to a closed shell ground state we discuss how to choose the most compact and non-redundant cluster operators. Although there exists a more elaborate spin-adapted JM-like ansatz of Datta and Mukherjee (known as combinatoric open-shell CC (COS-CC), its working equations are more complex. Results are compared with those from COS-CC, equation of motion coupled cluster methods, restricted open-shell Hartree-Fock coupled cluster, and full configuration interaction. We observe that our results are more accurate with respect to most other theories as a result of the use of the cluster expansion structure for our wave operator. Our results are comparable to those from the more involved COS-CC, indicating that our theory captures the most important aspects of physics with a considerably simpler scheme.
Jagau, Thomas-C.; Prochnow, Eric; Evangelista, Francesco A.; Gauss, Jürgen
2010-04-01
Analytic gradients for the state-specific multireference coupled-cluster method suggested by Mahapatra et al. [Mol. Phys. 94, 157 (1998)] (Mk-MRCC) are reported within the singles and doubles approximation using two-configurational self-consistent field (TCSCF) orbitals. The present implementation extends our previous work on Mk-MRCC gradients [E. Prochnow et al., J. Chem. Phys. 131, 064109 (2009)] which is based on restricted Hartree-Fock orbitals and consequently the main focus of the present paper is on the treatment of orbital relaxation at the TCSCF level using coupled-perturbed TCSCF theory. Geometry optimizations on m-arynes and nitrenes are presented to illustrate the influence of the orbitals on the computed equilibrium structures. The results are compared to those obtained at the single-reference coupled-cluster singles and doubles and at the Mk-MRCC singles and doubles level of theory when using restricted Hartree-Fock orbitals.
Simulation of the photodetachment spectrum of HHfO- using coupled-cluster calculations
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.
Haghdani, Shokouh; Åstrand, Per-Olof; Koch, Henrik
2016-02-01
We have calculated the electronic optical rotation of seven molecules using coupled cluster singles-doubles (CCSD) and the second-order approximation (CC2) employing the aug-cc-pVXZ (X = D, T, or Q) basis sets. We have also compared to time-dependent density functional theory (TDDFT) by utilizing two functionals B3LYP and CAM-B3LYP and the same basis sets. Using relative and absolute error schemes, our calculations demonstrate that the CAM-B3LYP functional predicts optical rotation with the minimum deviations compared to CCSD at λ = 355 and 589.3 nm. Furthermore, our results illustrate that the aug-cc-pVDZ basis set provides the optical rotation in good agreement with the larger basis sets for molecules not possessing small-angle optical rotation at λ = 589.3 nm. We have also performed several two-point inverse power extrapolations for the basis set convergence, i.e., OR(∞) + AX(-n), using the CC2 model at λ = 355 and 589.3 nm. Our results reveal that a two-point inverse power extrapolation with the aug-cc-pVTZ and aug-cc-pVQZ basis sets at n = 5 provides optical rotation deviations similar to those of aug-cc-pV5Z with respect to the basis limit.
Energy Technology Data Exchange (ETDEWEB)
Ibrahim, Khaled Z. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Epifanovsky, Evgeny [Q-Chem, Inc., Pleasanton, CA (United States); Williams, Samuel W. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Krylov, Anna I. [Univ. of Southern California, Los Angeles, CA (United States). Dept. of Chemistry
2016-07-26
Coupled-cluster methods provide highly accurate models of molecular structure by explicit numerical calculation of tensors representing the correlation between electrons. These calculations are dominated by a sequence of tensor contractions, motivating the development of numerical libraries for such operations. While based on matrix-matrix multiplication, these libraries are specialized to exploit symmetries in the molecular structure and in electronic interactions, and thus reduce the size of the tensor representation and the complexity of contractions. The resulting algorithms are irregular and their parallelization has been previously achieved via the use of dynamic scheduling or specialized data decompositions. We introduce our efforts to extend the Libtensor framework to work in the distributed memory environment in a scalable and energy efficient manner. We achieve up to 240 speedup compared with the best optimized shared memory implementation. We attain scalability to hundreds of thousands of compute cores on three distributed-memory architectures, (Cray XC30&XC40, BlueGene/Q), and on a heterogeneous GPU-CPU system (Cray XK7). As the bottlenecks shift from being compute-bound DGEMM's to communication-bound collectives as the size of the molecular system scales, we adopt two radically different parallelization approaches for handling load-imbalance. Nevertheless, we preserve a uni ed interface to both programming models to maintain the productivity of computational quantum chemists.
Sharma, Sandeep
2015-01-01
We propose a multireference linearized coupled cluster theory using matrix product states (MPS-LCC) which provides remarkably accurate ground-state energies, at a computational cost that has the same scaling as multireference configuration interaction singles and doubles (MRCISD), for a wide variety of electronic Hamiltonians. These range from first-row dimers at equilibrium and stretched geometries, to highly multireference systems such as the chromium dimer and lattice models such as periodic two-dimensional 1-band and 3-band Hubbard models. The MPS-LCC theory shows a speed up of several orders of magnitude over the usual DMRG algorithm while delivering energies in excellent agreement with converged DMRG calculations. Also, in all the benchmark calculations presented here MPS-LCC outperformed the commonly used multi-reference quantum chemistry methods in some cases giving energies in excess of an order of magnitude more accurate. As a size-extensive method that can treat large active spaces, MPS-LCC opens u...
A view on coupled cluster perturbation theory using a bivariational Lagrangian formulation
Kristensen, Kasper; Matthews, Devin A; Olsen, Jeppe; Jørgensen, Poul
2015-01-01
We consider two distinct coupled cluster (CC) perturbation series that both expand the difference between the energies of the CCSD (CC with single and double excitations) and CCSDT (CC with single, double, and triple excitations) models in orders of the M{\\o}ller-Plesset fluctuation potential. We initially introduce the E-CCSD(T-$n$) series, in which the CCSD amplitude equations are satisfied at the expansion point, and compare it to the recently developed CCSD(T-$n$) series [J. Chem. Phys. 140, 064108 (2014)], in which not only the CCSD amplitude, but also the CCSD multiplier equations are satisfied at the expansion point. Both series are term-wise size extensive and formally converge towards the CCSDT target energy. However, the two series are different, and the CCSD(T-$n$) series is found to exhibit a more rapid convergence up through the series, which we trace back to the fact that more information at the expansion point is utilized than for the E-CCSD(T-$n$) series. The present analysis can be generalize...
Kuś, Tomasz; Bartlett, Rodney J.
2008-09-01
The doublet and quartet excited states of the formyl radical have been studied by the equation-of-motion (EOM) coupled cluster (CC) method. The Sz spin-conserving singles and doubles (EOM-EE-CCSD) and singles, doubles, and triples (EOM-EE-CCSDT) approaches, as well as the spin-flipped singles and doubles (EOM-SF-CCSD) method have been applied, subject to unrestricted Hartree-Fock (HF), restricted open-shell HF, and quasirestricted HF references. The structural parameters, vertical and adiabatic excitation energies, and harmonic vibrational frequencies have been calculated. The issue of the reference function choice for the spin-flipped (SF) method and its impact on the results has been discussed using the experimental data and theoretical results available. The results show that if the appropriate reference function is chosen so that target states differ from the reference by only single excitations, then EOM-EE-CCSD and EOM-SF-CCSD methods give a very good description of the excited states. For the states that have a non-negligible contribution of the doubly excited configurations one is able to use the SF method with such a reference function, that in most cases the performance of the EOM-SF-CCSD method is better than that of the EOM-EE-CCSD approach.
Investigating tunnel and above-barrier ionization using complex-scaled coupled-cluster theory
Jagau, Thomas-C.
2016-11-01
The theory and implementation of the complex-scaled coupled-cluster method with singles and doubles excitations (cs-CCSD) for studying resonances induced by static electric fields are presented. Within this framework, Stark shifts and ionization rates are obtained directly from the real and imaginary parts of the complex energy. The method is applied to the ground states of hydrogen, helium, lithium, beryllium, neon, argon, and carbon at varying field strengths. Complex-scaled Hartree-Fock, second-order many-body perturbation theory, and CCSD results are reported and analyzed with a focus on the impact of electron correlation on the ionization process. cs-CCSD calculations with suitably augmented standard Gaussian basis sets are found to deliver accurate strong-field ionization rates over a range of six orders of magnitude. The field-induced resonances are characterized beyond energy and ionization rate through their dipole moments, second moments, as well as Dyson orbitals and comparisons are drawn to autoionizing and autodetaching resonances. Marked differences are found between the tunneling and above-barrier regimes allowing for a clear distinction of the two mechanisms.
Relativistic equation-of-motion coupled-cluster method using open-shell reference wavefunction
Pathak, Himadri; Nayak, Malaya K; Vaval, Nayana; Pal, Sourav
2016-01-01
The open-shell reference relativistic equation-of-motion coupled-cluster method within its four-component description is successfully implemented with the consideration of single- and double- excitation approximation. The one-body and two-body matrix elements required for the correlation calculation are generated using Dirac-Coulomb Hamiltonian. As a first attempt, the implemented method is employed to calculate a few of the low-lying ionized states of heavy atomic (Ag, Cs, Au, Fr, Lr) and valence ionization potential of molecular (HgH, PbF) systems, where the effect of relativity does really matter to obtain highly accurate results. Not only the relativistic effect, but also the effect of electron correlation is crucial in these heavy atomic and molecular systems. To justify the fact, we have taken two further approximations in the four-component relativistic equation-of-motion framework to quantify how the effect of electron correlation plays a role in the calculated values at different level of the approxi...
Natural triple excitations in local coupled cluster calculations with pair natural orbitals
Riplinger, Christoph; Sandhoefer, Barbara; Hansen, Andreas; Neese, Frank
2013-10-01
In this work, the extension of the previously developed domain based local pair-natural orbital (DLPNO) based singles- and doubles coupled cluster (DLPNO-CCSD) method to perturbatively include connected triple excitations is reported. The development is based on the concept of triples-natural orbitals that span the joint space of the three pair natural orbital (PNO) spaces of the three electron pairs that are involved in the calculation of a given triple-excitation contribution. The truncation error is very smooth and can be significantly reduced through extrapolation to the zero threshold. However, the extrapolation procedure does not improve relative energies. The overall computational effort of the method is asymptotically linear with the system size O(N). Actual linear scaling has been confirmed in test calculations on alkane chains. The accuracy of the DLPNO-CCSD(T) approximation relative to semicanonical CCSD(T0) is comparable to the previously developed DLPNO-CCSD method relative to canonical CCSD. Relative energies are predicted with an average error of approximately 0.5 kcal/mol for a challenging test set of medium sized organic molecules. The triples correction typically adds 30%-50% to the overall computation time. Thus, very large systems can be treated on the basis of the current implementation. In addition to the linear C150H302 (452 atoms, >8800 basis functions) we demonstrate the first CCSD(T) level calculation on an entire protein, Crambin with 644 atoms, and more than 6400 basis functions.
Krause, Christine; Werner, Hans-Joachim
2012-06-07
Explicitly correlated local coupled-cluster (LCCSD-F12) methods with pair natural orbitals (PNOs), orbital specific virtual orbitals (OSVs), and projected atomic orbitals (PAOs) are compared. In all cases pair-specific virtual subspaces (domains) are used, and the convergence of the correlation energy as a function of the domain sizes is studied. Furthermore, the performance of the methods for reaction energies of 52 reactions involving 58 small and medium sized molecules is investigated. It is demonstrated that for all choices of virtual orbitals much smaller domains are needed in the explicitly correlated methods than without the explicitly correlated terms, since the latter correct a large part of the domain error, as found previously. For PNO-LCCSD-F12 with VTZ-F12 basis sets on the average only 20 PNOs per pair are needed to obtain reaction energies with a root mean square deviation of less than 1 kJ mol(-1) from complete basis set estimates. With OSVs or PAOs at least 4 times larger domains are needed for the same accuracy. A new hybrid method that combines the advantages of the OSV and PNO methods is proposed and tested. While in the current work the different local methods are only simulated using a conventional CCSD program, the implications for low-order scaling local implementations of the various methods are discussed.
Unlocking the full potential of wave-matter nonlinear coupling in the epsilon-near-zero regime
Ciattoni, Alessandro; Marini, Andrea; Di Falco, Andrea; Faccio, Daniele; Scalora, Michael
2015-01-01
In recent years, unconventional metamaterial properties have triggered a revolution of electromagnetic research which has unveiled novel scenarios of wave-matter interaction. A very small dielectric permittivity is a leading example of such unusual features, since it produces an exotic static-like regime where the electromagnetic field is spatially slowly-varying over a physically large region. The so-called epsilon-near-zero metamaterials thus offer an ideal platform where to manipulate the inner details of the "stretched" field. Here we theoretically prove that a standard nonlinearity is able to operate such a manipulation to the point that even a thin slab produces a dramatic nonlinear pulse transformation, if the dielectric permittivity is very small within the field bandwidth. The predicted non-resonant releasing of full nonlinear coupling produced by the epsilon-near-zero condition does not resort to any field enhancement mechanisms and opens novel routes to exploiting matter nonlinearity for steering t...
Feller, David
2016-01-01
Benchmark quality adiabatic electron affinities for a collection of atoms and small molecules were obtained with the Feller-Peterson-Dixon composite coupled cluster theory method. Prior applications of this method demonstrated its ability to accurately predict atomization energies/heats of formation for more than 170 molecules. In the current work, the 1-particle expansion involved very large correlation consistent basis sets, ranging up to aug-cc-pV9Z (aug-cc-pV10Z for H and H2), with the goal of minimizing the residual basis set truncation error that must otherwise be approximated with extrapolation formulas. The n-particle expansion begins with coupled cluster calculations through iterative single and double excitations plus a quasiperturbative treatment of "connected" triple excitations (CCSD(T)) pushed to the complete basis set limit followed by CCSDT, CCSDTQ, or CCSDTQ5 corrections. Due to the small size of the systems examined here, it was possible in many cases to extend the n-particle expansion to the full configuration interaction wave function limit. Additional, smaller corrections associated with core/valence correlation, scalar relativity, anharmonic zero point vibrational energies, and non-adiabatic effects were also included. The overall root mean square (RMS) deviation was 0.005 eV (0.12 kcal/mol). This level of agreement was comparable to what was found with molecular heats of formation. A 95% confidence level corresponds to roughly twice the RMS value or 0.01 eV. While the atomic electron affinities are known experimentally to high accuracy, the molecular values are less certain. This contributes to the difficulty of gauging the accuracy of the theoretical results. A limited number of electron affinities were determined with the explicitly correlated CCSD(T)-F12b method. After extending the VnZ-F12 orbital basis sets with additional diffuse functions, the F12b method was found to accurately reproduce the best F/F- value obtained with standard
Proton-coupled electron transfer in [pyridine·(H2O)n]-, n = 3, 4, clusters
Archer, Kaye A.; Jordan, Kenneth D.
2016-09-01
The equation-of-motion method is used to map out one-dimensional potentials for proton-coupled electron transfer in the [pyridine·(H2O)n]-, n = 3, 4, clusters. In both cases there is an avoided crossing between valence-type pyridinyl·(OH-) (H2O)n-1 and dipole-bound pyridine·(H2O)n- anion species. For the n = 3 cluster, the mixing is sufficiently strong that both limiting structures are predicted to be sampled in the vibrational zero-point level.
Gauss, Jürgen; Ruud, Kenneth; Kállay, Mihály
2007-08-01
An implementation of the gauge-origin independent calculation of magnetizabilities and rotational g tensors at the coupled-cluster (CC) level is presented. The properties of interest are obtained as second derivatives of the energy with respect to the external magnetic field (in the case of the magnetizability) or with respect to magnetic field and rotational angular momentum (in the case of the rotational g tensor), while gauge-origin independence and fast basis-set convergence are ensured by using gauge-including atomic orbitals (London atomic orbitals) as well as their extension to treat rotational perturbations (rotational London atomic orbitals). The implementation within our existing CC analytic second-derivative code is described, focusing on the required modifications concerning integral evaluation and treatment of the unperturbed and perturbed two-particle density matrices. An extensive set of test calculations for LiH and BH (up to the full configuration-interaction limit), for a series of simple hydrides (HF, H2O, NH3, and CH4) as well as the more challenging molecules CO, N2, and O3 [employing the CC singles and doubles (CCSD) and the CCSD approximation augmented by a perturbative treatment of triple excitations] demonstrates the importance of electron correlation for high-accuracy predictions of magnetizabilities and rotational g tensors.
Energy Technology Data Exchange (ETDEWEB)
Hammond, Jeffrey R.; Govind, Niranjan; Kowalski, Karol; Autschbach, Jochen; Xantheas, Sotiris S.
2009-12-07
The static dipole polarizabilities of water clusters are determined at the Coupled-Cluster level of theory (CCSD). For the dipole polarizability of the water monomer it was determined that the role of the basis set is even more important than that of electron correlation and that the basis set augmentation converges with two sets of diffuse functions. The CCSD results are used to benchmark a variety of density functionals while the performance of several families of basis sets (Dunning, Pople and Sadlej) in producing accurate values for the polarizabilities was also examined. The Sadlej family of basis sets was found to produce accurate results when compared to the ones obtained with the much larger Dunning basis sets. It was furthermore determined that the PBE0 density functional with the aug-cc-pVDZ basis set produces overall remarkably accurate polarizabilities at a moderate computational cost.
Lei, Zhen; Pei, Xiao-Li; Guan, Zong-Jie; Wang, Quan-Ming
2017-06-12
An intensely luminescent gold(I)-silver(I) cluster [(C)(AuPPhpy2 )6 Ag6 (CF3 CO2 )3 ](BF4 )5 (PPhpy2 =bis(2-pyridyl)phenylphosphine) (3) is synthesized by the reaction of [(C)(AuPPhpy2 )6 Ag4 ](BF4 )6 with AgCF3 CO2 . All eight faces of the octahedral C@Au6 core in 3 are capped, that is, six faces are capped by silver ions and two by tetrafluoroborates. Cluster 3 is intensely luminescent in solution with a quantum yield of 92 %. Ligation of CF3 CO2(-) ions is vital for the construction and emission properties of 3, as confirmed by DFT calculations. BF4(-) ions are involved in the protecting sphere of the metal core, as evidenced by (19) F NMR data. The participation of phosphines, CF3 CO2(-) , and BF4(-) ions in the protection of the emissive core and the enhancement of the rigidity of the cluster result in the high emission efficiency. This is the first example of organic ligands and inorganic anions forming a rigid protecting sphere for luminescent coinage-metal clusters. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Zheng, Xu; Hao, Zhiyong; Wang, Xu; Mao, Jie
2016-06-01
High-speed-railway-train interior noise at low, medium, and high frequencies could be simulated by finite element analysis (FEA) or boundary element analysis (BEA), hybrid finite element analysis-statistical energy analysis (FEA-SEA) and statistical energy analysis (SEA), respectively. First, a new method named statistical acoustic energy flow (SAEF) is proposed, which can be applied to the full-spectrum HST interior noise simulation (including low, medium, and high frequencies) with only one model. In an SAEF model, the corresponding multi-physical-field coupling excitations are firstly fully considered and coupled to excite the interior noise. The interior noise attenuated by sound insulation panels of carriage is simulated through modeling the inflow acoustic energy from the exterior excitations into the interior acoustic cavities. Rigid multi-body dynamics, fast multi-pole BEA, and large-eddy simulation with indirect boundary element analysis are first employed to extract the multi-physical-field excitations, which include the wheel-rail interaction forces/secondary suspension forces, the wheel-rail rolling noise, and aerodynamic noise, respectively. All the peak values and their frequency bands of the simulated acoustic excitations are validated with those from the noise source identification test. Besides, the measured equipment noise inside equipment compartment is used as one of the excitation sources which contribute to the interior noise. Second, a full-trimmed FE carriage model is firstly constructed, and the simulated modal shapes and frequencies agree well with the measured ones, which has validated the global FE carriage model as well as the local FE models of the aluminum alloy-trim composite panel. Thus, the sound transmission loss model of any composite panel has indirectly been validated. Finally, the SAEF model of the carriage is constructed based on the accurate FE model and stimulated by the multi-physical-field excitations. The results show
A pair natural orbital implementation of the coupled cluster model CC2 for excitation energies.
Helmich, Benjamin; Hättig, Christof
2013-08-28
We demonstrate how to extend the pair natural orbital (PNO) methodology for excited states, presented in a previous work for the perturbative doubles correction to configuration interaction singles (CIS(D)), to iterative coupled cluster methods such as the approximate singles and doubles model CC2. The original O(N(5)) scaling of the PNO construction is reduced by using orbital-specific virtuals (OSVs) as an intermediate step without spoiling the initial accuracy of the PNO method. Furthermore, a slower error convergence for charge-transfer states is analyzed and resolved by a numerical Laplace transformation during the PNO construction, so that an equally accurate treatment of local and charge-transfer excitations is achieved. With state-specific truncated PNO expansions, the eigenvalue problem is solved by combining the Davidson algorithm with deflation to project out roots that have already been determined and an automated refresh with a generation of new PNOs to achieve self-consistency of the PNO space. For a large test set, we found that truncation errors for PNO-CC2 excitation energies are only slightly larger than for PNO-CIS(D). The computational efficiency of PNO-CC2 is demonstrated for a large organic dye, where a reduction of the doubles space by a factor of more than 1000 is obtained compared to the canonical calculation. A compression of the doubles space by a factor 30 is achieved by a unified OSV space only. Moreover, calculations with the still preliminary PNO-CC2 implementation on a series of glycine oligomers revealed an early break even point with a canonical RI-CC2 implementation between 100 and 300 basis functions.
Energy Technology Data Exchange (ETDEWEB)
Hirata, So; Fan, Peng-Dong; Auer, Alexander A.; Nooijen, Marcel; Piecuch, Piotr
2004-12-22
Various approximations of combined coupled-cluster (CC) and many-body perturbation theories (MBPT) have been derived and implemented into parallel execution programs that take account of spin, spatial (real Abelian), and permutation symmetries within the spin-orbital formalisms for closed- and open-shell molecules. The models range from CCSD(T), CCSD[T], CCSD(2)T, CCSD(2)TQ, CCSDT(2)Q to the completely renormalized CCSD(T) and CCSD[T], where CCSD (CCSDT) is the CC with connected single and double (and triple) excitation operators and subscripted or parenthesized 2, T, and Q indicate the order of perturbation or the rank of connected excitation operators in the correction. The derivation and implementation have been semi-automated by the algebraic and symbolic manipulation program. The computer-synthesized subroutines generate the tensors with the highest rank in a block-wise manner so that they never need to be stored in their entirety, reusing the other pre-calculated intermediate tensors defined also prioritizing the memory optimization (subroutines for these are also computer synthesized). Consequently, the overall memory cost for the perturbation corrections of connected triple and quadruple excitation operators scales as O(n4) and O(n6), respectively (n is the number of orbitals). For systems with different multi-reference character in their wave functions, we found the order of accuracy is roughly CCSD < CR-CCSD(T) ? CCSD(2)T ? CCSD(T) < CCSD(2)TQ ? CCSDT < CCSDT(2)Q, whereas CR-CCSD(T) is effective for extreme cases of quasi-degeneracy (particularly for stretched single bonds) and the operation costs of CCSD(2)TQ and CCSDT(2)Q in the present implementations scale as rather steep O(n9). The perturbation correction part of the CCSD(T)/cc-pVDZ calculations for azulene exhibited a 45-fold speedup upon a 64-fold increase in the number of processors to 512 processors.
Relativistic coupled-cluster calculations of transition properties in highly charged inert-gas ions
Nandy, D. K.
2016-11-01
We have carried out an extensive investigation of various spectroscopic properties of highly charged inert-gas ions using a relativistic coupled-cluster method through a one-electron detachment procedure. In particular, we have calculated the atomic states 2 s22 p53/2 2P, 2 s22 p51/2 2P, and 2 s 2 p61/2 2S in F-like inert-gas ions; 3 s23 p53/2 2P, 3 s23 p51/2 2P, and 3 s 3 p61/2 2S states in Cl-like Kr, Xe, and Rn; and 4 s24 p53/2 2P, 4 s24 p51/2 2P, and 4 s 4 p61/2 2S states in Br-like Xe and Rn. Starting from a single-reference Dirac-Hartree-Fock wave function, we construct our exact atomic states by including the dynamic correlation effects in an all-order perturbative fashion. Employing this method, we estimate the ionization potential energies of three low-lying orbitals present in their respective closed-shell configurations. Since the considered highly charged inert-gas ions exhibit huge relativistic effects, we have taken into account the corrections due to Breit interaction as well as from the dominant quantum electrodynamic correction such as vacuum polarization and self-energy effects in these systems. Using our calculated relativistic atomic wave functions and energies, we accurately determine various transition properties such as wavelengths, line strengths, oscillator strengths, transition probabilities, and lifetimes of the excited states.
A pair natural orbital implementation of the coupled cluster model CC2 for excitation energies
Helmich, Benjamin; Hättig, Christof
2013-08-01
We demonstrate how to extend the pair natural orbital (PNO) methodology for excited states, presented in a previous work for the perturbative doubles correction to configuration interaction singles (CIS(D)), to iterative coupled cluster methods such as the approximate singles and doubles model CC2. The original O(N^5) scaling of the PNO construction is reduced by using orbital-specific virtuals (OSVs) as an intermediate step without spoiling the initial accuracy of the PNO method. Furthermore, a slower error convergence for charge-transfer states is analyzed and resolved by a numerical Laplace transformation during the PNO construction, so that an equally accurate treatment of local and charge-transfer excitations is achieved. With state-specific truncated PNO expansions, the eigenvalue problem is solved by combining the Davidson algorithm with deflation to project out roots that have already been determined and an automated refresh with a generation of new PNOs to achieve self-consistency of the PNO space. For a large test set, we found that truncation errors for PNO-CC2 excitation energies are only slightly larger than for PNO-CIS(D). The computational efficiency of PNO-CC2 is demonstrated for a large organic dye, where a reduction of the doubles space by a factor of more than 1000 is obtained compared to the canonical calculation. A compression of the doubles space by a factor 30 is achieved by a unified OSV space only. Moreover, calculations with the still preliminary PNO-CC2 implementation on a series of glycine oligomers revealed an early break even point with a canonical RI-CC2 implementation between 100 and 300 basis functions.
Chembo Kouomou, Y; Woafo, P
2003-04-01
We study the spatiotemporal dynamics of a ring of diffusely coupled single-well Duffing oscillators. The transitions from spatiotemporal chaos to cluster and complete synchronization states are particularly investigated, as well as the Hopf bifurcations to instability. It is found that the underlying mechanism of these transitions relies on the motion of the representative points corresponding to the system's nondegenerated spatial transverse Fourier modes in the parametric Strutt diagram. A scaling law is used to demonstrate that the compact interval of the scalar coupling parameter values leading to cluster synchronization broadens in a square-power-like fashion as the number of oscillators is increased. The analytical approach is confirmed by numerical simulations.
Politikos, D.; Somarakis, S.; Tsiaras, K. P.; Giannoulaki, M.; Petihakis, G.; Machias, A.; Triantafyllou, G.
2015-11-01
A 3-D full life cycle population model for the North Aegean Sea (NAS) anchovy stock is presented. The model is two-way coupled with a hydrodynamic-biogeochemical model (POM-ERSEM). The anchovy life span is divided into seven life stages/age classes. Embryos and early larvae are passive particles, but subsequent stages exhibit active horizontal movements based on specific rules. A bioenergetics model simulates the growth in both the larval and juvenile/adult stages, while the microzooplankton and mesozooplankton fields of the biogeochemical model provide the food for fish consumption. The super-individual approach is adopted for the representation of the anchovy population. A dynamic egg production module, with an energy allocation algorithm, is embedded in the bioenergetics equation and produces eggs based on a new conceptual model for anchovy vitellogenesis. A model simulation for the period 2003-2006 with realistic initial conditions reproduced well the magnitude of population biomass and daily egg production estimated from acoustic and daily egg production method (DEPM) surveys, carried out in the NAS during June 2003-2006. Model simulated adult and egg habitats were also in good agreement with observed spatial distributions of acoustic biomass and egg abundance in June. Sensitivity simulations were performed to investigate the effect of different formulations adopted for key processes, such as reproduction and movement. The effect of the anchovy population on plankton dynamics was also investigated, by comparing simulations adopting a two-way or a one-way coupling of the fish with the biogeochemical model.
Jagau, Thomas-Christian
2012-01-01
Coupled-cluster (CC) theory is one of the most successful approaches in high-accuracy quantum chemistry. The present thesis makes a number of contributions to the determination of molecular properties and excitation energies within the CC framework. The multireference CC (MRCC) method proposed by Mukherjee and coworkers (Mk-MRCC) has been benchmarked within the singles and doubles approximation (Mk-MRCCSD) for molecular equilibrium structures. It is demonstrated that Mk-MRCCSD yields reliable...
Liakos, Dimitrios G; Neese, Frank
2015-09-08
The recently developed domain-based local pair natural orbital coupled cluster theory with single, double, and perturbative triple excitations (DLPNO-CCSD(T)) delivers results that are closely approaching those of the parent canonical coupled cluster method at a small fraction of the computational cost. A recent extended benchmark study established that, depending on the three main truncation thresholds, it is possible to approach the canonical CCSD(T) results within 1 kJ (default setting, TightPNO), 1 kcal/mol (default setting, NormalPNO), and 2-3 kcal (default setting, LoosePNO). Although thresholds for calculations with TightPNO are 2-4 times slower than those based on NormalPNO thresholds, they are still many orders of magnitude faster than canonical CCSD(T) calculations, even for small and medium sized molecules where there is little locality. The computational effort for the coupled cluster step scales nearly linearly with system size. Since, in many instances, the coupled cluster step in DLPNO-CCSD(T) is cheaper or at least not much more expensive than the preceding Hartree-Fock calculation, it is useful to compare the method against modern density functional theory (DFT), which requires an effort comparable to that of Hartree-Fock theory (at least if Hartree-Fock exchange is part of the functional definition). Double hybrid density functionals (DHDF's) even require a MP2-like step. The purpose of this article is to evaluate the cost vs accuracy ratio of DLPNO-CCSD(T) against modern DFT (including the PBE, B3LYP, M06-2X, B2PLYP, and B2GP-PLYP functionals and, where applicable, their van der Waals corrected counterparts). To eliminate any possible bias in favor of DLPNO-CCSD(T), we have chosen established benchmark sets that were specifically proposed for evaluating DFT functionals. It is demonstrated that DLPNO-CCSD(T) with any of the three default thresholds is more accurate than any of the DFT functionals. Furthermore, using the aug-cc-pVTZ basis set and
Degroote, Matthias; Henderson, Thomas M.; Zhao, Jinmo; Dukelsky, Jorge; Scuseria, Gustavo E.
2016-03-01
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 wave function. In between, we interpolate using a single parameter. The effective 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. 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 strengths. The numerical cost is polynomial in system size and the theory can be straightforwardly applied to any realistic Hamiltonian.
Lutnæs, Ola B.; Teale, Andrew M.; Helgaker, Trygve; Tozer, David J.; Ruud, Kenneth; Gauss, Jürgen
2009-10-01
An accurate set of benchmark rotational g tensors and magnetizabilities are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster single-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the results obtained is established for the rotational g tensors by careful comparison with experimental data, taking into account zero-point vibrational corrections. After an analysis of the basis sets employed, extrapolation techniques are used to provide estimates of the basis-set-limit quantities, thereby establishing an accurate benchmark data set. The utility of the data set is demonstrated by examining a wide variety of density functionals for the calculation of these properties. None of the density-functional methods are competitive with the CCSD or CCSD(T) methods. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of density-functional calculations constrained to give the same electronic density. The importance of current dependence in exchange-correlation functionals is discussed in light of this comparison.
Directory of Open Access Journals (Sweden)
Anita Raj
Full Text Available 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.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.Findings demonstrate that men can be engaged in FP programming in
Dong, Bing; Ding, G. H.; Lei, X. L.
2017-01-01
We present a theoretical investigation for the full counting statistics of the Andreev tunneling through a quantum dot (QD) embedded between superconducting (SC) and normal leads in the presence of a strong on-site electron-phonon interaction using nonequilibrium Green function method. For this purpose, we generalize the dressed tunneling approximation (DTA) recently developed in dealing with inelastic tunneling in a normal QD system to the Andreev transport issue. This method takes account of vibrational effect in evaluation of electronic tunneling self energy in comparison with other simple approaches and meanwhile allows us to derive an explicit analytical formula for the cumulant generating function at the subgap region. We then analyze the interplay of polaronic and SC proximity effects on the Andreev reflection spectrum, current-voltage characteristics, and current fluctuations of the hybrid system. Our main findings include: (1) no phonon side peaks in the linear Andreev conductance; (2) a negative differential conductance stemming from the suppressed Andreev reflection spectrum; (3) a novel inelastic resonant peak in the differential conductance due to phonon assisted Andreev reflection; (4) enhancement or suppression of shot noise for the symmetric or asymmetric tunnel-coupling system, respectively.
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.
Brinzanik, R.; Jensen, P. J.; Bennemann, K. H.
2003-11-01
For growing inhomogeneous thin films with an island nanostructure similar to that observed in experiment we determine the nonequilibrium and the equilibrium remanent magnetization. The single-island magnetic anisotropy, the dipole coupling, and the exchange interaction between magnetic islands are taken into account within a micromagnetic model. A cluster Monte Carlo method is developed which includes coherent magnetization changes of connected islands. This causes a fast relaxation towards equilibrium for irregularly connected systems. We analyze the transition from dipole coupled islands at low coverages to a strongly connected ferromagnetic film at high coverages during film growth. For coverages below the percolation threshold the dipole interaction induces a collective magnetic order with ordering temperatures of 1 10 K for the assumed model parameters. Anisotropy causes blocking temperatures of 10 100 K and thus pronounced nonequilibrium effects. The dipole coupling leads to a somewhat slower magnetic relaxation.
Fernández-García, Aurora; Revilla, Ana; Vázquez-de Parga, Elena; Vinogradova, Anna; Rakhmanova, Aza; Karamov, Eduard; Carrera, Cristina; Delgado, Elena; Pérez-Álvarez, Lucía; Nájera, Rafael; Osmanov, Saladin
2012-01-01
Abstract The HIV-1 epidemic in Russia has been insufficiently studied, with only 11 complete genome sequences from this country currently available, only three of which are of the locally predominant genetic form, the former Soviet Union (FSU) subtype A variant (AFSU). Here we analyze 10 newly derived AFSU near full-length genome sequences from Russia. Samples were selected based on phylogenetic clustering in protease-reverse transcriptase in two of the major AFSU clusters, V77IPR (n=6), widely circulating in Russia and other FSU countries, and ASP1 (n=4), predominant in St. Petersburg. The phylogenetic analysis shows that the V77IPR genomes group in a monophyletic cluster together with 10 previously obtained AFSU genome sequences from Uzbekistan, Kazakhstan, Russia, and Cyprus, all bearing the V77I substitution in protease. Similarly, the four ASP1 genomes group in a monophyletic cluster. These results therefore show that the monophyly of V77IPR and ASP1 AFSU clusters is supported in near complete genomes. PMID:22251084
Gasbarri, P.; Monti, R.; De Angelis, C.; Sabatini, M.
2014-01-01
One of the most important problems for performing a good design of the spacecraft attitude control law is connected to its robustness when some uncertainty parameters are present on the inertial and/or on the elastic characteristics of a satellite. These uncertainties are generally intrinsic on the modeling of complex structures and in the case of large flexible structures they can be also attributed to secondary effects associated to the elasticity. One of the most interesting issues in modeling large flexible space structures is associated to the evaluation of the inertia tensor which in general depends not only on the geometric ‘fixed' characteristic of the satellite but also on its elastic displacements which of course in turn modify the ‘shape' of the satellite. Usually these terms can be considered of a second order of magnitude if compared with the ones associated to the rigid part of a structure. However the increasing demand on the dimension of satellites due to the presence for instance of very large solar arrays (necessary to generate power) and/or large antennas has the necessity to investigate their effects on their global dynamic behavior in more details as a consequence. In the present paper a methodology based on classical Lagrangian approach coupled with a standard Finite Element tool has been used to derive the full dynamic equations of an orbiting flexible satellite under the actions of gravity, gravity gradient forces and attitude control. A particular attention has been paid to the study of the effects of flexibility on the inertial terms of the spacecraft which, as well known, influence its attitude dynamic behavior. Furthermore the effects of the attitude control authority and its robustness to the uncertainties on inertial and elastic parameters has been investigated and discussed.
Directory of Open Access Journals (Sweden)
Andrew E Bruno
Full Text Available Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be time-consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192 overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and to the insertion and correct placement of sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient, CDcoeff, appears to be robust in this application, and coupled with hierarchical clustering and the overlay of crystallization outcome, reveals information of biological relevance. While tested with a single example the
Energy Technology Data Exchange (ETDEWEB)
Hu, Hanshi; Bhaskaran-Nair, Kiran; Apra, Edoardo; Govind, Niranjan; Kowalski, Karol
2014-10-02
In this paper we discuss the application of novel parallel implementation of the coupled cluster (CC) and equation-of-motion coupled cluster methods (EOMCC) in calculations of excitation energies of triplet states in beta-carotene. Calculated excitation energies are compared with experimental data, where available. We also provide a detailed description of the new parallel algorithms for iterative CC and EOMCC models involving single and doubles excitations.
Pašteka, L. F.; Eliav, E.; Borschevsky, A.; Kaldor, U.; Schwerdtfeger, P.
2017-01-01
The first ionization potential (IP) and electron affinity (EA) of the gold atom have been determined to an unprecedented accuracy using relativistic coupled cluster calculations up to the pentuple excitation level including the Breit and QED contributions. We reach meV accuracy (with respect to the experimental values) by carefully accounting for all individual contributions beyond the standard relativistic coupled cluster approach. Thus, we are able to resolve the long-standing discrepancy between experimental and theoretical IP and EA of gold.
Korona, Tatiana; Jeziorski, Bogumil
2006-11-14
One-electron density matrices resulting from the explicitly connected commutator expansion of the expectation value were implemented at the singles and doubles coupled cluster (CCSD) level. In the proposed approach the one-electron density matrix is obtained at a little extra cost in comparison to the calculation of the CCSD correlation energy. Therefore, in terms of the computational time the new method is significantly less demanding than the conventional linear-response CCSD theory which requires additionally an expensive calculation of the left-hand solution of the CCSD equations. The quality of the new density matrices was investigated by computing a set of one-electron properties for a series of molecules of varying sizes and comparing the results with data obtained using the full configuration interaction method or higher level coupled cluster theory. It has been found that the results obtained using the new approach are of the same quality as those predicted by the linear-response CCSD method. The novel one-electron density matrices have also been applied to study the energy of the electrostatic interaction for a number of van der Waals complexes, including the benzene and azulene dimers.
Chaudhuri, Rajat K; Chattopadhyay, Sudip; Mahapatra, Uttam Sinha
2013-11-27
The coupled cluster based linear response theory (CCLRT) with four-component relativistic spinors is employed to compute the electric field gradients (EFG) of (35)Cl, (79)Br, and (127)I nuclei. The EFGs resulting from these calculations are combined with experimental nuclear quadrupole coupling constants (NQCC) to determine the nuclear quadrupole moments (NQM), Q of the halide nuclei. Our estimated NQMs [(35)Cl = -81.12 mb, (79)Br = 307.98 mb, and (127)I = -688.22 mb] agree well with the new atomic values [(35)Cl = -81.1(1.2), (79)Br = 302(5), and (127)I = -680(10) mb] obtained via Fock space multireference coupled cluster method with the Dirac-Coulomb-Breit Hamiltonian. Although our estimated Q((79)Br) value deviates from the accepted reference value of 313(3) mb, it agrees well with the recently recommended value, Q((79)Br) = 308.7(20) mb. Good agreement with current reference data indicates the accuracy of the proposed value for these halogen nuclei and lends credence to the results obtained via CCLRT approach. The electron affinities yielded by this method with no extra cost are also in good agreement with experimental values, which bolster our belief that the NQMs values for halogen nuclei derived here are reliable.
van den Boogaard, Noortje M; Kersten, Fleur A M; Goddijn, Mariëtte; Bossuyt, Patrick M M; van der Veen, Fulco; Hompes, Peter G A; Hermens, Rosella P M G; Braat, Didi D M; Mol, Ben Willem J; Nelen, Willianne L D M; Hoek, Annemieke
2013-01-01
BACKGROUND: Prognostic models in reproductive medicine can help to identify subfertile couples who would benefit from fertility treatment. Expectant management in couples with a good chance of natural conception, i.e., tailored expectant management (TEM), prevents unnecessary treatment and is theref
Boogaard, N.M. van den; Kersten, F.A.M.; Goddijn, M.; Bossuyt, P.M.; Veen, F. van der; Hompes, P.G.; Hermens, R.P.M.G.; Braat, D.D.M.; Mol, B.W.; Nelen, W.L.D.M.
2013-01-01
BACKGROUND: Prognostic models in reproductive medicine can help to identify subfertile couples who would benefit from fertility treatment. Expectant management in couples with a good chance of natural conception, i.e., tailored expectant management (TEM), prevents unnecessary treatment and is theref
Mitosis-coupled, microtubule-dependent clustering of endosomal vesicles around centrosomes.
Takatsu, Hiroyuki; Katoh, Yohei; Ueda, Tomoko; Waguri, Satoshi; Murayama, Takashi; Takahashi, Senye; Shin, Hye-Won; Nakayama, Kazuhisa
2013-01-01
Upon cell division, not only cells themselves but also their organelles undergo drastic shape changes, although the behaviors of organelles other than the Golgi apparatus remain poorly understood. We followed the spatiotemporal changes in the localization of transferrin receptor (TfnR) and other proteins. In early mitotic phases, a population of proteins cycling through the endocytic recycling compartment (ERC) exhibits a distinct spatiotemporal change from that of Golgi proteins. In prophase/prometaphase, when the cell surface-to-volume ratio is reaching its minimum, the ERC proteins are transiently assembled around the centrated centrosome in a microtubule- and dynein-dependent manner, and soon separated polewards into two clusters concomitant with separation of duplicated centrosomes. Electron microscopic analysis revealed that endosomal vesicles containing endocytosed transferrin cluster tightly around centrosomes without fusing with one another. As cytokinesis proceeds, the clusters gradually collapse, and the ERC proteins reassemble around the furrowing equatorial region. FRAP (fluorescence recovery after photobleaching) analyses of EGFP-TfnR-expressing cells revealed minimal membrane exchange between the endosomal clusters and other cellular compartments until anaphase/telophase, when membrane traffic resumes. Our observations indicate that ERC clustering around centrosomes plays a fundamental role in restricting membrane delivery to the plasma membrane during early mitotic phases, when the cell surface-to-volume ratio reaches its minimum.
Eriksen, Janus J; Matthews, Devin A; Jørgensen, Poul; Gauss, Jürgen
2016-05-21
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 set 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.
Evangelista, Francesco A.; Gauss, Jürgen
2012-06-01
We consider the recursive single commutator (RSC) approximation of the Baker-Campbell-Hausdorff expansion introduced by Yanai and Chan [T. Yanai, G.K.-L. Chan, J. Chem. Phys. 124 (2006) 194106] and apply it in order to approximate the similarity transformation of the Hamiltonian in both traditional and unitary coupled cluster theory. The equilibrium bond distance, harmonic vibrational frequency, and anharmonic constant of H2, HF, N2, CuH, and Cu2 were computed using the coupled cluster approach with single and double excitations (CCSD) and CCSD with the RSC approximation of the similarity-transformed Hamiltonian (CCSD-RSC). Our results demonstrate that the RSC approximation introduces substantial errors in the estimates of molecular properties. The leading pejorative effects of the RSC approximation can be traced back to the imbalanced description of diagrams arising from the term {1}/{2}[H^,T,T]. Following this analysis we consider a modified RSC scheme correct to fourth-order in the energy, which is found to reproduce CCSD results more closely. The RSC scheme is also applied in conjunction with the state-specific multireference coupled cluster approach of Mukherjee and co-workers [U.S. Mahapatra, B. Datta, D. Mukherjee, J. Chem. Phys. 110 (1999) 6171] to compute the potential energy curve of the BeH2 model, the vibrational frequencies of ozone, and the singlet-triplet splitting of p-benzyne. These examples show that the deterioration of the results caused by the RSC scheme is analogous to the one observed in the single-reference case. Implications for the formulation of approximate internally contracted multireference theories are discussed.
Application of a Relativistic Coupled-Cluster Theory to the Effective Electric Field in YbF
Abe, M; Hada, M; Das, B P; Tatewaki, H; Mukherjee, D
2014-01-01
An accurate determination of the effective electric field (Eeff) in YbF is important, as it can be combined with the results of future experiments to give an improved new limit for the electric dipole moment of the electron. We report a relativistic coupled-cluster calculation of this quantity in which all the core electrons were excited. It surpasses the approximations made in the previous reported calculations. We obtain a value of 23.1 GV/cm for Eeff in YbF with an estimated error of less than 10%. The crucial roles of the basis sets and the core excitations in our work are discussed.
DEFF Research Database (Denmark)
Silva-Junior, Mario R.; Sauer, Stephan P. A.; Schreiber, Marko;
2010-01-01
to those obtained previously with the smaller TZVP basis set. For each of the three coupled cluster methods, a correlation coefficient greater than 0.994 is found between the vertical excitation energies computed with the two basis sets. The deviations of the CC2 and CCSDR(3) results from the CC3 reference...... strengths and excited-state dipole moments, CC2 calculations with the aug-cc-pVTZ and TZVP basis sets give correlation coefficients of 0.966 and 0.833, respectively, implying that basis set convergence is slower for these one-electron properties....
DEFF Research Database (Denmark)
Thomsen, Bo; Hansen, Mikkel Bo; Seidler, Peter
2012-01-01
We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations...... with results from the recently reported [P. Seidler, M. B. Hansen, W. Györffy, D. Toffoli, and O. Christiansen, J. Chem. Phys. 132, 164105 (2010)] vibrational configuration interaction damped response function calculated using a symmetric Lanczos algorithm. Calculations of IR spectra of oxazole, cyclopropene...
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.
Baldi, Marco; Maccio, Andrea V
2011-01-01
We investigate the effects of a coupled Dark Energy (cDE) scalar field on the alignment between satellites and matter distributions in galaxy clusters. Using high-resolution N-body simulations for LCDM and cDE cosmological models, we compute the probability density distribution for the alignment angle between the satellite galaxies and underlying matter distributions, finding a difference between the two scenarios. With respect to LCDM, in cDE cosmologies the satellite galaxies are less preferentially located along the major axis of the matter distribution, possibly reducing the tension with obersevational data. A physical explanation is that the coupling between dark matter and dark energy acts as an additional tidal force on the satellite galaxies diminishing the alignments between their distribution and the matter one. Through a likelihood ratio test based on the generalized chi square statistics, the null hypothesis that the two probability distributions come from the same parent population is rejected at...
Energy Technology Data Exchange (ETDEWEB)
Minati, Ludovico, E-mail: lminati@ieee.org, E-mail: ludovico.minati@unitn.it [MR-Lab, Center for Mind/Brain Science, University of Trento, Italy and Scientific Department, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan (Italy)
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.
Wilke, Jeremiah J; Schaefer, Henry F
2011-08-01
R12 methods have now been established to improve both the efficiency and accuracy of wave function-based theories. While closed-shell and spin-orbital methodologies for coupled cluster theory are well-studied, R12 corrections based on an open-shell, spin-restricted formalism have not been well developed. We present an efficient spin-restricted R12 method based on the symmetric exchange or Z-averaged approach that reduces the number of variational parameters. The current formalism reduces spin contamination relative to unrestricted methods but remains rigorously size consistent in contrast to other spin-adapted formulations. The theory is derived entirely in spin-orbital quantities, but Z-averaged symmetries are exploited to minimize the computational work in the residual equations. R12 corrections are formulated in a perturbative manner and are therefore obtained with little extra cost relative to the standard coupled cluster problem. R12 results with only a triple-ζ basis are competitive with conventional aug-cc-pV5Z and aug-cc-pV6Z results, demonstrating the utility of the method in thermochemical problems for high-spin open-shell systems.
Eriksen, Janus Juul; Jørgensen, Poul; Gauss, Jürgen
2015-01-01
The accuracy with which total energies of open-shell species may be calculated using coupled cluster perturbative triples expansions is investigated. In particular, the acclaimed CCSD(T) model, in which a non-iterative correction for the effect of triple excitations is added to the coupled cluster singles and doubles (CCSD) energy, is compared to the second- through sixth-order models of the recently proposed CCSD(T-n) triples series 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 set of 18 atoms and small radicals with comparable RHF-based results, it is found that not only the numerical consistency of the CCSD(T) model, but also its fortuitous cancellation of errors for closed-shell systems break down in the transition from closed- to open-shell systems. For the higher-order models of the CCSD(T-n) series, however, no behavioral differences are found between the correlated descriptions of c...
Institute of Scientific and Technical Information of China (English)
SUN Peiyan; BAO Mutai; GAO Zhenhui; LI Mei; ZHAO Yuhui; WANG Xinping; ZHOU Qing; WANG Xiulin
2006-01-01
By gas chromatogram, six crude oils fingerprinting distributed in four oilfields and four oil platforms were analyzed and the corresponding normal paraffin hydrocarbon (including pristane and phytane) concentration was obtained by the internal standard method. The normal paraffin hydrocarbon distribution patterns of six crude oils were built and compared. The cluster analysis on the normal paraffin hydrocarbon concentration was conducted for classification and some ratios of oils were used for oils comparison. The results indicated: there was a clear difference within different crude oils in different oil fields and a small difference between the crude oils in the same oil platform. The normal paraffin hydrocarbon distribution pattern and ratios, as well as the cluster analysis on the normal paraffin hydrocarbon concentration can have a better differentiation result for the crude oils with small difference than the original gas chromatogram.
Wang, Zhifan; Tu, Zheyan; Wang, Fan
2014-12-09
Excitation energies of closed-shell systems based on the equation-of-motion (EOM) coupled-cluster theory at the singles and doubles (CCSD) level with spin-orbit coupling (SOC) included in the post-Hartree-Fock treatment are implemented in the present work. SOC can be included in both the CC and EOM steps (EOM-SOC-CCSD) or only in the EOM part (SOC-EOM-CCSD). The latter approach is an economical way to account for SOC effects, but excitation energies with this approach are not size-intensive. When the unlinked term in the latter approach is neglected (cSOC-EOM-CCSD), size-intensive excitation energies can be obtained. Time-reversal symmetry and spatial symmetry are exploited to reduce the computational effort. Imposing time-reversal symmetry results in a real matrix representation for the similarity-transformed Hamiltonian, which facilitates the requirement of time-reversal symmetry for new trial vectors in Davidson's algorithm. Results on some closed-shell atoms and molecules containing heavy elements show that EOM-SOC-CCSD can provide excitation energies and spin-orbit splittings with reasonable accuracy. On the other hand, the SOC-EOM-CCSD approach is able to afford accurate estimates of SOC effects for valence electrons of systems containing elements up to the fifth row, while cSOC-EOM-CCSD is less accurate for spin-orbit splittings of transitions involving p1/2 spinors, even for Kr.
Bartlett, Rodney J; Musiał, Monika
2006-11-28
The nCC hierarchy of coupled-cluster approximations, where n guarantees exactness for n electrons and all products of n electrons are derived and applied to several illustrative problems. The condition of exactness for n=2 defines nCCSD=2CC, with nCCSDT=3CC and nCCSDTQ=4CC being exact for three and four electrons. To achieve this, the minimum number of diagrams is evaluated, which is less than in the corresponding CC model. For all practical purposes, nCC is also the proper definition of a size-extensive CI. 2CC is also an orbitally invariant coupled electron pair approximation. The numerical results of nCC are close to those for the full CC variant, and in some cases are closer to the full CI reference result. As 2CC is exact for separated electron pairs, it is the natural zeroth-order approximation for the correlation problem in molecules with other effects introduced as these units start to interact. The nCC hierarchy of approximations has all the attractive features of CC including its size extensivity, orbital invariance, and orbital insensitivity, but in a conceptually appealing form suited to bond breaking, while being computationally less demanding. Excited states from the equation of motion (EOM-2CC) are also reported, which show results frequently approaching those of EOM-CCSDT.
Full simulation study of the top Yukawa coupling at the ILC at $\\sqrt{s}$ = 1 TeV
Price, Tony; Strube, Jan; Tanabe, Tomohiko
2015-01-01
We present a study of the expected precision for measurement of the top Yukawa coupling, yt, in e+e- collisions at a center-of-mass energy of 1 TeV and assuming a beam polarization of P (e-, e+) = (-0.8,+0.2). Independent analyses of ttH final states containing at least six hadronic jets are performed, based on detailed simulations of SiD and ILD, the two candidate detector concepts for the ILC. We estimate that a statistical precision of yt of 4% can be obtained with an integrated luminosity of 1 $\\mathrm{ab}^{-1}$.
Energy Technology Data Exchange (ETDEWEB)
Yomba, Emmanuel, E-mail: emmanuel.yomba@csun.edu; Zakeri, Gholam-Ali, E-mail: ali.zakeri@csun.edu
2016-02-05
We investigate the existence of various solitary wave solutions in coupled Schrödinger equations with specific cubic and quintic nonlinearities. This system arises in wave propagation in fiber optics with focusing and defocusing with modulated nonlinearities. We obtain front–front, bright–bright, dark–dark, and dark–bright like solitons using a direct approach, and then, by reducing the system of equations to a single auxiliary equation of a Duffing-type ordinary differential equation, we provide a large class of Jacobi-elliptic solutions. These solutions are presented in the exact form and analyzed. We find a class of wide localized and snake-like (in both space and time) vector solitons. One of the novel aspects of this study is that we have shown that the qualitative behavior of the solutions is independent of the choice of similarity variables. Numerical results show that the solutions of the above system are stable with up to 10% white noises. - Highlights: • Dynamics of wide and snake-like pulses is analyzed for coupled Schrödinger equations. • Qualitative appearance of solutions is analyzed using various similarity variables. • Effect of change in parameter-values on dynamics of the solutions is investigated. • Vectors front–front, bright–bright, dark–dark and dark–bright solitons are obtained.
Full simulation study of the top Yukawa coupling at the ILC at √(s) = 1 TeV
Energy Technology Data Exchange (ETDEWEB)
Price, T. [University of Birmingham, Birmingham (United Kingdom); Roloff, P. [CERN, Geneva (Switzerland); Strube, J. [Tohoku University, Sendai (Japan); Pacific Northwest National Laboratory, Richland, WA (United States); Tanabe, T. [ICEPP, The University of Tokyo, Tokyo (Japan)
2015-07-15
We present a study of the expected precision for the measurement of the top Yukawa coupling, y{sub t} in e{sup +}e{sup -} collisions at a center-of-mass energy of 1 TeV. Independent analyses of t anti tH final states containing at least six hadronic jets are performed, based on detailed simulations of SiD and ILD, the two candidate detector concepts for the ILC. We estimate that a statistical precision on y{sub t} of 4.5 % can be obtained with an integrated luminosity of 1 ab{sup -1} that is split equally between two configurations for the beam polarization P(e{sup -},e{sup +}), (-80 %, +20 %) and (+80 %, -20 %). This estimate improves to 4 % if the 1 ab{sup -1} sample is assumed to be fully in the P(e{sup -},e{sup +}) = (-80 %, +20 %) configuration. (orig.)
Mani, B. K.; Chattopadhyay, S.; Angom, D.
2017-04-01
We report the development of a parallel FORTRAN code, RCCPAC, to solve the relativistic coupled-cluster equations for closed-shell and one-valence atoms and ions. The parallelization is implemented through the use of message passing interface, which is suitable for distributed memory computers. The coupled-cluster equations are defined in terms of the reduced matrix elements, and solved iteratively using Jacobi method. The ground and excited states of coupled-cluster wave functions obtained from the code could be used to compute different properties of closed-shell and one-valence atom or ion. As an example we compute the ground state correlation energy, attachment energies, E1 reduced matrix elements and hyperfine structure constants.
Energy Technology Data Exchange (ETDEWEB)
Jung, Hyunsung; Yu, Young-Sang; Lee, Ki-Suk; Im, Mi-Young; Fischer, Peter; Bocklage, Lars; Vogel, Andreas; Bolte, Markus; Meier, Guido; Kim, Sang-Koog
2010-09-01
We employed time-and space-resolved full-field magnetic transmission soft x-ray microscopy to observe vortex-core gyrations in a pair of dipolar-coupled vortex-state Permalloy (Ni{sub 80}Fe{sub 20}) disks. The 70 ps temporal and 20 nm spatial resolution of the microscope enabled us to simultaneously measure vortex gyrations in both disks and to resolve the phases and amplitudes of both vortex-core positions. We observed their correlation for a specific vortex-state configuration. This work provides a robust and direct method of studying vortex gyrations in dipolar-coupled vortex oscillators.
Peng, Bo; Kowalski, Karol
2016-12-01
In this paper we derive basic properties of the Green's-function matrix elements stemming from the exponential coupled-cluster (CC) parametrization of the ground-state wave function. We demonstrate that all intermediates used to express the retarded (or, equivalently, ionized) part of the Green's function in the ω representation can be expressed only through connected diagrams. Similar properties are also shared by the first-order ω derivative of the retarded part of the CC Green's function. Moreover, the first-order ω derivative of the CC Green's function can be evaluated analytically. This result can be generalized to any order of ω derivatives. Through the Dyson equation, derivatives of the corresponding CC self-energy operator can be evaluated analytically. In analogy to the CC Green's function, the corresponding CC self-energy operator can be represented by connected terms. Our analysis can easily be generalized to the advanced part of the CC Green's function.
Matthews, Devin A.; Stanton, John F.
2015-02-01
The theory of non-orthogonal spin-adaptation for closed-shell molecular systems is applied to coupled cluster methods with quadruple excitations (CCSDTQ). Calculations at this level of detail are of critical importance in describing the properties of molecular systems to an accuracy which can meet or exceed modern experimental techniques. Such calculations are of significant (and growing) importance in such fields as thermodynamics, kinetics, and atomic and molecular spectroscopies. With respect to the implementation of CCSDTQ and related methods, we show that there are significant advantages to non-orthogonal spin-adaption with respect to simplification and factorization of the working equations and to creating an efficient implementation. The resulting algorithm is implemented in the CFOUR program suite for CCSDT, CCSDTQ, and various approximate methods (CCSD(T), CC3, CCSDT-n, and CCSDT(Q)).
Pillió, Zoltán; Tajti, Attila; Szalay, Péter G
2012-09-11
A new algorithm is presented for the calculation of the ladder-type term of the coupled cluster singles and doubles (CCSD) equations using two-electron integrals in atomic orbital (AO) basis. The method is based on an orbital grouping scheme, which results in an optimal partitioning of the AO integral matrix into sparse and dense blocks allowing efficient matrix multiplication. Carefully chosen numerical tests have been performed to analyze the performance of all aspects of the new algorithm. It is shown that the suggested scheme allows an efficient utilization of modern highly parallel architectures and devices in CCSD calculations. Details of the implementation in the development version of CFOUR quantum chemical program package are also presented.
DEFF Research Database (Denmark)
Thomsen, Bo; Hansen, Mikkel Bo; Seidler, Peter
2012-01-01
We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations....... The absorption spectrum can in this formulation be seen as a matrix function of the characteristic VCC Jacobian response matrix. The asymmetric matrix version of the Lanczos method is used to generate a tridiagonal representation of the VCC response Jacobian. Solving the complex response equations...... in the relevant Lanczos space provides a method for calculating the VCC damped response functions and thereby subsequently the absorption spectra. The convergence behaviour of the algorithm is discussed theoretically and tested for different levels of completeness of the VCC expansion. Comparison is made...
Tu, Zhe-Yan; Wang, Wen-Liang; Li, Ren-Zhong; Xia, Cai-Juan; Li, Lian-Bi
2016-07-01
The CCSD(T) approach based on two-component relativistic effective core potential with spin-orbit interaction just included in coupled cluster iteration is adopted to study the spectroscopic constants of ground states of Kr2, Xe2 and Rn2 dimers. The spectroscopic constants have significant basis set dependence. Extrapolation to the complete basis set limit provides the most accurate values. The spin-orbit interaction hardly affects the spectroscopic constants of Kr2 and Xe2. However, the equilibrium bond length is shortened about 0.013 Å and the dissociation energy is augmented about 18 cm-1 by the spin-orbit interaction for Rn2 in the complete basis set limit.
Savukov, I.; Safronova, U. I.; Safronova, M. S.
2015-11-01
Excitation energies, term designations, g factors, transition rates, and lifetimes of U2 + are determined using a relativistic configuration interaction (CI) + linearized-coupled-cluster (LCC) approach. The CI-LCC energies are compared with CI + many-body-perturbation-theory (MBPT) and available experimental energies. Close agreement has been found with experiment, within hundreds of cm-1. In addition, lifetimes of higher levels have been calculated for comparison with three experimentally measured lifetimes, and close agreement has been found within the experimental error. CI-LCC calculations constitute a benchmark test of the CI + all-order method in complex relativistic systems such as actinides and their ions with many valence electrons. The theory yields many energy levels, g factors, transition rates, and lifetimes of U2 + that are not available from experiment. The theory can be applied to other multivalence atoms and ions, which would be of interest to many applications.
McAlexander, Harley R; Crawford, T Daniel
2016-01-12
We have investigated the performance of the reduced-scaling coupled cluster method based on projected atomic orbitals (PAOs), pair natural orbitals (PNOs), and orbital specific virtuals (OSVs) for the prediction of linear response properties. These methods introduce different degrees of controllable sparsity in the ground-state and perturbed coupled cluster wave functions, leading to localization errors in properties such as dynamic polarizabilities and specific optical rotations. Using a series of chiral test compounds, we find that the inherent costs associated with computing response properties are significantly greater than those for determining the ground-state energy. As the dimensionality of the molecular system increases-from (pseudo)linear structures, such as fluoroalkanes, to cagelike structures, such as β-pinene-the crossover point between canonical-orbital and localized-orbital algorithms increases substantially. Furthermore, both the OSV and PNO methods provide greater reduction in cost (as measured by the size of the double-excitation space) than do PAOs, and PNOs provide the greatest level of sparsity for the systems examined here. Single-excitation truncation induces much larger errors than corresponding doubles truncation due to the fact that the first-order contribution to the one-electron perturbed wave function appears in the singles amplitudes. Both the PNO and OSV methods perform reasonably well for frequency-dependent polarizabilities provided appropriate thresholds are used for the occupation-number and weak-pair cutoffs on which each method depends. Specific rotations, however, are very sensitive to wave function truncation, to the extent that aggressive thresholds can yield the incorrect sign of the rotation, due to the delicate balance of positive and negative wave function contributions to the mixed electric-/magnetic-field response.
Send, Robert; Kaila, Ville R I; Sundholm, Dage
2011-06-07
We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes.
Yomba, Emmanuel; Zakeri, Gholam-Ali
2016-02-01
We investigate the existence of various solitary wave solutions in coupled Schrödinger equations with specific cubic and quintic nonlinearities. This system arises in wave propagation in fiber optics with focusing and defocusing with modulated nonlinearities. We obtain front-front, bright-bright, dark-dark, and dark-bright like solitons using a direct approach, and then, by reducing the system of equations to a single auxiliary equation of a Duffing-type ordinary differential equation, we provide a large class of Jacobi-elliptic solutions. These solutions are presented in the exact form and analyzed. We find a class of wide localized and snake-like (in both space and time) vector solitons. One of the novel aspects of this study is that we have shown that the qualitative behavior of the solutions is independent of the choice of similarity variables. Numerical results show that the solutions of the above system are stable with up to 10% white noises.
Li, Xiangzhu; Paldus, Josef
The reduced multireference coupled-cluster method with singles and doubles (RMR CCSD) and its RMR CCSD(T) version are employed to study the energetics of 1,n-didehydro-polyenes. The RMR CCSD method accounts for quasi-degeneracy by exploiting a multireference (MR) CISD wave function as an external source of the most important (primary) triples and quadruples while the subsequent perturbative correction for the secondary triples leads to RMR CCSD(T). The resulting energies are compared with those yielded by the standard single-reference (SR) CCSD and CCSD(T) approaches. We first determine the optimal geometry for each species considered. Using the CC methods just mentioned we then compute the energy of the lowest-lying singlet and triplet states, the implied singlet-triplet splitting, and determine the spin multiplicity of the ground state. We point out the relationship between the degree of the diradical character, the extent of quasi-degeneracy or the MR nature of the state considered, the distance separating the radical centers and, finally, the size of the largest doubly excited cluster amplitude in the CC wave functions.
球状泡群内气泡的耦合振动∗%Coupled oscillation of bubbles in a spherical bubble cluster
Institute of Scientific and Technical Information of China (English)
王成会; 莫润阳; 胡静; 陈时
2015-01-01
The pressure wave emitted by a pulsating bubble affects the motions of other bubbles, so in an acoustic field bubbles are in a state of coupled oscillation. In this paper, a cluster with cavitation bubbles inside is considered, and a mathematical model is developed to describe the dynamics of the bubbles of the same radius inside a spherical cluster when the effects of coupled oscillation are included. Based on this new model, the nonlinear acoustic response of cavitation bubbles is analyzed numerically. Comparison of our model with those in the literature, shows that bubbles are suppressed heavily. Because of the coupled oscillations of bubbles, the motions of a bubble are affected by more constraints in the system, which cause the decrease of natural frequency of the bubbles. The nonlinear acoustical response of bubbles is improved by the coupled oscillation in a bubble cluster. With the rise in number density of the cluster, the suppression of bubble oscillation is enhanced. For a cluster of 1 mm radius, when the bubble number is below 500, the change of bubble number may cause a sharp decrease of maximum radial displacement of the bubbles. In cavitation region, there are bubble clusters and large-sized bubble, and the moving large bubble can absorb small bubbles from the surface of bubble cluster, so the bubble numbers inside a cluster varies with time, which may change the acoustic response of coupled oscillating bubbles. The increase of the liquid static pressure can suppress the oscillation of bubbles too, and there is a sensitive region (1–2 atm) that affects remarkably the acoustical response of bubbles. Driving ultrasound can affect the motion of bubble greatly. The range of cavitation bubble size is narrowed when the wave frequency increases. The bubbles whose initial radii are close to 5 µm are easy to be activated by ultrasound under given acoustic conditions, i.e. sizes of bubble cluster, surrounding liquid and inner gas. The cluster oscillation of
DEFF Research Database (Denmark)
Sauer, Stephan P. A.
1997-01-01
A new modification of the second-order polarization propagator approximation (SOPPA) is presented. In the new method, called SOPPA(CCSD), all first-order Møller - Plesset doubles and second-order Møller - Plesset singles correlation coefficients are replaced with the corresponding coupled......-cluster singles and doubles (CCSD) T2 and T1 amplitudes. This is in contrast to the earlier coupled-cluster polarization propagator approximation (CCSDPPA) in which only one of the doubles correlation coefficients was replaced in the unrelaxed second-order density matrix. The importance of this modification...
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.
Yang, MinDong; Teng, Bin; Xiao, LongFei; Ning, DeZhi; Shi, ZhongMin; Qu, Yan
2014-01-01
A new full time-domain nonlinear coupled method has been established and then applied to predict the responses of a Truss Spar in irregular wave. For the coupled analysis, a second-order time-domain approach is developed to calculate the wave forces, and a finite element model based on rod theory is established in three dimensions in a global coordinate system. In numerical implementation, the higher-order boundary element method (HOBEM) is employed to solve the velocity potential, and the 4th-order Adams-Bashforth-Moultn scheme is used to update the second-order wave surface. In deriving convergent solutions, the hull displacements and mooring tensions are kept consistent at the fairlead and the motion equations of platform and mooring-lines/risers are solved simultaneously using Newmark- β integration scheme including Newton-Raphson iteration. Both the coupled quasi-static analysis and the coupled dynamic analysis are performed. The numerical simulation results are also compared with the model test results, and they coincide very well as a whole. The slow-drift responses can be clearly observed in the time histories of displacements and mooring tensions. Some important characteristics of the coupled responses are concluded.
van Dam, Hubertus J J; Vishnu, Abhinav; de Jong, Wibe A
2011-01-11
In the past couple of decades, the massive computational power provided by the most modern supercomputers has resulted in simulation of higher-order computational chemistry methods, previously considered intractable. As the system sizes continue to increase, the computational chemistry domain continues to escalate this trend using parallel computing with programming models such as Message Passing Interface (MPI) and Partitioned Global Address Space (PGAS) programming models such as Global Arrays. The ever increasing scale of these supercomputers comes at a cost of reduced Mean Time Between Failures (MTBF), currently on the order of days and projected to be on the order of hours for upcoming extreme scale systems. While traditional disk-based check pointing methods are ubiquitous for storing intermediate solutions, they suffer from high overhead of writing and recovering from checkpoints. In practice, checkpointing itself often brings the system down. Clearly, methods beyond checkpointing are imperative to handling the aggravating issue of reducing MTBF. In this paper, we address this challenge by designing and implementing an efficient fault tolerant version of the Coupled Cluster (CC) method with NWChem, using in-memory data redundancy. We present the challenges associated with our design, including an efficient data storage model, maintenance of at least one consistent data copy, and the recovery process. Our performance evaluation without faults shows that the current design exhibits a small overhead. In the presence of a simulated fault, the proposed design incurs negligible overhead in comparison to the state of the art implementation without faults.
Emergent properties of nuclei from ab initio coupled-cluster calculations
Hagen, G; Hjorth-Jensen, M; Papenbrock, T
2016-01-01
Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO$_{\\rm sat}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to $^{56}$Ni. We derive an efficient scheme for including continuum effects in coupled-clust...
Tandon, Santokh S; Bunge, Scott D; Sanchiz, Joaquin; Thompson, Laurence K
2012-03-05
Reactions between 2,6-diformyl-4-methylphenol (DFMF) and tris(hydroxymethyl) aminomethane (THMAM = H(3)L2) in the presence of copper(II) salts, CuX(2) (X = CH(3)CO(2)(-), BF(4)(-), ClO(4)(-), Cl(-), NO(3)(-)) and Ni(CH(3)CO(2))(2) or Ni(ClO(4))(2)/NaC(6)H(5)CO(2), sodium azide (NaN(3)), and triethylamine (TEA), in one pot self-assemble giving a coordination polymer consisting of repeating pentanuclear copper(II) clusters {[Cu(2)(H(5)L(2-))(μ-N(3))](2)[Cu(N(3))(4)]·2CH(3)OH}(n) (1) and hexanuclear Ni(II) complexes [Ni(6)(H(3)L1(-))(2)(HL2(2-))(2)(μ-N(3))(4)(CH(3)CO(2))(2)]·6C(3)H(7)NO·C(2)H(5)OH (2) and [Ni(6)(H(3)L1(-))(2)(HL2(2-))(2)(μ-N(3))(4)(C(6)H(5)CO(2))(2)]·3C(3)H(7)NO·3H(2)O·CH(3)OH (3). In 1, H(5)L(2-) and in 2 and 3 H(3)L1(-) and HL2(2-) represent doubly deprotonated, singly deprotonated, and doubly deprotonated Schiff-base ligands H(7)L and H(4)L1 and a tripodal ligand H(3)L2, respectively. 1 has a novel double-stranded ladder-like structure in which [Cu(N(3))(4)](2-) anions link single chains comprised of dinuclear cationic subunits [Cu(2)(H(5)L(2-))(μ-N(3))](+), forming a 3D structure of interconnected ladders through H bonding. Nickel(II) clusters 2 and 3 have very similar neutral hexanuclear cores in which six nickel(II) ions are bonded to two H(4)L1, two H(3)L2, four μ-azido, and two μ-CH(3)CO(2)(-)/μ-C(6)H(5)CO(2)(-) ligands. In each structure two terminal dinickel (Ni(2)) units are connected to the central dinickel unit through four doubly bridging end-on (EO) μ-azido and four triply bridging μ(3)-methoxy bridges organizing into hexanuclear units. In each terminal dinuclear unit two nickel centers are bridged through one μ-phenolate oxygen from H(3)L1(-), one μ(3)-methoxy oxygen from HL2(2-), and one μ-CH(3)CO(2)(-) (2)/μ-C(6)H(5)CO(2)(-) (3) ion. Bulk magnetization measurements on 1 show moderately strong antiferromagnetic coupling within the [Cu(2)] building block (J(1) = -113.5 cm(-1)). Bulk magnetization measurements on 2
Relativistic equation-of-motion coupled-cluster method for the electron attachment problem
Pathak, Himadri; Nayak, Malaya K; Vaval, Nayana; Pal, Sourav
2016-01-01
The article considers the successful implementation of relativistic equation-of-motion coupled clus- ter method for the electron attachment problem (EA-EOMCC) at the level of single- and double- excitation approximation. The Dirac-Coulomb Hamiltonian is used to generate the single particle orbitals and two-body matrix elements. The implemented relativistic EA-EOMCC method is em- ployed to calculate ionization potential values of alkali metal atoms (Li, Na, K, Rb, Cs, Fr) and the vertical electron affinity values of LiX (X=H, F, Cl, Br), NaY (Y=H, F, Cl) starting from their closed-shell configuration. We have taken C 2 as an example to understand what should be the na- ture of the basis and cut off in the orbital energies that can be used for the correlation calculations without loosing a considerable amount of accuracy in the computed values. Both four-component and X2C calculations are done for all the opted systems to understand the effect of relativity in our calculations as well as to justify the fact tha...
Cluster synchronization in oscillatory networks
Belykh, Vladimir N.; Osipov, Grigory V.; Petrov, Valentin S.; Suykens, Johan A. K.; Vandewalle, Joos
2008-09-01
Synchronous behavior in networks of coupled oscillators is a commonly observed phenomenon attracting a growing interest in physics, biology, communication, and other fields of science and technology. Besides global synchronization, one can also observe splitting of the full network into several clusters of mutually synchronized oscillators. In this paper, we study the conditions for such cluster partitioning into ensembles for the case of identical chaotic systems. We focus mainly on the existence and the stability of unique unconditional clusters whose rise does not depend on the origin of the other clusters. Also, conditional clusters in arrays of globally nonsymmetrically coupled identical chaotic oscillators are investigated. The design problem of organizing clusters into a given configuration is discussed.
DEFF Research Database (Denmark)
Sauer, Stephan P. A.; Haq, Inam U.; Sabin, John R.
2013-01-01
Using an asymmetric-Lanczos-chain algorithm for the calculation of the coupled cluster linear response functions at the CCSD and CC2 levels of approximation, we have calculated the mean excitation energies of the noble gases He, Ne and Ar, and of the hydrogen molecule H2. Convergence with respect...
Energy Technology Data Exchange (ETDEWEB)
Wykes, M., E-mail: mikewykes@gmail.com; Parambil, R.; Gierschner, J. [Madrid Institute for Advanced Studies, IMDEA Nanoscience, Calle Faraday 9, Campus Cantoblanco, 28049 Madrid (Spain); Beljonne, D. [Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc 20, 7000 Mons (Belgium)
2015-09-21
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 fluorescence 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.
Chen, Xu-Lin; Yu, Rongmin; Wu, Xiao-Yuan; Liang, Dong; Jia, Ji-Hui; Lu, Can-Zhong
2016-06-21
Correction for 'A strongly greenish-blue-emitting Cu4Cl4 cluster with an efficient spin-orbit coupling (SOC): fast phosphorescence versus thermally activated delayed fluorescence' by Xu-Lin Chen et al., Chem. Commun., 2016, 52, 6288-6291.
Energy Technology Data Exchange (ETDEWEB)
Borschevsky, A.; Eliav, E.; Kaldor, U. [School of Chemistry, Tel Aviv University, 69978 Tel Aviv, (Israel); Vilkas, M.J.; Ishikawa, Y. [Department of Chemistry, University of Puerto Rico, P.O. Box 23346, San Juan, Puerto Rico 00931-3346 (United States)
2007-07-01
Complete text of publication follows: Measurements of the spectroscopic properties of the superheavy elements present a serious challenge to the experimentalist. Their short lifetimes and the low quantities of their production necessitate reliable prediction of transition energies to avoid the need for broad wavelength scans and to assist in identifying the lines. Thus, reliable high-accuracy calculations are necessary prior and parallel to experimental research. Nobelium and Lawrencium are at present the two most likely candidates for spectroscopic measurements, with the first experiments planned at GSI, Darmstadt. The intermediate Hamiltonian (IH) coupled cluster method is applied to the ionization potentials, electron affinities, and excitation energies of atomic nobelium and lawrencium. Large basis sets are used (37s31p26d21f16g11h6i). All levels of a particular atom are obtained simultaneously by diagonalizing the IH matrix. The matrix elements correspond to all excitations from correlated occupied orbitals to virtual orbitals in a large P space, and are 'dressed' by folding in excitations to higher virtual orbitals (Q space) at the coupled cluster singles-and-doubles level. Lamb-shift corrections are included. The same approach was applied to the lighter homologues of Lr and No, lutetium and ytterbium, for which many transition energies are experimentally known, in order to assess the accuracy of the calculation. The average absolute error of 20 excitation energies of Lu is 423 cm{sup -1}, and the error limits for Lr are therefore put at 700 cm{sup -1}. Predicted Lr excitations with large transition moments in the prime range for the planned experiment, 20,000-30,000 cm{sup -1}, are 7p {yields} 8s at 20,100 cm{sup -1} and 7p {yields}p 7d at 28,100 cm{sup -1}. In case of Yb, the calculated ionization potential was within 20 cm{sup -1} of the experiment, and the average error of the 20 lowest calculated excitations was about 300 cm{sup -1}. Hence, the
Directory of Open Access Journals (Sweden)
S. H. Li
2014-01-01
Full Text Available Under complicated driving situations, such as cornering brake, lane change, or barrier avoidance, the vertical, lateral, and longitudinal dynamics of a vehicle are coupled and interacted obviously. This work aims to propose the suitable vehicle and driver models for researching full vehicle dynamics in complicated conditions. A nonlinear three-directional coupled lumped parameters (TCLP model of a heavy-duty vehicle considering the nonlinearity of suspension damping and tire stiffness is built firstly. Then a modified preview driver model with nonlinear time delay is proposed and connected to the TCLP model to form a driver-vehicle closed-loop system. The presented driver-vehicle closed-loop system is evaluated during a double-lane change and compared with test data, traditional handling stability vehicle model, linear full vehicle model, and other driver models. The results show that the new driver model has better lane keeping performances than the other two driver models. In addition, the effects of driver model parameters on lane keeping performances, handling stability, ride comfort, and roll stability are discussed. The models and results of this paper are useful to enhance understanding the effects of driver behaviour on full vehicle dynamics.
Teale, Andrew M; Lutnæs, Ola B; Helgaker, Trygve; Tozer, David J; Gauss, Jürgen
2013-01-14
Accurate sets of benchmark nuclear-magnetic-resonance shielding constants and spin-rotation constants are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the calculated coupled-cluster constants is established by a careful comparison with experimental data, taking into account zero-point vibrational corrections. Coupled-cluster basis-set convergence is analyzed and extrapolation techniques are employed to estimate basis-set-limit quantities, thereby establishing an accurate benchmark data set. Together with the set provided for rotational g-tensors and magnetizabilities in our previous work [O. B. Lutnæs, A. M. Teale, T. Helgaker, D. J. Tozer, K. Ruud, and J. Gauss, J. Chem. Phys. 131, 144104 (2009)], it provides a substantial source of consistently calculated high-accuracy data on second-order magnetic response properties. The utility of this benchmark data set is demonstrated by examining a wide variety of Kohn-Sham exchange-correlation functionals for the calculation of these properties. None of the existing approximate functionals provide an accuracy competitive with that provided by CCSD or CCSD(T) theory. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of Kohn-Sham calculations constrained to give the same electronic density. Routes to future improvements are discussed in light of this comparison.
New redox states observed in [FeFe] hydrogenases reveal redox coupling within the H-cluster.
Adamska-Venkatesh, Agnieszka; Krawietz, Danuta; Siebel, Judith; Weber, Katharina; Happe, Thomas; Reijerse, Edward; Lubitz, Wolfgang
2014-08-13
Active [FeFe] hydrogenases can be obtained by expressing the unmaturated enzyme in Escherichia coli followed by incubation with a synthetic precursor of the binuclear [2Fe] subcluster, namely: [NEt4]2[Fe2(adt)(CO)4(CN)2] (adt = [S-CH2-NH-CH2-S](2-)). The binuclear subsite Fe2(adt)(CO)3(CN)2 is attached through a bridging cysteine side chain to a [4Fe-4S] subcluster already present in the unmaturated enzyme thus yielding the intact native "H-cluster". We present FTIR electrochemical studies of the [FeFe] hydrogenase from Chlamydomonas reinhardtii, CrHydA1, maturated with the precursor of the native cofactor [Fe2(adt)(CO)4(CN)2](2-) as well as a non-natural variant [Fe2(pdt)(CO)4(CN)2](2-) in which the bridging amine functionality is replaced by CH2. The obtained active enzyme CrHydA1(adt) shows the same redox states in the respective potential range as observed for the native system (E(ox/red) = -400 mV, E(red/sred) = -470 mV). For the Hox → Hred transition the reducing equivalent is stored on the binuclear part, ([4Fe-4S](2+)Fe(II)Fe(I) → [4Fe-4S](2+)Fe(I)Fe(I)), while the Hred → Hsred transition is characterized by a reduction of the [4Fe-4S] part of the H-cluster ([4Fe-4S](2+)Fe(I)Fe(I) → [4Fe-4S](+)Fe(I)Fe(I)). A similar transition is reported here for the CO inhibited state of the H-cluster: ([4Fe-4S](2+)Fe(I)Fe(II)CO → [4Fe-4S](+)Fe(I)Fe(II)CO). An FTIR electrochemical study of the inactive variant with the pdt ligand, CrHydA1(pdt), identified two redox states H(pdt)-ox and H(pdt)-"red". Both EPR and FTIR spectra of H(pdt)-ox are virtually identical to those of the H(adt)-ox and the native Hox state. The H(pdt)-"red" state is also characterized by a reduced [4Fe-4S] subcluster. In contrast to CrHydA1(adt), the H(pdt)-ox state of CrHydA1(pdt) is stable up to rather high potentials (+200 mV). This study demonstrates the distinct redox coupling between the two parts of the H-cluster and confirms that the [4Fe-4S]H subsite is also redox active and as
Pathak, Himadri; Sasmal, Sudip; Nayak, Malaya K.; Vaval, Nayana; Pal, Sourav
2016-08-01
The open-shell reference relativistic equation-of-motion coupled-cluster method within its four-component description is successfully implemented with the consideration of single- and double- excitation approximations using the Dirac-Coulomb Hamiltonian. At the first attempt, the implemented method is employed to calculate ionization potential value of heavy atomic (Ag, Cs, Au, Fr, and Lr) and molecular (HgH and PbF) systems, where the effect of relativity does really matter to obtain highly accurate results. Not only the relativistic effect but also the effect of electron correlation is crucial in these heavy atomic and molecular systems. To justify the fact, we have taken two further approximations in the four-component relativistic equation-of-motion framework to quantify how the effect of electron correlation plays a role in the calculated values at different levels of theory. All these calculated results are compared with the available experimental data as well as with other theoretically calculated values to judge the extent of accuracy obtained in our calculations.
Tenerani, A; Le Contel, O; Califano, F; Pegoraro, F; Robert, P; Cornilleau-Wehrlin, N; Sauvaud, J A
2012-10-12
We present a new model of self-consistent coupling between low frequency, ion-scale coherent structures with high frequency whistler waves in order to interpret Cluster data. The idea relies on the possibility of trapping whistler waves by inhomogeneous external fields where they can be spatially confined and propagate for times much longer than their characteristic electronic time scale. Here we take the example of a slow magnetosonic soliton acting as a wave guide in analogy with the ducting properties of an inhomogeneous plasma. The soliton is characterized by a magnetic dip and density hump that traps and advects high frequency waves over many ion times. The model represents a new possible way of explaining space measurements often detecting the presence of whistler waves in correspondence to magnetic depressions and density humps. This approach, here given by means of slow solitons, but more general than that, is alternative to the standard approach of considering whistler wave packets as associated with nonpropagating magnetic holes resulting from a mirror-type instability.
Bozkaya, Uğur; Sherrill, C David
2016-05-07
An efficient implementation is presented for analytic gradients of the coupled-cluster singles and doubles (CCSD) method with the density-fitting approximation, denoted DF-CCSD. Frozen core terms are also included. When applied to a set of alkanes, the DF-CCSD analytic gradients are significantly accelerated compared to conventional CCSD for larger molecules. The efficiency of our DF-CCSD algorithm arises from the acceleration of several different terms, which are designated as the "gradient terms": computation of particle density matrices (PDMs), generalized Fock-matrix (GFM), solution of the Z-vector equation, formation of the relaxed PDMs and GFM, back-transformation of PDMs and GFM to the atomic orbital (AO) basis, and evaluation of gradients in the AO basis. For the largest member of the alkane set (C10H22), the computational times for the gradient terms (with the cc-pVTZ basis set) are 2582.6 (CCSD) and 310.7 (DF-CCSD) min, respectively, a speed up of more than 8-folds. For gradient related terms, the DF approach avoids the usage of four-index electron repulsion integrals. Based on our previous study [U. Bozkaya, J. Chem. Phys. 141, 124108 (2014)], our formalism completely avoids construction or storage of the 4-index two-particle density matrix (TPDM), using instead 2- and 3-index TPDMs. The DF approach introduces negligible errors for equilibrium bond lengths and harmonic vibrational frequencies.
The coupled-cluster approach to quantum many-body problem in a three-Hilbert-space reinterpretation
Bishop, Raymond F
2013-01-01
The quantum many-body bound-state problem in its computationally successful coupled cluster method (CCM) representation is reconsidered. In conventional practice one factorizes the ground-state wave functions $|\\Psi\\rangle= e^S |\\Phi\\rangle$ which live in the "physical" Hilbert space ${\\cal H}^{(P)}$ using an elementary ansatz for $|\\Phi\\rangle$ plus a formal expansion of $S$ in an operator basis of multi-configurational creation operators. In our paper a reinterpretation of the method is proposed. Using parallels between the CCM and the so called quasi-Hermitian, alias three-Hilbert-space (THS), quantum mechanics, the CCM transition from the known microscopic Hamiltonian (denoted by usual symbol $H$), which is self-adjoint in ${\\cal H}^{(P)}$, to its effective lower-case isospectral avatar $\\hat{h}=e^{-S} H e^S$, is assigned a THS interpretation. In the opposite direction, a THS-prescribed, non-CCM, innovative reinstallation of Hermiticity is shown to be possible for the CCM effective Hamiltonian $\\hat{h}$, ...
Eriksen, Janus J; Jørgensen, Poul; Gauss, Jürgen
2016-01-01
We extend our assessment of the potential of perturbative coupled cluster (CC) expansions for a test set of open-shell species to the description of quadruple excitations. In doing so, we compare the prominent CCSDT(Q) and lambda-CCSDT(Q) (a-CCSDT(Q)) models, in which the CC singles, doubles, and triples (CCSDT) energy is augmented by similar corrections for quadruple excitations, to the second- through sixth-order models of the CCSDT(Q-n) quadruples series, which is based on a CCSDT rather than an HF zeroth-order state. By comparing the models in terms of the size-intensive recovery of as well as the total deviation from the quadruples contribution to CC singles, doubles, triples, and quadruples (CCSDTQ) energies, we find (i) that the accuracy offered by the CCSDT(Q) and a-CCSDT(Q) models is strongly dependent on the spin of the molecular ground state - like for the CCSD(T) model in the first part of the present series [arXiv:1512.02846] - and (ii) that the performance of the CCSDT(Q-n) models is practically...
Ovchinnikov, Vasily A; Sundholm, Dage
2014-04-21
The 0-0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations. Excitation energies have also been calculated at the linear-response time-dependent density functional theory (TDDFT) level using the B3LYP functional. Large basis sets have been employed for ensuring that the obtained excitation energies are close to the basis-set limit. Zero-point vibrational energy corrections have been calculated at the B3LYP and CC2 levels for the ground and excited states rendering direct comparisons with high-precision spectroscopy measurements feasible. The obtained excitation energies for the 0-0 transitions of the first excited states of guanine tautomers are in good agreement with experimental values confirming the experimental assignment of the energetic order of the tautomers of the DNA bases. For the experimentally detected guanine tautomers, the first excited state corresponds to a π→π* transition, whereas for the tautomers of adenine, thymine, and the lowest tautomer of cytosine the transition to the first excited state has n →π* character. The calculations suggest that the 0-0 transitions of adenine, thymine, and cytosine are not observed in the absorption spectrum due to the weak oscillator strength of the formally symmetry-forbidden transitions, while 0-0 transitions of thymine have been detected in fluorescence excitation spectra.
Ichino, Takatoshi; Cheng, Lan; Stanton, John F.
2016-06-01
The innovative application of the ion-trap technique by Wester and coworkers has yielded definitive experimental values of photodetachment cross sections for the atomic oxygen radical anion (Obullet -) [Hlavenka et al., J. Chem. Phys. 130, 061105 (2009)]. In the present study, equation-of-motion coupled-cluster (EOM-CC) calculations have been performed to derive theoretical values of photodetachment cross sections for the negative ions of atoms in the first two periods of the periodic table as well as of those which belong to the alkali metal and halogen groups. Two methods have been employed to derive the cross sections. One involves the Dyson orbitals obtained from EOM-CC calculations and plane wave functions for the detached electron in the transition dipole moment integrals. The other method utilizes the moment theory following EOM-CC calculations of transition dipole moments for a large number of pseudo-states. The cross sections so evaluated for Obullet - match the experimental values very well. Generally good agreement has been found between the theoretical and experimental values of the cross sections for the atoms in the first two periods, while the present calculations cast some doubt on reported experimental values for some atoms beyond the second period. Substantial relativistic effects on the cross section have been observed for heavy elements in the alkali metal and halogen groups.
Walwyn, Wendy; John, Scott; Maga, Matthew; Evans, Christopher J; Hales, Tim G
2009-07-01
Recombinant micro and delta opioid receptors expressed in cell lines can form heterodimers with distinctive properties and trafficking. However, a role for opioid receptor heterodimerization in neurons has yet to be identified. The inhibitory coupling of opioid receptors to voltage-dependent Ca(2+) channels (VDCCs) is a relatively inefficient process and therefore provides a sensitive assay of altered opioid receptor function and expression. We examined micro-receptor coupling to VDCCs in dorsal root ganglion neurons of delta(+/+), delta(+/-), and delta(-/-) mice. Neurons deficient in delta receptors exhibited reduced inhibition of VDCCs by morphine and [D-Ala(2),Phe(4),Gly(5)-ol]-enkephalin (DAMGO). An absence of delta receptors caused reduced efficacy of DAMGO without affecting potency. An absence of delta receptors reduced neither the density of VDCCs nor their inhibition by either the GABA(B) receptor agonist baclofen or intracellular guanosine 5'-O-(3-thio)triphosphate. Flow cytometry revealed a reduction in micro-receptor surface expression in delta(-/-) neurons without altered DAMGO-induced internalization. There was no change in micro-receptor mRNA levels. D-Phe-Cys-Tyr-D-Trp-Arg-Thr-Pen-Thr-NH(2)-sensitive mu-receptor-coupling efficacy was fully restored to delta(+/+) levels in delta(-/-) neurons by expression of recombinant delta receptors. However, the dimerization-deficient delta-15 construct expressed in delta(-/-) neurons failed to fully restore the inhibitory coupling of micro-receptors compared with that seen in delta(+/+) neurons, suggesting that, although not essential for micro-receptor function, micro-delta receptor dimerization contributes to full micro-agonist efficacy. Because DAMGO exhibited a similar potency in delta(+/+) and delta(-/-) neurons and caused similar levels of internalization, the role for heterodimerization is probably at the level of receptor biosynthesis.
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Minnis AM
2015-05-01
Full Text Available Alexandra M Minnis,1,2 Irene A Doherty,1,3 Tracy L Kline,1 William A Zule,1 Bronwyn Myers,4,5 Tara Carney,4 Wendee M Wechsberg1,3,6,7 1RTI International, Research Triangle Park, NC, 2School of Public Health, University of California, Berkeley, CA, 3University of North Carolina, Chapel Hill, NC, USA; 4Alcohol, Tobacco and Other Drug Research Unit, South African Medical Research Council, 5Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; 6North Carolina State University, Raleigh, 7Duke University School of Medicine, Durham, NC, USA Background: Inequitable gender-based power in relationships and intimate partner violence contribute to persistently high rates of HIV infection among South African women. We examined the effects of two group-based HIV prevention interventions that engaged men and their female partners together in a couples intervention (Couples Health CoOp [CHC] and a gender-separate intervention (Men’s Health CoOp/Women’s Health CoOp [MHC/WHC] on women’s reports of power, communication, and conflict in relationships. Methods: The cluster-randomized field experiment included heterosexual couples from a high-density South African township in which neighborhoods were randomized to one of the intervention arms or a control arm that received the WHC only. Participants completed in-person study visits at baseline and 6-month follow-up. We examined group differences using one-way analysis of variance and multivariable regression models.Results: Of the 290 couples enrolled, 255 women remained in the same partnership over 6 months. Following the intervention, women in the CHC arm compared with those in the WHC arm were more likely to report an increase in relationship control (ß=0.92, 95% confidence interval [CI]: 0.02, 1.83, P=0.045 and gender norms supporting female autonomy in relationships (ß=0.99, 95% CI: 0.07, 1.91, P=0.035. Women in the MHC/WHC arm were more likely to report increases
Boström, Jonas; Pitoňák, Michal; Aquilante, Francesco; Neogrády, Pavel; Pedersen, Thomas Bondo; Lindh, Roland
2012-06-12
We compute noncovalent intermolecular interaction energies for the S22 test set [Phys. Chem. Chem. Phys.2006, 8, 1985-1993] of molecules at the Møller-Plesset and coupled cluster levels of supermolecular theory using density fitting (DF) to approximate all two-electron integrals. The error due to the DF approximation is analyzed for a range of auxiliary basis sets derived from Cholesky decomposition (CD) in conjunction with correlation consistent and atomic natural orbital valence basis sets. A Cholesky decomposition threshold of 10(-4)Eh for full molecular CD and its one-center approximation (1C-CD) generally yields errors below 0.03 kcal/mol, whereas 10(-3)Eh is sufficient to obtain the same level of accuracy or better with the atomic CD (aCD) and atomic compact CD (acCD) auxiliary basis sets. Comparing to commonly used predefined auxiliary basis sets, we find that while the aCD and acCD sets are larger by a factor of 2-4 with triple-ζ AO basis sets, they provide results 1-2 orders of magnitude more accurate.
Jang, Jinwoo; Smyth, Andrew W.
2017-01-01
The objective of structural model updating is to reduce inherent modeling errors in Finite Element (FE) models due to simplifications, idealized connections, and uncertainties of material properties. Updated FE models, which have less discrepancies with real structures, give more precise predictions of dynamic behaviors for future analyses. However, model updating becomes more difficult when applied to civil structures with a large number of structural components and complicated connections. In this paper, a full-scale FE model of a major long-span bridge has been updated for improved consistency with real measured data. Two methods are applied to improve the model updating process. The first method focuses on improving the agreement of the updated mode shapes with the measured data. A nonlinear inequality constraint equation is used to an optimization procedure, providing the capability to regulate updated mode shapes to remain within reasonable agreements with those observed. An interior point algorithm deals with nonlinearity in the objective function and constraints. The second method finds very efficient updating parameters in a more systematic way. The selection of updating parameters in FE models is essential to have a successful updating result because the parameters are directly related to the modal properties of dynamic systems. An in-depth sensitivity analysis is carried out in an effort to precisely understand the effects of physical parameters in the FE model on natural frequencies. Based on the sensitivity analysis, cluster analysis is conducted to find a very efficient set of updating parameters.
de Lara-Castells, M. P.; Villarreal, P.; Delgado-Barrio, G.; Mitrushchenkov, A. O.
2009-11-01
An efficient full-configuration-interaction nuclear orbital treatment has been recently developed as a benchmark quantum-chemistry-like method to calculate ground and excited "solvent" energies and wave functions in small doped ΔEest clusters (N ≤4) [M. P. de Lara-Castells, G. Delgado-Barrio, P. Villarreal, and A. O. Mitrushchenkov, J. Chem. Phys. 125, 221101 (2006)]. Additional methodological and computational details of the implementation, which uses an iterative Jacobi-Davidson diagonalization algorithm to properly address the inherent "hard-core" He-He interaction problem, are described here. The convergence of total energies, average pair He-He interaction energies, and relevant one- and two-body properties upon increasing the angular part of the one-particle basis set (expanded in spherical harmonics) has been analyzed, considering Cl2 as the dopant and a semiempirical model (T-shaped) He-Cl2(B) potential. Converged results are used to analyze global energetic and structural aspects as well as the configuration makeup of the wave functions, associated with the ground and low-lying "solvent" excited states. Our study reveals that besides the fermionic nature of H3e atoms, key roles in determining total binding energies and wave-function structures are played by the strong repulsive core of the He-He potential as well as its very weak attractive region, the most stable arrangement somehow departing from the one of N He atoms equally spaced on equatorial "ring" around the dopant. The present results for N =4 fermions indicates the structural "pairing" of two H3e atoms at opposite sides on a broad "belt" around the dopant, executing a sort of asymmetric umbrella motion. This pairing is a compromise between maximizing the H3e-H3e and the He-dopant attractions, and suppressing at the same time the "hard-core" repulsion. Although the He-He attractive interaction is rather weak, its contribution to the total energy is found to scale as a power of three and it thus
Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C. S.
1985-01-01
The cluster correlation function xi sub c(r) is compared with the particle correlation function, xi(r) in cosmological N-body simulations with a wide range of initial conditions. The experiments include scale-free initial conditions, pancake models with a coherence length in the initial density field, and hybrid models. Three N-body techniques and two cluster-finding algorithms are used. In scale-free models with white noise initial conditions, xi sub c and xi are essentially identical. In scale-free models with more power on large scales, it is found that the amplitude of xi sub c increases with cluster richness; in this case the clusters give a biased estimate of the particle correlations. In the pancake and hybrid models (with n = 0 or 1), xi sub c is steeper than xi, but the cluster correlation length exceeds that of the points by less than a factor of 2, independent of cluster richness. Thus the high amplitude of xi sub c found in studies of rich clusters of galaxies is inconsistent with white noise and pancake models and may indicate a primordial fluctuation spectrum with substantial power on large scales.
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Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C.S.
1985-08-01
The cluster correlation function xi sub c(r) is compared with the particle correlation function, xi(r) in cosmological N-body simulations with a wide range of initial conditions. The experiments include scale-free initial conditions, pancake models with a coherence length in the initial density field, and hybrid models. Three N-body techniques and two cluster-finding algorithms are used. In scale-free models with white noise initial conditions, xi sub c and xi are essentially identical. In scale-free models with more power on large scales, it is found that the amplitude of xi sub c increases with cluster richness; in this case the clusters give a biased estimate of the particle correlations. In the pancake and hybrid models (with n = 0 or 1), xi sub c is steeper than xi, but the cluster correlation length exceeds that of the points by less than a factor of 2, independent of cluster richness. Thus the high amplitude of xi sub c found in studies of rich clusters of galaxies is inconsistent with white noise and pancake models and may indicate a primordial fluctuation spectrum with substantial power on large scales. 30 references.
We propose to investigate, with MINIBALL coupled to T-REX, the one-valence-proton $^{133}$Sb nucleus by the cluster transfer reaction of $^{132}$Sn on $^{7}$Li. The excited $^{133}$Sb will be populated by transfer of a triton into $^{132}$Sn, followed by the emission of an $\\alpha$-particle (detected in T-REX) and 2 neutrons. The aim of the experiment is to locate states arising from the coupling of the valence proton of $^{133}$Sb to the collective low-lying phonon excitations of $^{132}$Sn (in particular the 3$^−$). According to calculations in the weak-coupling approach, these states lie in the 4$\\, - \\,$5 MeV excitation energy region and in the spin interval 1/2$\\, - \\,$ 19/2, i.e., in the region populated by the cluster transfer reaction. The results will be used to perform advanced tests of different types of nuclear interactions, usually employed in the description of particle-phonon coupled excitations. States arising from couplings of the proton with simpler core excitations, involving few nucleons...
Eriksen, Janus J.; Matthews, Devin A.; Jørgensen, Poul; Gauss, Jürgen
2016-05-01
We extend our assessment of the potential of perturbative coupled cluster (CC) expansions for a test set of open-shell atoms and organic radicals to the description of quadruple excitations. Namely, the second- through sixth-order models of the recently proposed CCSDT(Q-n) quadruples series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)] are compared to the prominent CCSDT(Q) and ΛCCSDT(Q) models. From a comparison of the models in terms of their recovery of total CC singles, doubles, triples, and quadruples (CCSDTQ) energies, we find that the performance of the CCSDT(Q-n) models is independent of the reference used (unrestricted or restricted (open-shell) Hartree-Fock), in contrast to the CCSDT(Q) and ΛCCSDT(Q) models, for which the accuracy is strongly dependent on the spin of the molecular ground state. By further comparing the ability of the models to recover relative CCSDTQ total atomization energies, the discrepancy between them is found to be even more pronounced, stressing how a balanced description of both closed- and open-shell species—as found in the CCSDT(Q-n) models—is indeed of paramount importance if any perturbative CC model is to be of chemical relevance for high-accuracy applications. In particular, the third-order CCSDT(Q-3) model is found to offer an encouraging alternative to the existing choices of quadruples models used in modern computational thermochemistry, since the model is still only of moderate cost, albeit markedly more costly than, e.g., the CCSDT(Q) and ΛCCSDT(Q) models.
Bishop, R. F.; Li, P. H. Y.; Zinke, R.; Darradi, R.; Richter, J.; Farnell, D. J. J.; Schulenburg, J.
2017-04-01
We use the coupled cluster method (CCM) to study the ground-state properties and lowest-lying triplet excited state of the spin-half XXZ antiferromagnet on the square lattice. The CCM is applied to it to high orders of approximation by using an efficient computer code that has been written by us and which has been implemented to run on massively parallelized computer platforms. We are able therefore to present precise data for the basic quantities of this model over a wide range of values for the anisotropy parameter Δ in the range - 1 ≤ Δ 1) regimes, where Δ → ∞ represents the Ising limit. We present results for the ground-state energy, the sublattice magnetization, the zero-field transverse magnetic susceptibility, the spin stiffness, and the triplet spin gap. Our results provide a useful yardstick against which other approximate methods and/or experimental studies of relevant antiferromagnetic square-lattice compounds may now compare their own results. We also focus particular attention on the behaviour of these parameters for the easy-axis system in the vicinity of the isotropic Heisenberg point (Δ = 1) , where the model undergoes a phase transition from a gapped state (for Δ > 1) to a gapless state (for Δ ≤ 1), and compare our results there with those from spin-wave theory (SWT). Interestingly, the nature of the criticality at Δ = 1 for the present model with spins of spin quantum number s =1/2 that is revealed by our CCM results seems to differ qualitatively from that predicted by SWT, which becomes exact only for its near-classical large-s counterpart.
Eriksen, Janus J; Matthews, Devin A; Jørgensen, Poul; Gauss, Jürgen
2016-05-21
We extend our assessment of the potential of perturbative coupled cluster (CC) expansions for a test set of open-shell atoms and organic radicals to the description of quadruple excitations. Namely, the second- through sixth-order models of the recently proposed CCSDT(Q-n) quadruples series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)] are compared to the prominent CCSDT(Q) and ΛCCSDT(Q) models. From a comparison of the models in terms of their recovery of total CC singles, doubles, triples, and quadruples (CCSDTQ) energies, we find that the performance of the CCSDT(Q-n) models is independent of the reference used (unrestricted or restricted (open-shell) Hartree-Fock), in contrast to the CCSDT(Q) and ΛCCSDT(Q) models, for which the accuracy is strongly dependent on the spin of the molecular ground state. By further comparing the ability of the models to recover relative CCSDTQ total atomization energies, the discrepancy between them is found to be even more pronounced, stressing how a balanced description of both closed- and open-shell species-as found in the CCSDT(Q-n) models-is indeed of paramount importance if any perturbative CC model is to be of chemical relevance for high-accuracy applications. In particular, the third-order CCSDT(Q-3) model is found to offer an encouraging alternative to the existing choices of quadruples models used in modern computational thermochemistry, since the model is still only of moderate cost, albeit markedly more costly than, e.g., the CCSDT(Q) and ΛCCSDT(Q) models.
Peng, Bo; Kowalski, Karol
2017-09-12
The representation and storage of two-electron integral tensors are vital in large-scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this work, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition of the two-electron integral tensor in our implementation. For the size of the atomic basis set, Nb, ranging from ∼100 up to ∼2,000, the observed numerical scaling of our implementation shows [Formula: see text] versus [Formula: see text] cost of performing single CD on the two-electron integral tensor in most of the other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic orbital (AO) two-electron integral tensor from [Formula: see text] to [Formula: see text] with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled cluster formalism employing single and double excitations (CCSD) on several benchmark systems including the C60 molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10(-4) to 10(-3) to give acceptable compromise between efficiency and accuracy.
Wang, Yue; Xu, Shijie
2014-12-01
The motion of a rigid body in a uniformly rotating second degree and order gravity field is a good model for the gravitationally coupled orbit-attitude motion of a spacecraft in the close proximity of an asteroid. The relative equilibria of this full dynamics model are investigated using geometric mechanics from a global point of view. Two types of relative equilibria are found based on the equilibrium conditions: one is the Lagrangian relative equilibria, at which the circular orbit of the rigid body is in the equatorial plane of the central body; the other is the non-Lagrangian relative equilibria, at which the circular orbit is parallel to but not in the equatorial plane of central body. The existences of the Lagrangian and non-Lagrangian relative equilibria are discussed numerically with respect to the parameters of the gravity field and the rigid body. The effect of the gravitational orbit-attitude coupling is especially assessed. The existence region of the Lagrangian relative equilibria is given on the plane of the system parameters. Numerical results suggest that the negative C 20 with a small absolute value and a negative C 22 with a large absolute value favor the existence of the non-Lagrangian relative equilibria. The effect of the gravitational orbit-attitude coupling of the rigid body on the existence of the non-Lagrangian relative equilibria can be positive or negative, which depends on the harmonics C 20 and C 22, and the angular velocity of the rotation of the gravity field.
Yuan, Shuping; Si, Hongzong; Fu, Aiping; Chu, Tianshu; Tian, Fenghui; Duan, Yun-Bo; Wang, Jianguo
2011-02-10
Titanium silicalite-1 (TS-1) is an important catalyst for selective oxidation reactions. However, the nature and structure of the active sites and the mechanistic details of the catalytic reactions over TS-1 have not been well-understood, leaving a continuous debate on the genesis of active sites on the TS-1 surface in the literature. In this work, the location of Si vacancies and [Ti(OSi)(4)] and [Ti(OSi)(3)OH] sites in the MFI (Framework Type Code of ZSM-5 (Zeolite Socony Mobile-Five)) framework has been studied using a full ab initio method with 40T clusters with a Si:Ti molar ratio of 39:1. It was shown that the former four energetically favorable sites for Si vacancies are T6, T12, T4, and T8 and for Ti centers of [Ti(OSi)(4)] are T10, T4, T8 and T11, being partially the same sites. Whether by replacing Si vacancies or substituting the fully coordinated Si sites, the most preferential site for Ti is T10, which indicates that the insertion mechanism does not affect the favorable sites of Ti in the MFI lattice. For the defective [Ti(OSi)(3)OH] sites, it was found that the Si vacancy at T6 with a Ti at its neighboring T9 site (T6-def-T9-Ti pair) is the most energetically favorable one, followed by a T6-def-T5-Ti pair with a small energy gap. These findings are significant to elucidate the nature of the active sites and the mechanism of reactions catalyzed by TS-1 and to design the TS-1 catalyst.
Cerrillo, Javier; Buser, Maximilian; Brandes, Tobias
2016-12-01
Nonequilibrium transport properties of quantum systems have recently become experimentally accessible in a number of platforms in so-called full-counting experiments that measure transient and steady-state nonequilibrium transport dynamics. We show that the effect of the measurement back-action can be exploited to establish general relationships between transport coefficients in the transient regime which take the form of fluctuation-dissipation theorems in the steady state. This result becomes most conspicuous in the transient dynamics of open quantum systems under strong-coupling to non-Markovian environments in nonequilibrium settings. In order to explore this regime, a new simulation method based in a hierarchy of equations of motion has been developed. We instantiate our proposal with the study of energetic conductance between two baths connected via a few level system.
Directory of Open Access Journals (Sweden)
JONG WOON KIM
2014-04-01
In this paper, we introduce a modified scattering kernel approach to avoid the unnecessarily repeated calculations involved with the scattering source calculation, and used it with parallel computing to effectively reduce the computation time. Its computational efficiency was tested for three-dimensional full-coupled photon-electron transport problems using our computer program which solves the multi-group discrete ordinates transport equation by using the discontinuous finite element method with unstructured tetrahedral meshes for complicated geometrical problems. The numerical tests show that we can improve speed up to 17∼42 times for the elapsed time per iteration using the modified scattering kernel, not only in the single CPU calculation but also in the parallel computing with several CPUs.
Gervais, B; Zanuttini, D; Douady, J
2016-05-21
We analyze the role of the spin-orbit (SO) coupling in the dissociative dynamics of excited alkali atoms at the surface of small rare gas clusters. The electronic structure of the whole system is deduced from a one-electron model based on core polarization pseudo-potentials. It allows us to obtain in the same footing the energy, forces, and non-adiabatic couplings used to simulate the dynamics by means of a surface hopping method. The fine structure state population is analyzed by considering the relative magnitude of the SO coupling ξ, with respect to the spin-free potential energy. We identify three regimes of ξ-values leading to different evolution of adiabatic state population after excitation of the system in the uppermost state of the lowest np (2)P shell. For sufficiently small ξ, the final population of the J=12 atomic states, P12, grows up linearly from P12=13 at ξ = 0 after a diabatic dynamics. For large values of ξ, we observe a rather adiabatic dynamics with P12 decreasing as ξ increases. For intermediate values of ξ, the coupling is extremely efficient and a complete transfer of population is observed for the set of parameters associated to NaAr3 and NaAr4 clusters.
Energy Technology Data Exchange (ETDEWEB)
Choi, Jae-Gu; Choi, Young-Wook; Ham, Tae-Hee [Korea Electrotechnology Research Institute, Ansan (Korea, Republic of); Park, Hye-Suk; Kim, Ye-Seul; Kim, Hee-Joung [Yonsei University, Wonju (Korea, Republic of)
2012-02-15
We have developed a prototype full-field digital breast tomosynthesis (DBT) system by using a complementary-metal-oxide semiconductive (CMOS) array coupled with a columnar CsI(Tl) scintillator. The imaging system consists of a matrix with an active detector area of 3072 x 3888 pixels and a pixel pitch of 74.8 μm. For tomosynthesis imaging, the X-ray tube is automatically rotated in 3 .deg. increments in the shoot mode to acquire projection images at 15 different angles over a ±21 .deg. angular range in less than 10 s. The digital detector is stationary during image acquisition. In this research, we also carried out evaluation studies to characterize the performance of the system in different operational modes designed for the DBT system, e.g., binning mode and the range of view angles, in terms of the modulation transfer function (MTF), the normalized noise power spectra (NNPS), and the detective quantum efficiency (DQE): The MTF value measured at the Nyquist frequency was 18.49%, the NNPS value at zero frequency was about 1.93 x 10{sup -5} (mm{sup 2}), and the maximum value of DQE was about 47.09% for the full resolution. For the pixel binning mode, the MTF decreased more than it did for the full resolution mode due to the increased effective pixel size. However, the full resolution mode was more sensitive to noise than the pixel binning mode. For the scan angle of the DBT system, oblique incidence of X-rays on a detector caused blurring that reduced resolution. These results seem to be promising for the use of the DBT system in potential clinical applications and will provide important information when comparisons with other DBT systems are made.
Directory of Open Access Journals (Sweden)
Nobuhide Doi
Full Text Available The G protein-coupled receptors (GPCRs, which form the largest group of transmembrane proteins involved in signal transduction, are major targets of currently available drugs. Thus, the search for cognate and surrogate peptide ligands for GPCRs is of both basic and therapeutic interest. Here we describe the application of an in vitro DNA display technology to screening libraries of peptide ligands for full-length GPCRs expressed on whole cells. We used human angiotensin II (Ang II type-1 receptor (hAT1R as a model GPCR. Under improved selection conditions using hAT1R-expressing Chinese hamster ovary (CHO-K1 cells as bait, we confirmed that Ang II gene could be enriched more than 10,000-fold after four rounds of selection. Further, we successfully selected diverse Ang II-like peptides from randomized peptide libraries. The results provide more precise information on the sequence-function relationships of hAT1R ligands than can be obtained by conventional alanine-scanning mutagenesis. Completely in vitro DNA display can overcome the limitations of current display technologies and is expected to prove widely useful for screening diverse libraries of mutant peptide and protein ligands for receptors that can be expressed functionally on the surface of CHO-K1 cells.
Evidence for a chemical enrichment coupling of globular clusters and field stars in the Fornax dSph
Hendricks, Benjamin; Johnson, Christian I; Frank, Matthias J; Koch, Andreas; Mateo, Mario; Bailey, John I
2016-01-01
The globular cluster H4, located in the center of the Fornax dwarf spheroidal galaxy, is crucial for understanding the formation and chemical evolution of star clusters in low-mass galactic environments. H4 is peculiar because the cluster is significantly more metal-rich than the galaxy's other clusters, is located near the galaxy center, and may also be the youngest cluster in the galaxy. In this study, we present detailed chemical abundances derived from high-resolution (R~28000) spectroscopy of an isolated H4 member star for comparison with a sample of 22 nearby Fornax field stars. We find the H4 member to be depleted in the alpha-elements Si, Ca, and Ti with [Si/Fe]=-0.35+-0.34, [Ca/Fe]=+0.05+-0.08, and [Ti/Fe]=-0.27+-0.23, resulting in an average [alpha/Fe]=-0.19+-0.14. If this result is representative of the average cluster properties, H4 is the only known system with a low [alpha/Fe] ratio and a moderately low metallicity embedded in an intact birth environment. For the field stars we find a clear sequ...
Directory of Open Access Journals (Sweden)
von Baum Heike
2006-07-01
Full Text Available Abstract Background Spread of antibiotic resistance in hospitals is a well-known problem, but studies investigating the importance of factors potentially related to the spread of resistant bacteria in outpatients are sparse. Methods Stool samples were obtained from 206 healthy couples in a community setting in Southern Germany in 2002–2003. E. coli was cultured and minimal inhibition concentrations were tested. Prevalences of E. coli resistance to commonly prescribed antibiotics according to potential risk factors were ascertained. Results Prevalences of ampicillin resistance were 15.7% and 19.4% for women and men, respectively. About ten percent and 15% of all isolates were resistant to cotrimoxazole and doxycycline, respectively. A partner carrying resistance was the main risk factor for being colonized with resistant E. coli. Odds ratios (95% CI for ampicillin and cotrimoxazole resistance given carriage of resistant isolates by the partner were 6.9 (3.1–15.5 and 3.3 (1.5–18.0, respectively. Conclusion Our data suggest that conjugal transmission may be more important for the spread of antibiotic resistance in the community setting than commonly suspected risk factors such as previous antibiotic intake or hospital contacts.
Yoo, Jaiyul; Seljak, Uros; Zaldarriaga, Matias
2012-01-01
Kaiser redshift-space distortion formula describes well the clustering of galaxies in redshift surveys on small scales, but there are numerous additional terms that arise on large scales. Some of these terms can be described using Newtonian dynamics and have been discussed in the literature, while the others require proper general relativistic description that was only recently developed. Accounting for these terms in galaxy clustering is the first step toward tests of general relativity on horizon scales. The effects can be classified as two terms that represent the velocity and the gravitational potential contributions. Their amplitude is determined by effects such as the volume and luminosity distance fluctuation effects and the time evolution of galaxy number density and Hubble parameter. We compare the Newtonian approximation often used in the redshift-space distortion literature to the fully general relativistic equation, and show that Newtonian approximation accounts for most of the terms contributing ...
Directory of Open Access Journals (Sweden)
Qi Zhang
2014-01-01
Full Text Available With the aim to analyze field-to-line coupling effects based on energy spectrum, parallel finite-difference time-domain (FDTD method is applied to calculate the induced voltage on overhead lines under high-power electromagnetic (HPEM environment. Firstly, the energy distribution laws of HEMP (IEC 61000-2-9, HEMP (Bell Laboratory, HEMP (Paulino et al., 2010, and LEMP (IEC61000-4-5 are given. Due to the air-earth stratified medium, both the absorbing boundary and the connecting boundary applied to scattering by finite-length objects are separately set in aerial and underground parts. Moreover, the influence of line length on induced voltage is analyzed and discussed. The results indicate that the half-peak width is wider with the increase of the line length. But the steepness of induced voltage on the overhead line is invariable. There is no further increase in the peak of induced voltage especially when the line length increases to be equivalent to the wavelength of the frequency bands with the maximum energy.
Soriano, Nicolas; Vincent, Pascal; Auger, Gabriel; Cariou, Marie-Estelle; Moullec, Séverine; Lagente, Vincent; Ygout, Jean-François; Kayal, Samer; Faili, Ahmad
2015-01-22
Here, we announce the complete annotated genome sequence of a Streptococcus pyogenes M/emm83 strain, STAB1101, isolated from clustered cases in homeless persons in Brittany (France). The genome is composed of 1,709,790 bp, with a G+C content of 38.4% and 1,550 identified coding sequences (CDS), and it harbors a Tn916-like transposon.
Umetsu, Keiichi; Broadhurst, Tom; Zitrin, Adi; Okabe, Nobuhiro; Hsieh, Bau-Ching; Molnar, Sandor M
2009-01-01
We derive an accurate mass distribution of the rich galaxy cluster Cl0024+1654 (z=0.395) based on deep Subaru BR_{c}z' imaging and our recent comprehensive strong lensing analysis of HST/ACS/NIC3 observations. We define an undiluted background population of red and blue galaxies by carefully combining all color and positional information. Unlike previous work, the weak and strong lensing are in excellent agreement where the data overlap. The joint mass profile continuously steepens out to the virial radius, 2300kpc/h, with only a minor contribution, \\sim 10% in the mass, from known subcluster at a projected distance of \\sim 700kpc/h. The projected mass distribution for the entire cluster is well fitted with a single Navarro-Frenk-White model with a virial mass, M_{vir} = (1.2 \\pm 0.2) \\times 10^{15} M_{sun}/h, and a concentration, c_{vir} = 9 \\pm 1. Careful examination and interpretation of X-ray and dynamical data, based on recent high-resolution cluster collision simulations, strongly suggest that this clus...
Sarkar, Kanchan; Bhattacharyya, S P
2013-08-21
We propose and implement a simple adaptive heuristic to optimize the geometries of clusters of point charges or ions with the ability to find the global minimum energy configurations. The approach uses random mutations of a single string encoding the geometry and accepts moves that decrease the energy. Mutation probability and mutation intensity are allowed to evolve adaptively on the basis of continuous evaluation of past explorations. The resulting algorithm has been called Completely Adaptive Random Mutation Hill Climbing method. We have implemented this method to search through the complex potential energy landscapes of parabolically confined 3D classical Coulomb clusters of hundreds or thousands of charges--usually found in high frequency discharge plasmas. The energy per particle (EN∕N) and its first and second differences, structural features, distribution of the oscillation frequencies of normal modes, etc., are analyzed as functions of confinement strength and the number of charges in the system. Certain magic numbers are identified. In order to test the feasibility of the algorithm in cluster geometry optimization on more complex energy landscapes, we have applied the algorithm for optimizing the geometries of MgO clusters, described by Coulomb-Born-Mayer potential and finding global minimum of some Lennard-Jones clusters. The convergence behavior of the algorithm compares favorably with those of other existing global optimizers.
Role of Asymmetric Clusters in Desynchronization of Coherent Motion
DEFF Research Database (Denmark)
Popovych, O.; Maistrenko, Y.; Mosekilde, Erik
2002-01-01
The transition from full synchronization (coherent motion) to two-cluster dynamics is studied for a system of N globally coupled logistic maps. When increasing the nonlinearity parameter of the individual map, new periodic and strongly asymmetric two-cluster states are found to emerge in the same...... order as the periodic windows arise in the logistic map. These strongly asymmetric two-cluster states are generally first to stabilize when reducing the coupling strength. Similar phenomena are also observed for a system of globally coupled Henon maps.......The transition from full synchronization (coherent motion) to two-cluster dynamics is studied for a system of N globally coupled logistic maps. When increasing the nonlinearity parameter of the individual map, new periodic and strongly asymmetric two-cluster states are found to emerge in the same...
Energy Technology Data Exchange (ETDEWEB)
Riplinger, Christoph; Pinski, Peter; Becker, Ute; Neese, Frank, E-mail: frank.neese@cec.mpg.de, E-mail: evaleev@vt.edu [Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr (Germany); Valeev, Edward F., E-mail: frank.neese@cec.mpg.de, E-mail: evaleev@vt.edu [Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061 (United States)
2016-01-14
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
Directory of Open Access Journals (Sweden)
Li Jing-shan
2014-06-01
Full Text Available This study is concerned with the design and implementation of a real-time processing system of full resolution quick-look image of HJ-1 environmental satellite C SAR based on high-performance clusters. The system processes the first quick-look SAR image on December 9, 2012. The results show that the design and implementation of the quick-look processing system satisfies the real-time SAR image processing performance requirements at full resolution. Moreover, this system is the first real-time business system of full-resolution quick-look spaceborne SAR images in China.
Energy Technology Data Exchange (ETDEWEB)
Berardo, Enrico; Kaplan, Ferdinand; Bhaskaran Nair, Kiran; Shelton, William A.; Van Setten, Michiel J.; Kowalski, Karol; Zwijnenburg, Martijn A.
2017-08-01
We study the vertical ionisation potential, electron affinity, fundamental gap and exciton binding energy values of small bare and hydroxylated TiO2 nanoclusters to understand how the excited state properties change as a function of size and hydroxylation. In addition, we have employed a range of many-body methods; including G0W0, qsGW, EA/IP-EOM-CCSD and DFT (B3LYP, PBE), to compare the performance and predictions of the different classes of methods. We demonstrate that for bare (i.e. non-hydroxylated) clusters all many-body methods predict the same trend with cluster size. The highest occupied and lowest unoccupied DFT orbitals follow the same trends as the electron affinity and ionisation potentials predicted by the many-body methods but are generally far too shallow and deep respectively in absolute terms. In contrast, the ΔDFT method is found to yield values in the correct energy window. However, its predictions depend on the functional used and do not necessarily follow trends based on the many-body methods. The effect of hydroxylation of the clusters is to open up both the optical and fundamental gap. Finally, a simple microscopic explanation for the observed trends with cluster size and upon hydroxylation is proposed in terms of the Madelung onsite potential.
Peng, Degao; van Aggelen, Helen; Steinmann, Stephan; Yang, Yang; Yang, Weitao; Duke University Team
2014-03-01
The particle-particle random-phase approximation (pp-RPA) recently attracts extensive interests in quantum chemistry recently. Pp-RPA is a versatile model to calculate ground-state correlation energies, and double ionization potential/double electron affinity. We inspect particle-particle random-phase approximation in different perspectives to further understand its theoretical fundamentals. Viewed as summation of all ladder diagrams, the pp-RPA correlation energy is proved to be analytically equivalent to the ladder coupled-cluster doubles (ladder-CCD) theory. With this equivalence, we can make use of various well-established coupled-cluster techniques to study pp-RPA. Furthermore, we establish linear-response time-dependent density-functional theory with pairing fields (TDDFT-PF), where pp-RPA can be interpreted as the mean-field approximation to a general theory. TDDFT-PF is closely related to the density-functional theory of superconductors, but is applied to normal systems to capture exact N plus/minus 2 excitations. In the linear-response regime, both the adiabatic and non-adiabatic TDDFT-PF equations are established. This sets the fundamentals for further density-functional developments aiming for pp-RPA. These theoretical perspectives will be very helpful for future study.
Wasilewska, B.; Bednarczyk, P.; Boiano, C.; Brambilla, S.; Camera, F.; Ciemała, M.; Dorvaux, O.; Giaz, A.; Jastrzab, M.; Kihel, S.; Kmiecik, M.; Maj, A.; Matea, I.; Massarczyk, R.; Mazumdar, I.; Mentana, A.; Napiorkowski, P.; Sowicki, B.; Schwengner, R.; Riboldi, S.; Ziebliński, M.; PARIS Collaboration
2015-06-01
The first cluster of the constructed PARIS calorimeter was assembled and tested at the γELBE facility at HZDR, Dresden, Germany. The experiment was aimed at the evaluation of the performance of each detector separately as well as the whole PARIS cluster with discrete γ-ray energies seen by the PARIS ranging up to 8.9 MeV. As the detectors use phoswich configuration, with 2" × 2" × 2" LaBr3(Ce) crystal coupled to 2" × 2" × 6" NaI(Tl) one, great care must be taken during the data analysis process to obtain the best possible values for energy resolution. Two algorithms for data transformation from matrices created with slow vs fast pulse shaping to energy spectra were tested from which one was chosen for further analysis. An algorithm for adding back energies of γ-rays scattered inside the cluster was prepared, as well. Energy resolution for γ-rays in 2-8 MeV range was estimated and is presented in this paper.
Godtliebsen, Ian H; Christiansen, Ove
2013-07-07
We describe new methods for the calculation of IR and Raman spectra using vibrational response theory. Using damped linear response functions that incorporate a Lorentzian line-shape function from the outset, it is shown how the calculation of Raman spectra can be carried out through the calculation of a set of vibrational response functions in the same manner as described previously for IR spectra. The necessary set of response functions can be calculated for both vibrational coupled cluster (VCC) and vibrational configuration interaction (VCI) anharmonic vibrational wave-functions. For the efficient and simultaneous calculation of the full set of necessary response functions, a non-hermitian band Lanczos algorithm is implemented for VCC, and a hermitian band Lanczos algorithm is implemented for VCI. It is shown that the simultaneous calculation of several response functions is often advantageous. Sample calculations are presented for pyridine and the complex between pyridine and the silver cation.
Reerink, T.J.; van de Wal, R.S.W.; Borsboom, P.-P.
2009-01-01
To overcome the mechanical coupling of an ice sheet with an ice shelf, one single set of velocity equations is presented covering both the sheet and the shelf. This set is obtained by applying shared sheet-shelf approximations. The hydrostatic approximation and a constant density are the only approx
Blossier, B; De soto, F; Gravina, M; Morenas, V; Pène, O; Rodríguez-Quintero, J
2010-01-01
Some very recent computations of $\\alpha_{\\bar{\\rm MS}}(M_Z)$ from $N_f=1+1$ lattice simulations and of the running of the Strong coupling, obtained from the lattice ghost-gluon vertex, over a large momentum window are very briefly reviewed.
Institute of Scientific and Technical Information of China (English)
李睿; 张玲玲; 郭世月
2012-01-01
Co-citation and citing coupling are widely applied in documents clustering. However, for patents clustering, which one is more suitable is still a question, considering patent is not only technological document but also legal document under patent law. This paper compares them on stability, time-effectiveness, objectivity and integrity, combination with logic of patent law, and so on, and ar- gues that performance advantages of eitin~ CouDlin~ in patents clusterin~ ~r,~ ,~virl,~,lt%同被引聚类与引用耦合聚类是两种常用的文献聚类方法，本文从聚类的时效性和实际可操作性、聚类结果的完整性和稳定性、聚类原理与专利法理逻辑和创新协同效应的契合性等方面对两种方法进行对比分析，发现引用耦合聚类方法在揭示专利间的相似性方面更具优势，同被引聚类方法则更适用于发现基础专利和揭示技术演化规律。两者若结合使用，则能在解决实际问题的过程中实现优势互补。
Zhang, Jie; Carver, Chase M; Choveau, Frank S; Shapiro, Mark S
2016-10-19
The fidelity of neuronal signaling requires organization of signaling molecules into macromolecular complexes, whose components are in intimate proximity. The intrinsic diffraction limit of light makes visualization of individual signaling complexes using visible light extremely difficult. However, using super-resolution stochastic optical reconstruction microscopy (STORM), we observed intimate association of individual molecules within signaling complexes containing ion channels (M-type K(+), L-type Ca(2+), or TRPV1 channels) and G protein-coupled receptors coupled by the scaffolding protein A-kinase-anchoring protein (AKAP)79/150. Some channels assembled as multi-channel supercomplexes. Surprisingly, we identified novel layers of interplay within macromolecular complexes containing diverse channel types at the single-complex level in sensory neurons, dependent on AKAP79/150. Electrophysiological studies revealed that such ion channels are functionally coupled as well. Our findings illustrate the novel role of AKAP79/150 as a molecular coupler of different channels that conveys crosstalk between channel activities within single microdomains in tuning the physiological response of neurons.
Lipparini, Filippo; Kirsch, Till; Köhn, Andreas; Gauss, Jürgen
2017-07-11
We combine internally contracted multireference coupled cluster theory with a four-component treatment of scalar-relativistic effects based on the spin-free Dirac-Coulomb Hamiltonian. This strategy allows for a rigorous treatment of static and dynamic correlation as well as scalar-relativistic effects, which makes it viable to describe molecules containing heavy transition elements. The use of a spin-free formalism limits the impact of the four-component treatment on the computational cost to the non-rate-determining steps of the calculations. We apply the newly developed method to the lowest singlet and triplet states of the monoxides of titanium, zirconium, and hafnium and show how the interplay between electronic correlation and relativistic effects explains the electronic structure of such molecules.
Indian Academy of Sciences (India)
Lalitha Ravichandran; Debarati Bhattacharya; Nayana Vaval; Sourav Pal
2012-01-01
Dipole moment calculations of SF and ClO radicals have been carried out using the recently developed partial triples correction to Fock-space multi-reference coupled cluster method. Theoretical calculation of the doublet SF and ClO radicals is useful due to their importance in atmospheric chemistry. The dipole moments of these radicals are extremely sensitive to correlation effects. A brief insight to the way the triples correction has been implemented is presented. We compare the results obtained from our analytic response treatment with that of restricted open Hartree-Fock (ROHF) calculations. Results are presented for both relaxed and non-relaxed approach in the ROHF method. Results suggest the importance of triples corrections. The effects of orbital relaxation are also analysed from the results.
Nandy, D K; Sahoo, B K
2014-01-01
We report the implementation of equation-of-motion coupled-cluster (EOMCC) method in the four-component relativistic framework with the spherical atomic potential to generate the excited states from a closed-shell atomic configuration. This theoretical development will be very useful to carry out high precision calculations of varieties of atomic properties in many atomic systems. We employ this method to calculate excitation energies of many low-lying states in a few Ne-like highly charged ions, such as Cr XV, Fe XVII, Co XVIII and Ni XIX ions, and compare them against their corresponding experimental values to demonstrate the accomplishment of the EOMCC implementation. The considered ions are apt to substantiate accurate inclusion of the relativistic effects in the evaluation of the atomic properties and are also interesting for the astrophysical studies. Investigation of the temporal variation of the fine structure constant (\\alpha) from the astrophysical observations is one of the modern research problems...
Godtliebsen, Ian H; Christiansen, Ove
2015-10-07
It is demonstrated how vibrational IR and Raman spectra can be calculated from damped response functions using anharmonic vibrational wave function calculations, without determining the potentially very many eigenstates of the system. We present an implementation for vibrational configuration interaction and vibrational coupled cluster, and describe how the complex equations can be solved using iterative techniques employing only real trial vectors and real matrix-vector transformations. Using this algorithm, arbitrary frequency intervals can be scanned independent of the number of excited states. Sample calculations are presented for the IR-spectrum of water, Raman spectra of pyridine and a pyridine-silver complex, as well as for the infra-red spectrum of oxazole, and vibrational corrections to the polarizability of formaldehyde.
Small, David W; Head-Gordon, Martin
2017-07-14
The Coupled Cluster Valence Bond (CCVB) method, previously presented for closed-shell (CS) systems, is extended to open-shell (OS) systems. The theoretical development is based on embedding the basic OS CCVB wavefunction in a fictitious singlet super-system. This approach reveals that the OS CCVB amplitude equations are quite similar to those of CS CCVB, and thus that OS CCVB requires the same level of computational effort as CS CCVB, which is an inexpensive method. We present qualitatively correct CCVB potential energy curves for all low-lying spin states of P2 and Mn2(+). CCVB is successfully applied to the low-lying spin states of some model linear polycarbenes, systems that appear to be a hindrance to standard density functionals. We examine an octa-carbene dimer in a side-by-side orientation, which, in the monomer dissociation limit, exhibits maximal strong correlation over the length of the polycarbene.
Shen, Jun; Piecuch, Piotr
2012-04-01
We have recently suggested the CC(P;Q) methodology that can correct energies obtained in the active-space coupled-cluster (CC) or equation-of-motion (EOM) CC calculations, which recover much of the nondynamical and some dynamical electron correlation effects, for the higher-order, mostly dynamical, correlations missing in the active-space CC/EOMCC considerations. It is shown that one can greatly improve the description of biradical transition states, both in terms of the resulting energy barriers and total energies, by combining the CC approach with singles, doubles, and active-space triples, termed CCSDt, with the CC(P;Q)-style correction due to missing triple excitations defining the CC(t;3) approximation.
Energy Technology Data Exchange (ETDEWEB)
Bhaskaran-Nair, Kiran [Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70802 (United States); Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Kowalski, Karol, E-mail: karol.kowalski@pnnl.gov [William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, K8-91, P.O.Box 999, Richland, Washington 99352 (United States); Moreno, Juana; Jarrell, Mark [Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70802 (United States); Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Shelton, William A. [Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803 (United States)
2014-08-21
In both molecular and periodic solid-state systems there is a need for the accurate determination of the ionization potential and the electron affinity for systems ranging from light harvesting polymers and photocatalytic compounds to semiconductors. The development of a Green's function approach based on the coupled cluster (CC) formalism would be a valuable tool for addressing many properties involving many-body interactions along with their associated correlation functions. As a first step in this direction, we have developed an accurate and parallel efficient approach based on the equation of motion-CC technique. To demonstrate the high degree of accuracy and numerical efficiency of our approach we calculate the ionization potential and electron affinity for C{sub 60} and C{sub 70}. Accurate predictions for these molecules are well beyond traditional molecular scale studies. We compare our results with experiments and both quantum Monte Carlo and GW calculations.
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.
Bistoni, Giovanni
2017-06-12
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 applied 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, AlF3, CaF2, CuF, GaF3, YF3, AgF, InF3, HfF4 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 sub-valence 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.
Hansen, Jared A; Ehara, Masahiro; Piecuch, Piotr
2013-10-10
The left-eigenstate completely renormalized coupled-cluster (CC) method with singles, doubles, and noniterative triples [CR-CC(2,3)] and a few representative density functional theory (DFT) approaches have been applied to methanol oxidation to formic acid on a Au8(-) cluster, which is a model for aerobic oxidations on gold nanoparticles. It is demonstrated that CR-CC(2,3) supports the previous exothermic reaction mechanism, placing the initial rate-determining transition state, which corresponds to hydrogen transfer from the methoxy species to the molecular oxygen, at about 20 kcal/mol above the reactants, less than 40 kcal/mol above the O2 and CH3O(-) species coadsorbed on Au8(-), and considerably above the remaining two transition states along the reaction pathway. The DFT calculations using the previously exploited M06 hybrid functional show reasonable agreement with CR-CC(2,3), but B3LYP offers additional improvements in the description of the relevant activation energies. Pure functionals, including M06-L, BP86, and TPSS, do not work well, significantly underestimating the activation barriers, but dispersion corrections, as in B97-D, bring the results closer to the M06 accuracy level.
Mukherjee, Saikat; Bandyopadhyay, Sudip; Paul, Amit Kumar; Adhikari, Satrajit
2013-04-25
We present the molecular symmetry (MS) adapted treatment of nonadiabatic coupling terms (NACTs) for the excited electronic states (2(2)E' and 1(2)A1') of Na3 cluster, where the adiabatic potential energy surfaces (PESs) and the NACTs are calculated at the MRCI level by using an ab initio quantum chemistry package (MOLPRO). The signs of the NACTs at each point of the configuration space (CS) are determined by employing appropriate irreducible representations (IREPs) arising due to MS group, and such terms are incorporated into the adiabatic to diabatic transformation (ADT) equations to obtain the ADT angles. Since those sign corrected NACTs and the corresponding ADT angles demonstrate the validity of curl condition for the existence of three-state (2(2)E' and 1(2)A1') sub-Hilbert space, it becomes possible to construct the continuous, single-valued, symmetric, and smooth 3 × 3 diabatic Hamiltonian matrix. Finally, nuclear dynamics has been carried out on such diabatic surfaces to explore whether our MS-based treatment of diabatization can reproduce the pattern of the experimental spectrum for system B of Na3 cluster.
Non-convex polygons clustering algorithm
Directory of Open Access Journals (Sweden)
Kruglikov Alexey
2016-01-01
Full Text Available A clustering algorithm is proposed, to be used as a preliminary step in motion planning. It is tightly coupled to the applied problem statement, i.e. uses parameters meaningful only with respect to it. Use of geometrical properties for polygons clustering allows for a better calculation time as opposed to general-purpose algorithms. A special form of map optimized for quick motion planning is constructed as a result.
Energy Technology Data Exchange (ETDEWEB)
Datta, Dipayan, E-mail: datta@uni-mainz.de; Gauss, Jürgen, E-mail: gauss@uni-mainz.de [Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz (Germany)
2014-09-14
An analytic scheme is presented for the evaluation of first derivatives of the energy for a unitary group based spin-adapted coupled cluster (CC) theory, namely, the combinatoric open-shell CC (COSCC) approach within the singles and doubles approximation. The widely used Lagrange multiplier approach is employed for the derivation of an analytical expression for the first derivative of the energy, which in combination with the well-established density-matrix formulation, is used for the computation of first-order electrical properties. Derivations of the spin-adapted lambda equations for determining the Lagrange multipliers and the expressions for the spin-free effective density matrices for the COSCC approach are presented. Orbital-relaxation effects due to the electric-field perturbation are treated via the Z-vector technique. We present calculations of the dipole moments for a number of doublet radicals in their ground states using restricted open-shell Hartree-Fock (ROHF) and quasi-restricted HF (QRHF) orbitals in order to demonstrate the applicability of our analytic scheme for computing energy derivatives. We also report calculations of the chlorine electric-field gradients and nuclear quadrupole-coupling constants for the CCl, CH{sub 2}Cl, ClO{sub 2}, and SiCl radicals.
Energy Technology Data Exchange (ETDEWEB)
Azar, Richard Julian, E-mail: julianazar2323@berkeley.edu; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu [Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)
2015-05-28
Your correspondents develop and apply fully nonorthogonal, local-reference perturbation theories describing non-covalent interactions. Our formulations are based on a Löwdin partitioning of the similarity-transformed Hamiltonian into a zeroth-order intramonomer piece (taking local CCSD solutions as its zeroth-order eigenfunction) plus a first-order piece coupling the fragments. If considerations are limited to a single molecule, the proposed intermolecular similarity-transformed perturbation theory represents a frozen-orbital variant of the “(2)”-type theories shown to be competitive with CCSD(T) and of similar cost if all terms are retained. Different restrictions on the zeroth- and first-order amplitudes are explored in the context of large-computation tractability and elucidation of non-local effects in the space of singles and doubles. To accurately approximate CCSD intermolecular interaction energies, a quadratically growing number of variables must be included at zeroth-order.
Xu, Xuefei; Zhang, Wenjing; Tang, Mingsheng; Truhlar, Donald G
2015-05-12
Coupled-cluster (CC) methods have been extensively used as the high-level approach in quantum electronic structure theory to predict various properties of molecules when experimental results are unavailable. It is often assumed that CC methods, if they include at least up to connected-triple-excitation quasiperturbative corrections to a full treatment of single and double excitations (in particular, CCSD(T)), and a very large basis set, are more accurate than Kohn-Sham (KS) density functional theory (DFT). In the present work, we tested and compared the performance of standard CC and KS methods on bond energy calculations of 20 3d transition metal-containing diatomic molecules against the most reliable experimental data available, as collected in a database called 3dMLBE20. It is found that, although the CCSD(T) and higher levels CC methods have mean unsigned deviations from experiment that are smaller than most exchange-correlation functionals for metal-ligand bond energies of transition metals, the improvement is less than one standard deviation of the mean unsigned deviation. Furthermore, on average, almost half of the 42 exchange-correlation functionals that we tested are closer to experiment than CCSD(T) with the same extended basis set for the same molecule. The results show that, when both relativistic and core-valence correlation effects are considered, even the very high-level (expensive) CC method with single, double, triple, and perturbative quadruple cluster operators, namely, CCSDT(2)Q, averaged over 20 bond energies, gives a mean unsigned deviation (MUD(20) = 4.7 kcal/mol when one correlates only valence, 3p, and 3s electrons of transition metals and only valence electrons of ligands, or 4.6 kcal/mol when one correlates all core electrons except for 1s shells of transition metals, S, and Cl); and that is similar to some good xc functionals (e.g., B97-1 (MUD(20) = 4.5 kcal/mol) and PW6B95 (MUD(20) = 4.9 kcal/mol)) when the same basis set is used. We
Datta, Dipayan; Kossmann, Simone; Neese, Frank
2016-09-01
The domain-based local pair-natural orbital coupled-cluster (DLPNO-CC) theory has recently emerged as an efficient and powerful quantum-chemical method for the calculation of energies of molecules comprised of several hundred atoms. It has been demonstrated that the DLPNO-CC approach attains the accuracy of a standard canonical coupled-cluster calculation to about 99.9% of the basis set correlation energy while realizing linear scaling of the computational cost with respect to system size. This is achieved by combining (a) localized occupied orbitals, (b) large virtual orbital correlation domains spanned by the projected atomic orbitals (PAOs), and (c) compaction of the virtual space through a truncated pair natural orbital (PNO) basis. In this paper, we report on the implementation of an analytic scheme for the calculation of the first derivatives of the DLPNO-CC energy for basis set independent perturbations within the singles and doubles approximation (DLPNO-CCSD) for closed-shell molecules. Perturbation-independent one-particle density matrices have been implemented in order to account for the response of the CC wave function to the external perturbation. Orbital-relaxation effects due to external perturbation are not taken into account in the current implementation. We investigate in detail the dependence of the computed first-order electrical properties (e.g., dipole moment) on the three major truncation parameters used in a DLPNO-CC calculation, namely, the natural orbital occupation number cutoff used for the construction of the PNOs, the weak electron-pair cutoff, and the domain size cutoff. No additional truncation parameter has been introduced for property calculation. We present benchmark calculations on dipole moments for a set of 10 molecules consisting of 20-40 atoms. We demonstrate that 98%-99% accuracy relative to the canonical CCSD results can be consistently achieved in these calculations. However, this comes with the price of tightening the
Localized attack on clustering networks
Dong, Gaogao; Du, Ruijin; Shao, Shuai; Stanley, H Eugene; Shlomo, Havlin
2016-01-01
Clustering network is one of which complex network attracting plenty of scholars to discuss and study the structures and cascading process. We primarily analyzed the effect of clustering coefficient to other various of the single clustering network under localized attack. These network models including double clustering network and star-like NON with clustering and random regular (RR) NON of ER networks with clustering are made up of at least two networks among which exist interdependent relation among whose degree of dependence is measured by coupling strength. We show both analytically and numerically, how the coupling strength and clustering coefficient effect the percolation threshold, size of giant component, critical coupling point where the behavior of phase transition changes from second order to first order with the increase of coupling strength between the networks. Last, we study the two types of clustering network: one type is same with double clustering network in which each subnetwork satisfies ...
de Lara-Castells, María Pilar; Aguirre, Néstor F.; Villarreal, Pablo; Barrio, Gerardo Delgado; Mitrushchenkov, Alexander O.
2010-05-01
A full-configuration-interaction nuclear orbital treatment has been recently developed as a benchmark quantum-chemistry-like method to study small doped H3e clusters [M. P. de Lara-Castells et al., J. Chem. Phys. 125, 221101 (2006)]. Our objective in this paper is to extend our previous study on (H3e)N-Cl2(B) clusters, using an enhanced implementation that allows employing very large one-particle basis sets [M. P. de Lara-Castells et al., J. Chem. Phys. 131, 194101 (2009)], and apply the method to the (H3e)N-Cl2(X) case, using both a semiempirical T-shaped and an ab initio He-dopant potential with minima at both T-shaped and linear conformations. Calculations of the ground and low-lying excited solvent states stress the key role played by the anisotropy of the He-dopant interaction in determining the global energies and the structuring of the H3e atoms around the dopant. Whereas H3e atoms are localized in a broad belt around the molecular axis in ground-state N-sized complexes with N =1-3, irrespective of using the T-shaped or the ab initio He-dopant potential function, the dopant species becomes fully coated by just four H3e atoms when the He-dopant potential also has a minimum at linear configurations. However, excited solvent states with a central ring-type clustering of the host molecule are found to be very close in energy with the ground state by using the ab initio potential function. A microscopic analysis of this behavior is provided. Additional simulations of the molecular rovibrational Raman spectra, also including excited solvent states, provide further insights into the importance of proper modeling the anisotropy of the He-dopant interaction in these weakly bound systems and of taking into account the low-lying excitations.
Energy Technology Data Exchange (ETDEWEB)
Yassin Hassan
2001-11-30
Develop a state-of-the-art non-intrusive diagnostic tool to perform simultaneous measurements of both the temporal and three-dimensional spatial velocity of the two phases of a bubbly flow. These measurements are required to provide a foundation for studying the constitutive closure relations needed in computational fluid dynamics and best-estimate thermal hydraulic codes employed in nuclear reactor safety analysis and severe accident simulation. Such kinds of full-field measurements are not achievable through the commonly used point-measurement techniques, such as hot wire, conductance probe, laser Doppler anemometry, etc. The results can also be used in several other applications, such as the dynamic transport of pollutants in water or studies of the dispersion of hazardous waste.
Garza, Alejandro J; Alencar, Ana G Sousa; Sun, Jianwei; Perdew, John P; Scuseria, Gustavo E
2015-01-01
Contrary to standard coupled cluster doubles (CCD) and Brueckner doubles (BD), singlet-paired analogues of CCD and BD (denoted here as CCD0 and BD0) do not break down when static correlation is present, but neglect substantial amounts of dynamic correlation. In fact, CCD0 and BD0 do not account for any contributions from multielectron excitations involving only same-spin electrons at all. We exploit this feature to add---without introducing double counting, self-interaction, or increase in cost---the missing correlation to these methods via meta-GGA density functionals (TPSS and SCAN). Furthermore, we improve upon these CCD0+DFT blends by invoking range separation: the short- and long-range correlations absent in CCD0/BD0 are evaluated with DFT and the direct random phase approximation (dRPA), respectively. This corrects the description of long-range van der Waals forces. Comprehensive benchmarking shows that the combinations presented here are very accurate for weakly correlated systems, while also providing...
Feldman, G.; Fulton, T.; Liaw, S. S.; Lindgren, I.
1990-02-01
The results from two approaches, those from the coupled cluster expansion (CCA), and those from the Green's function formalism (GFF), are compared in perturbation theory. The atoms discussed consist of a nondegenerate core, plus or minus two electrons (two particle (2P) and two hole (2H) systems), such that the resulting atoms also have non-degenerate ground states. The specific cases considered are the He++ -He pair through third order, and, very briefly, the Be++ -Be pair in second order. The corresponding 2-electron non-relativistic (NR) Bethe-Salpeter (BS) Green's functions are 0-, 2-, or 4-electron (rather than just 0-electron, i.e., vacuum) expectation values. The general equivalence of the various approaches is demonstrated in detail for He: On the one hand, the 2P and 2H versions of the CCA are shown to give the same result for the ground state energy in these orders, provided the same atom is described in both versions. On the other hand, the CCA and the GFF are shown to yield equal results.
Bistoni, Giovanni; Auer, Alexander A; Neese, Frank
2017-01-18
The interaction of Lewis acids and bases in both classical Lewis adducts and frustrated Lewis pairs (FLPs) is investigated to elucidate the role that London dispersion plays in different situations. The analysis comprises 14 different adducts between tris(pentafluorophenyl)borane and a series of phosphines, carbenes, and amines with various substituents, differing in both steric and electronic properties. The domain-based local pair natural orbital coupled-cluster (DLPNO-CCSD(T)) method is used in conjunction with the recently introduced local energy decomposition (LED) analysis to obtain state-of-the-art dissociation energies and, at the same time, a clear-cut definition of the London dispersion component of the interaction, with the ultimate goal of aiding in the development of designing principles for acid/base pairs with well-defined bonding features and reactivity. In agreement with previous DFT investigations, it is found that the London dispersion dominates the interaction energy in FLPs, and is also remarkably strong in Lewis adducts. In these latter systems, its magnitude can be easily modulated by modifying the polarizability of the substituents on the basic center, which is consistent with the recently introduced concept of dispersion energy donors. By counteracting the destabilizing energy contribution associated with the deformation of the monomers, the London dispersion drives the stability of many Lewis adducts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Wang, Ying; Qian, Hu-Jun; Morokuma, Keiji; Irle, Stephan
2012-07-05
Ab initio coupled cluster and density functional theory studies of atomic hydrogen addition to the central region of pyrene and coronene as molecular models for graphene hydrogenation were performed. Fully relaxed potential energy curves (PECs) were computed at the spin-unrestricted B3LYP/cc-pVDZ level of theory for the atomic hydrogen attack of a center carbon atom (site A), the midpoint of a neighboring carbon bond (site B), and the center of a central hexagon (site C). Using the B3LYP/cc-pVDZ PEC geometries, we evaluated energies at the PBE density functional, as well as ab initio restricted open-shell ROMP2, ROCCSD, and ROCCSD(T) levels of theory, employing cc-pVDZ and cc-pVTZ basis sets, and performed a G2MS extrapolation to the ROCCSD(T)/cc-pVTZ level of theory. In agreement with earlier studies, we find that only site A attack leads to chemisorption. The G2MS entrance channel barrier heights, binding energies, and PEC profiles are found to agree well with a recent ab initio multireference wave function theory study (Bonfanti et al. J. Chem. Phys.2011, 135, 164701), indicating that single-reference open-shell methods including B3LYP are sufficient for the theoretical treatment of the interaction of graphene with a single hydrogen atom.
Bravaya, Ksenia B; Zuev, Dmitry; Epifanovsky, Evgeny; Krylov, Anna I
2013-03-28
Theory and implementation of complex-scaled variant of equation-of-motion coupled-cluster method for excitation energies with single and double substitutions (EOM-EE-CCSD) is presented. The complex-scaling formalism extends the EOM-EE-CCSD model to resonance states, i.e., excited states that are metastable with respect to electron ejection. The method is applied to Feshbach resonances in atomic systems (He, H(-), and Be). The dependence of the results on one-electron basis set is quantified and analyzed. Energy decomposition and wave function analysis reveal that the origin of the dependence is in electron correlation, which is essential for the lifetime of Feshbach resonances. It is found that one-electron basis should be sufficiently flexible to describe radial and angular electron correlation in a balanced fashion and at different values of the scaling parameter, θ. Standard basis sets that are optimized for not-complex-scaled calculations (θ = 0) are not sufficiently flexible to describe the θ-dependence of the wave functions even when heavily augmented by additional sets.
Energy Technology Data Exchange (ETDEWEB)
Peng, Bo; Kowalski, Karol
2016-12-23
In this paper we derive basic properties of the Green’s function matrix elements stemming from the exponential coupled cluster (CC) parametrization of the ground-state wave function. We demon- strate that all intermediates used to express retarded (or equivalently, ionized) part of the Green’s function in the ω-representation can be expressed through connected diagrams only. Similar proper- ties are also shared by the first order ω-derivatives of the retarded part of the CC Green’s function. This property can be extended to any order ω-derivatives of the Green’s function. Through the Dyson equation of CC Green’s function, the derivatives of corresponding CC self-energy can be evaluated analytically. In analogy to the CC Green’s function, the corresponding CC self-energy is expressed in terms of connected diagrams only. Moreover, the ionized part of the CC Green’s func- tion satisfies the non-homogeneous linear system of ordinary differential equations, whose solution may be represented in the exponential form. Our analysis can be easily generalized to the advanced part of the CC Green’s function.
Clark, Cari Jo; Spencer, Rachael A; Shrestha, Binita; Ferguson, Gemma; Oakes, J Michael; Gupta, Jhumka
2017-01-13
Intimate partner violence (IPV) is a significant public health issue that affects 1 in 3 women globally and a similarly large number of women in Nepal. Over the past decade, important policy and programmatic steps have been taken to address violence against women in Nepal. There remains a dearth of evidence on the effectiveness of primary violence prevention strategies. The Change Starts at Home study begins to fill this gap by utilizing a multi-component social behaviour change communication (SBCC) strategy involving a radio drama and community mobilization to shift attitudes, norms and behaviours that underpin IPV perpetration in Nepal. The study uses a concurrent mixed-methods design. The quantitative aspect of the evaluation is a pair-matched, repeated cross-sectional 2-armed, single-blinded cluster trial (RCT: N = 36 clusters, 1440 individuals), comparing a social behaviour change communication (SBCC) strategy to radio programming alone for its impact on physical and / or sexual IPV at the end of programming (12 months' post-baseline) and 6-months post the cessation of project activities (18-months post baseline). The qualitative aspects of the design include several longitudinal approaches to understand the impact of the intervention and to examine mechanisms of change including in-depth interviews with participants (N = 18 couples), and focus group discussions with community leaders (N = 3 groups), and family members of participants (N = 12 groups). Treatment effects will be estimated with generalized logistic mixed models specified to compare differences in primary outcome from baseline to 12-month follow-up, and baseline to 18-months follow-up in accordance with intention-to-treat principles. The study rigorously evaluates the effectiveness of a promising strategy to prevent IPV. The results of the trial will be immediately useful for governmental, nongovernmental, and donor funded programs targeting partner violence or social norms that
Synchronization of coupled chaotic dynamics on networks
Indian Academy of Sciences (India)
R E Amritkar; Sarika Jalan
2005-03-01
We review some recent work on the synchronization of coupled dynamical systems on a variety of networks. When nodes show synchronized behaviour, two interesting phenomena can be observed. First, there are some nodes of the floating type that show intermittent behaviour between getting attached to some clusters and evolving independently. Secondly, two different ways of cluster formation can be identified, namely self-organized clusters which have mostly intra-cluster couplings and driven clusters which have mostly inter-cluster couplings.
Mondal, Bhaskar; Neese, Frank; Ye, Shengfa
2015-08-03
The development of efficient catalysts with base metals for CO2 hydrogenation has always been a major thrust of interest. A series of experimental and theoretical work has revealed that the catalytic cycle typically involves two key steps, namely, base-promoted heterolytic H2 splitting and hydride transfer to CO2, either of which can be the rate-determining step (RDS) of the entire reaction. To explore the determining factor for the nature of RDS, we present herein a comparative mechanistic investigation on CO2 hydrogenation mediated by [M(H)(η(2)-H2)(PP3(Ph))](n+) (M = Fe(II), Ru(II), and Co(III); PP3(Ph) = tris(2-(diphenylphosphino)phenyl)phosphine) type complexes. In order to construct reliable free energy profiles, we used highly correlated wave function based ab initio methods of the coupled cluster type alongside the standard density functional theory. Our calculations demonstrate that the hydricity of the metal-hydride intermediate generated by H2 splitting dictates the nature of the RDS for the Fe(II) and Co(III) systems, while the RDS for the Ru(II) catalyst appears to be ambiguous. CO2 hydrogenation catalyzed by the Fe(II) complex that possesses moderate hydricity traverses an H2-splitting RDS, whereas the RDS for the high-hydricity Co(III) species is found to be the hydride transfer. Thus, our findings suggest that hydricity can be used as a practical guide in future catalyst design. Enhancing the electron-accepting ability of low-hydricity catalysts is likely to improve their catalytic performance, while increasing the electron-donating ability of high-hydricity complexes may speed up CO2 conversion. Moreover, we also established the active roles of base NEt3 in directing the heterolytic H2 splitting and assisting product release through the formation of an acid-base complex.
Minenkov, Yury; Bistoni, Giovanni; Riplinger, Christoph; Auer, Alexander A; Neese, Frank; Cavallo, Luigi
2017-04-05
In this work, we tested canonical and domain based pair natural orbital coupled cluster methods (CCSD(T) and DLPNO-CCSD(T), respectively) for a set of 32 ligand exchange and association/dissociation reaction enthalpies involving ionic complexes of Li, Be, Na, Mg, Ca, Sr, Ba and Pb(ii). Two strategies were investigated: in the former, only valence electrons were included in the correlation treatment, giving rise to the computationally very efficient FC (frozen core) approach; in the latter, all non-ECP electrons were included in the correlation treatment, giving rise to the AE (all electron) approach. Apart from reactions involving Li and Be, the FC approach resulted in non-homogeneous performance. The FC approach leads to very small errors (core (sub-valence) orbitals of metals and the valence orbitals of oxygen and halogens in the molecular orbitals treated as core, and due to neglecting core-core and core-valence correlation effects. These large errors are reduced to a few kcal mol(-1) if the AE approach is used or the sub-valence orbitals of metals are included in the correlation treatment. On the technical side, the CCSD(T) and DLPNO-CCSD(T) results differ by a fraction of kcal mol(-1), indicating the latter method as the perfect choice when the CPU efficiency is essential. For completely black-box applications, as requested in catalysis or thermochemical calculations, we recommend the DLPNO-CCSD(T) method with all electrons that are not covered by effective core potentials included in the correlation treatment and correlation-consistent polarized core valence basis sets of cc-pwCVQZ(-PP) quality.
Minenkov, Yury
2017-03-07
In this work, we tested canonical and domain based pair natural orbital coupled cluster methods (CCSD(T) and DLPNO-CCSD(T), respectively) for a set of 32 ligand exchange and association/dissociation reaction enthalpies involving ionic complexes of Li, Be, Na, Mg, Ca, Sr, Ba and Pb(ii). Two strategies were investigated: in the former, only valence electrons were included in the correlation treatment, giving rise to the computationally very efficient FC (frozen core) approach; in the latter, all non-ECP electrons were included in the correlation treatment, giving rise to the AE (all electron) approach. Apart from reactions involving Li and Be, the FC approach resulted in non-homogeneous performance. The FC approach leads to very small errors (<2 kcal mol-1) for some reactions of Na, Mg, Ca, Sr, Ba and Pb, while for a few reactions of Ca and Ba deviations up to 40 kcal mol-1 have been obtained. Large errors are both due to artificial mixing of the core (sub-valence) orbitals of metals and the valence orbitals of oxygen and halogens in the molecular orbitals treated as core, and due to neglecting core-core and core-valence correlation effects. These large errors are reduced to a few kcal mol-1 if the AE approach is used or the sub-valence orbitals of metals are included in the correlation treatment. On the technical side, the CCSD(T) and DLPNO-CCSD(T) results differ by a fraction of kcal mol-1, indicating the latter method as the perfect choice when the CPU efficiency is essential. For completely black-box applications, as requested in catalysis or thermochemical calculations, we recommend the DLPNO-CCSD(T) method with all electrons that are not covered by effective core potentials included in the correlation treatment and correlation-consistent polarized core valence basis sets of cc-pwCVQZ(-PP) quality.
Gao, Yi; Neuhauser, Daniel
2013-05-14
We show how to obtain the correct electronic response of a large system by embedding; a small region is propagated by TDDFT (time-dependent density functional theory) simultaneously with a classical electrodynamics evolution using the Near-Field method over a larger external region. The propagations are coupled through a combined time-dependent density yielding a common Coulomb potential. We show that the embedding correctly describes the plasmonic response of a Mg(0001) slab and its influence on the dynamical charge transfer between an adsorbed H2O molecule and the substrate, giving the same spectral shape as full TDDFT (similar plasmon peak and molecular-dependent differential spectra) with much less computational effort. The results demonstrate that atomistic embedding electrodynamics is promising for nanoplasmonics and nanopolaritonics.
Li, Jilai; Zhou, Shaodong; Zhang, Jun; Schlangen, Maria; Weiske, Thomas; Usharani, Dandamudi; Shaik, Sason; Schwarz, Helmut
2016-06-29
The reactivity of the homo- and heteronuclear oxide clusters [XYO2](+) (X, Y = Al, Si, Mg) toward methane was studied using Fourier transform ion cyclotron resonance mass spectrometry, in conjunction with high-level quantum mechanical calculations. The most reactive cluster by both experiment and theory is [Al2O2](•+). In its favorable pathway, this cluster abstracts a hydrogen atom by means of proton-coupled electron transfer (PCET) instead of following the conventional hydrogen-atom transfer (HAT) route. This mechanistic choice originates in the strong Lewis acidity of the aluminum site of [Al2O2](•+), which cleaves the C-H bond heterolytically to form an Al-CH3 entity, while the proton is transferred to the bridging oxygen atom of the cluster ion. In addition, a comparison of the reactivity of heteronuclear and homonuclear oxide clusters [XYO2](+) (X, Y = Al, Si, Mg) reveals a striking doping effect by aluminum. Thus, the vacant s-p hybrid orbital on Al acts as an acceptor of the electron pair from methyl anion (CH3(-)) and is therefore eminently important for bringing about thermal methane activation by PCET. For the Al-doped cluster ions, the spin density at an oxygen atom, which is crucial for the HAT mechanism, acts here as a spectator during the course of the PCET mediated C-H bond cleavage. A diagnostic plot of the deformation energy vis-à-vis the barrier shows the different HAT/PCET reactivity map for the entire series. This is a strong connection to the recently discussed mechanism of oxidative coupling of methane on magnesium oxide surfaces proceeding through Grignard-type intermediates.
Directory of Open Access Journals (Sweden)
Jin-Zhong Wu
2013-01-01
Full Text Available A simple and reliable method of high-performance liquid chromatography with photodiode array detection (HPLC-DAD was developed to evaluate the quality of Receptaculum Nelumbinis (dried receptacle of Nelumbo nucifera through establishing chromatographic fingerprint and simultaneous determination of five flavonol glycosides, including hyperoside, isoquercitrin, quercetin-3-O-β-d-glucuronide, isorhamnetin-3-O-β-d-galactoside and syringetin-3-O-β-d-glucoside. In quantitative analysis, the five components showed good regression (R > 0.9998 within linear ranges, and their recoveries were in the range of 98.31%–100.32%. In the chromatographic fingerprint, twelve peaks were selected as the characteristic peaks to assess the similarities of different samples collected from different origins in China according to the State Food and Drug Administration (SFDA requirements. Furthermore, hierarchical cluster analysis (HCA was also applied to evaluate the variation of chemical components among different sources of Receptaculum Nelumbinis in China. This study indicated that the combination of quantitative and chromatographic fingerprint analysis can be readily utilized as a quality control method for Receptaculum Nelumbinis and its related traditional Chinese medicinal preparations.
Cluster Synchronization Algorithms
Xia, Weiguo; Cao, Ming
2010-01-01
This paper presents two approaches to achieving cluster synchronization in dynamical multi-agent systems. In contrast to the widely studied synchronization behavior, where all the coupled agents converge to the same value asymptotically, in the cluster synchronization problem studied in this paper,
Cieluch, Ewelina; Pietryga, Krzysztof; Sarewicz, Marcin; Osyczka, Artur
2010-01-01
Cytochrome c1 of Rhodobacter (Rba.) species provides a series of mutants which change barriers for electron transfer through the cofactor chains of cytochrome bc1 by modifying heme c1 redox midpoint potential. Analysis of post-flash electron distribution in such systems can provide useful information about the contribution of individual reactions to the overall electron flow. In Rba. capsulatus, the non-functional low-potential forms of cytochrome c1 which are devoid of the disulfide bond naturally present in this protein revert spontaneously by introducing a second-site suppression (mutation A181T) that brings the potential of heme c1 back to the functionally high levels, yet maintains it some 100 mV lower from the native value. Here we report that the disulfide and the mutation A181T can coexist in one protein but the mutation exerts a dominant effect on the redox properties of heme c1 and the potential remains at the same lower value as in the disulfide-free form. This establishes effective means to modify a barrier for electron transfer between the FeS cluster and heme c1 without breaking disulfide. A comparison of the flash-induced electron transfers in native and mutated cytochrome bc1 revealed significant differences in the post-flash equilibrium distribution of electrons only when the connection of the chains with the quinone pool was interrupted at the level of either of the catalytic sites by the use of specific inhibitors, antimycin or myxothiazol. In the non-inhibited system no such differences were observed. We explain the results using a kinetic model in which a shift in the equilibrium of one reaction influences the equilibrium of all remaining reactions in the cofactor chains. It follows a rather simple description in which the direction of electron flow through the coupled chains of cytochrome bc1 exclusively depends on the rates of all reversible partial reactions, including the Q/QH2 exchange rate to/from the catalytic sites. PMID:19917265
Saitow, Masaaki; Becker, Ute; Riplinger, Christoph; Valeev, Edward F; Neese, Frank
2017-04-28
The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable molecular electronic wave functions and energies for many molecular systems around their equilibrium geometries. However, the high computational cost, which is well-known to scale as O(N(6)) with system size N, has limited its practical application to small systems consisting of not more than approximately 20-30 atoms. To overcome these limitations, low-order scaling approximations to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The production level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell unrestricted Hartree-Fock reference wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approximations have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is
Document Clustering Based on Semi-Supervised Term Clustering
Directory of Open Access Journals (Sweden)
Hamid Mahmoodi
2012-05-01
Full Text Available The study is conducted to propose a multi-step feature (term selection process and in semi-supervised fashion, provide initial centers for term clusters. Then utilize the fuzzy c-means (FCM clustering algorithm for clustering terms. Finally assign each of documents to closest associated term clusters. While most text clustering algorithms directly use documents for clustering, we propose to first group the terms using FCM algorithm and then cluster documents based on terms clusters. We evaluate effectiveness of our technique on several standard text collections and compare our results with the some classical text clustering algorithms.
Chen, Lei; Wang, Zhigang; Li, Zhengqiang; Zhang, Rui-Qin
2017-07-01
Using density functional theory, this work presents a comprehensive analysis of nonresonant surface-enhanced Raman scattering enhancement of pyridine on M@Ag12 (M = V-, Nb-, Ta-, Cr, Mo, W, Mn+, Tc+, Re+). Computational results indicate that the chemical enhancement of pyridine on M@Ag12 is closely associated with the charge properties of silver-caged clusters. Pyridine on negative clusters exhibits the strongest chemical enhancement with a factor of about 103, while the chemical enhancement is only about 102 for pyridine on neutral clusters and 10 for pyridine on positive clusters. The polarizability analyses elucidate the nature of the chemical enhancement that delocalized electrons of negative adsorption systems occupy higher molecular orbitals than those of neutral and positive adsorption systems, which can lead to stronger nonresonant chemical enhancement.
Chen, Lei; Wang, Zhigang; Li, Zhengqiang; Zhang, Rui-Qin
2016-10-01
Using density functional theory, this work presents a comprehensive analysis of nonresonant surface-enhanced Raman scattering enhancement of pyridine on M@Ag12 (M = V-, Nb-, Ta-, Cr, Mo, W, Mn+, Tc+, Re+). Computational results indicate that the chemical enhancement of pyridine on M@Ag12 is closely associated with the charge properties of silver-caged clusters. Pyridine on negative clusters exhibits the strongest chemical enhancement with a factor of about 103, while the chemical enhancement is only about 102 for pyridine on neutral clusters and 10 for pyridine on positive clusters. The polarizability analyses elucidate the nature of the chemical enhancement that delocalized electrons of negative adsorption systems occupy higher molecular orbitals than those of neutral and positive adsorption systems, which can lead to stronger nonresonant chemical enhancement.
Cardiac mitochondria exhibit dynamic functional clustering
Directory of Open Access Journals (Sweden)
Felix Tobias Kurz
2014-09-01
Full Text Available Multi-oscillatory behavior of mitochondrial inner membrane potential ΔΨm in self-organized cardiac mitochondrial networks can be triggered by metabolic or oxidative stress. Spatio-temporal analyses of cardiac mitochondrial networks have shown that mitochondria are heterogeneously organized in synchronously oscillating clusters in which the mean cluster frequency and size are inversely correlated, thus suggesting a modulation of cluster frequency through local inter-mitochondrial coupling. In this study, we propose a method to examine the mitochondrial network's topology through quantification of its dynamic local clustering coefficients. Individual mitochondrial ΔΨm oscillation signals were identified for each cardiac myocyte and cross-correlated with all network mitochondria using previously described methods (Kurz et al., 2010. Time-varying inter-mitochondrial connectivity, defined for mitochondria in the whole network whose signals are at least 90% correlated at any given time point, allowed considering functional local clustering coefficients. It is shown that mitochondrial clustering in isolated cardiac myocytes changes dynamically and is significantly higher than for random mitochondrial networks that are constructed using the Erdös-Rényi model based on the same sets of vertices. The network's time-averaged clustering coefficient for cardiac myocytes was found to be 0.500 ± 0.051 (N=9 versus 0.061 ± 0.020 for random networks, respectively. Our results demonstrate that cardiac mitochondria constitute a network with dynamically connected constituents whose topological organization is prone to clustering. Cluster partitioning in networks of coupled oscillators has been observed in scale-free and chaotic systems and is therefore in good agreement with previous models of cardiac mitochondrial networks (Aon et al., 2008.
Marketing research cluster analysis
Directory of Open Access Journals (Sweden)
Marić Nebojša
2002-01-01
Full Text Available One area of applications of cluster analysis in marketing is identification of groups of cities and towns with similar demographic profiles. This paper considers main aspects of cluster analysis by an example of clustering 12 cities with the use of Minitab software.
Kempgens, Pierre; Rosé, Jacky
2011-03-01
Two-dimensional ⁵⁹Co correlation spectroscopy (COSY) and double-quantum-filtered (DQF) COSY NMR experiments are reported for the tetrahedral mixed-metal cluster HFeCo₃(CO)₁₀(PCyH₂)(PPh₂[CH₂C(O)Ph]), which consists from the point of view of ⁵⁹Co NMR spectroscopy, of an AMX system of three-spin S=7/2. Both 2D NMR spectra prove the existence of a J scalar coupling constant between non-equivalent ⁵⁹Co nuclei. By contrast to what happens with the conventional 2D ⁵⁹Co COSY NMR spectrum, it was possible to simulate the 2D ⁵⁹Co DQF-COSY NMR spectrum by density matrix calculations in order to extract the values of the ¹J(⁵⁹Co-⁵⁹Co) coupling constants. The comparison between experimental and theoretical 2D NMR spectra gives spin-couplings constants of several hundreds Hertz for this cluster. Copyright © 2010 Elsevier Inc. All rights reserved.
Institute of Scientific and Technical Information of China (English)
王国红; 贾楠; 邢蕊
2013-01-01
Competition outside of the region may lead to the overall migration and the cavitation in the develop-ment process of industrial clusters. Fostering innovation incubator network for SMEs is an effective way to deal with cluster risks. The paper defines the meaning of innovation incubation network and collaborative innovation network of SMEs in clusters, analyzes the relation schema, and determines the coupling domain between the two. System dynamics is used to analyze the coupling mechanism. Policy advices to improve the effect of coupling and the regional innovation capacity are put forward. Dalian Double D Innovation Incubator is analyzed as an ex-emplary case.% 在产业集群的发展过程中，区域外的竞争可能会导致集群的整体迁移和空洞现象，培育面向中小企业的创新孵化网络是应对集群风险的有效途径。界定了创新孵化网络与集群中小企业协同创新网络的内涵，分析了二者之间的关系模式，确定了二者的耦合域，应用系统动力学方法分析了二者之间的耦合作用机制，提出了促进二者之间耦合作用、提高区域创新能力的政策建议，并以大连双D港创业孵化中心为对象进行了案例分析。
Energy Technology Data Exchange (ETDEWEB)
Kowalski, Karol; Krishnamoorthy, Sriram; Villa, Oreste; Hammond, Jeffrey R.; Govind, Niranjan
2010-04-21
The development of efficient parallel implementations of electronic structure methods enables not only the study of excited states of large molecular systems but also a unique opportunity to assess the role of various correlation effects in describing excitation energies for systems composed of hundreds of electrons. In this article, we discuss the impact of triply excited configurations in Equation-of-Motion Coupled Cluster (EOMCC) formalism. As a benchmark system we chose the fused porphyrin dimer, which is described by the basis set composed of 942 functions and where 270 electrons were correlated in the EOMCC calculations.
Energy Technology Data Exchange (ETDEWEB)
Schunk, P.R.; Sackinger, P.A.; Rao, R.R. [and others
1996-01-01
GOMA is a two- and three-dimensional finite element program which excels in analyses of manufacturing processes, particularly those involving free or moving interfaces. Specifically, the full-Newton-coupled heat, mass, momentum, and pseudo-solid mesh motion algorithm makes GOMA ideally suited for simulating processes in which the bulk fluid transport is closely coupled to the interfacial physics. Examples include, but are not limited to, coating and polymer processing flows, soldering, crystal growth, and solid-network or solution film drying. The code is based on the premise that any boundary can be (1) moving or free, with an apriori unknown position dictated by the distinguishing physics, (2) fixed, according to a global analytical representation, or (3) moving in time and space under user-prescribed kinematics. The goal is to enable the user to predict boundary position or motion simultaneously with the physics of the problem being analyzed and to pursue geometrical design studies and fluid-structure interaction problems. The moving mesh algorithm treats the entire domain as a computational Lagrangian solid that deforms subject to the physical principles which dictate boundary position. As an added benefit, the same Lagrangian solid mechanics can be exploited to solve multi-field problems for which the solid motion and stresses interact with other transport phenomena, either within the same material phase (e.g. shrinking coating) or in neighboring material phases (e.g. flexible blade coating). Thus, analyses of many fluid-structure interaction problems and deformable porous media problems are accessible. This document serves as a user`s guide and reference for GOMA and provides a brief overview of GOMA`s capabilities, theoretical background, and classes of problems for which it is targeted.
Energy Technology Data Exchange (ETDEWEB)
Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long; Li, Hui, E-mail: Prof-huili@jlu.edu.cn [Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023 (China)
2016-01-07
The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H{sub 2}O–Ar, which explicitly incorporates interdependence on the intramolecular (Q{sub 1}, Q{sub 2}, Q{sub 3}) normal-mode coordinates of the H{sub 2}O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v{sub 1}, v{sub 2}, v{sub 3}) = (0, 0, 0), (0, 0, 1), (1, 0, 0), (0, 1, 0) states of H{sub 2}O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm{sup −1}, and required only 58 parameters. With the 3D PESs of H{sub 2}O–Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm{sup −1} for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H{sub 2}O in H{sub 2}O–Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear
Coupled transfers; Transferts couples
Energy Technology Data Exchange (ETDEWEB)
Nicolas, X.; Lauriat, G.; Jimenez-Rondan, J. [Universite de Marne-la-Vallee, Lab. d' Etudes des Transferts d' Energie et de Matiere (LETEM), 77 (France); Bouali, H.; Mezrhab, A. [Faculte des Sciences, Dept. de Physique, Lab. de Mecanique et Energetique, Oujda (Morocco); Abid, C. [Ecole Polytechnique Universitaire de Marseille, IUSTI UMR 6595, 13 Marseille (France); Stoian, M.; Rebay, M.; Lachi, M.; Padet, J. [Faculte des Sciences, Lab. de Thermomecanique, UTAP, 51 - Reims (France); Mladin, E.C. [Universitaire Polytechnique Bucarest, Faculte de Genie Mecanique, Bucarest (Romania); Mezrhab, A. [Faculte des Sciences, Lab. de Mecanique et Energetique, Dept. de Physique, Oujda (Morocco); Abid, C.; Papini, F. [Ecole Polytechnique, IUSTI, 13 - Marseille (France); Lorrette, C.; Goyheneche, J.M.; Boechat, C.; Pailler, R. [Laboratoire des Composites ThermoStructuraux, UMR 5801, 33 - Pessac (France); Ben Salah, M.; Askri, F.; Jemni, A.; Ben Nasrallah, S. [Ecole Nationale d' Ingenieurs de Monastir, Lab. d' Etudes des Systemes Thermiques et Energetiques (Tunisia); Grine, A.; Desmons, J.Y.; Harmand, S. [Laboratoire de Mecanique et d' Energetique, 59 - Valenciennes (France); Radenac, E.; Gressier, J.; Millan, P. [ONERA, 31 - Toulouse (France); Giovannini, A. [Institut de Mecanique des Fluides de Toulouse, 31 (France)
2005-07-01
This session about coupled transfers gathers 30 articles dealing with: numerical study of coupled heat transfers inside an alveolar wall; natural convection/radiant heat transfer coupling inside a plugged and ventilated chimney; finite-volume modeling of the convection-conduction coupling in non-stationary regime; numerical study of the natural convection/radiant heat transfer coupling inside a partitioned cavity; modeling of the thermal conductivity of textile reinforced composites: finite element homogenization on a full periodical pattern; application of the control volume method based on non-structured finite elements to the problems of axisymmetrical radiant heat transfers in any geometries; modeling of convective transfers in transient regime on a flat plate; a conservative method for the non-stationary coupling of aero-thermal engineering codes; measurement of coupled heat transfers (forced convection/radiant transfer) inside an horizontal duct; numerical simulation of the combustion of a water-oil emulsion droplet; numerical simulation study of heat and mass transfers inside a reactor for nano-powders synthesis; reduction of a combustion and heat transfer model of a direct injection diesel engine; modeling of heat transfers inside a knocking operated spark ignition engine; heat loss inside an internal combustion engine, thermodynamical and flamelet model, composition effects of CH{sub 4}H{sub 2} mixtures; experimental study and modeling of the evolution of a flame on a solid fuel; heat transfer for laminar subsonic jet of oxygen plasma impacting an obstacle; hydrogen transport through a A-Si:H layer submitted to an hydrogen plasma: temperature effects; thermal modeling of the CO{sub 2} laser welding of a magnesium alloy; radiant heat transfer inside a 3-D environment: application of the finite volume method in association with the CK model; optimization of the infrared baking of two types of powder paints; optimization of the emission power of an infrared
Bricmont, J; Bricmont J; Kupiainen A
1994-01-01
We consider a lattice of weakly coupled expanding circle maps. We construct, via a cluster expansion of the Perron-Frobenius operator, an invariant measure for these infinite dimensional dynamical systems which exhibits space-time-chaos.
Institute of Scientific and Technical Information of China (English)
谢帆; 张波; 丘东元
2014-01-01
The loosely coupled inductive power transfer system is an effective and safe method of power transmission,which uses electromagnetic induction technology to achieve non-contact transmission of energy while solving the shortcoming of traditional power supply with wires.The nonlinear bifurcation phenomenon of the full-bridge resonant converter is analyzed with the change of the coupling coefficient of the loosely coupled transformer.The state equations and nonlinear models of the system are built based on the mutual inductance modeling.The nonlinear behaviors are numerically analyzed when the system resonates,and the complex three-dimensional bifurcation diagram is obtained with the coupling coefficient as the bifurcation parameter.The complex bifurcation behaviors of the system are validated by circuit simulation.Moreover,the border collision phenomenon and the characteristics of the time and frequency domains are analyzed.This study expands nonlinear research on the switching converter to the wireless power transfer system,providing important guidance for reliability design of the wireless power transfer system.%松散耦合感应电能传输系统利用电磁感应技术，实现了能量的非接触传输，解决了传统导线直接供电的缺陷，是一种有效、安全的电能传输方法。文中以全桥谐振变换器为例，基于松散耦合变压器分析了系统随着耦合系数的改变而发生的非线性分岔现象。通过互感模型建立系统的状态方程及其非线性模型，分析了系统谐振时的非线性行为，得到以耦合系数为分岔参数的系统复杂三维分岔图。电路仿真验证了系统的复杂分岔行为，并且进一步分析了系统在分岔过程中经历的边界碰撞现象以及准周期状态下系统的时域与频域特征。该研究将开关变换器的非线性研究拓展到无线电能传输系统中，对无线电能传输系统的可靠设计具有重要指导意义。
Sherrill, C David; Takatani, Tait; Hohenstein, Edward G
2009-09-24
Large, correlation-consistent basis sets have been used to very closely approximate the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] complete basis set potential energy curves of several prototype nonbonded complexes, the sandwich, T-shaped, and parallel-displaced benzene dimers, the methane-benzene complex, the H2S-benzene complex, and the methane dimer. These benchmark potential energy curves are used to assess the performance of several methods for nonbonded interactions, including various spin-component-scaled second-order perturbation theory (SCS-MP2) methods, the spin-component-scaled coupled-cluster singles and doubles method (SCS-CCSD), density functional theory empirically corrected for dispersion (DFT-D), and the meta-generalized-gradient approximation functionals M05-2X and M06-2X. These approaches generally provide good results for the test set, with the SCS methods being somewhat more robust. M05-2X underbinds for the test cases considered, while the performances of DFT-D and M06-2X are similar. Density fitting, dual basis, and local correlation approximations all introduce only small errors in the interaction energies but can speed up the computations significantly, particulary when used in combination.
Ghadar, Yasaman; Clark, Aurora E
2012-02-07
The interaction potentials between immiscible polar and non-polar solvents are a major driving force behind the formation of liquid:liquid interfaces. In this work, the interaction energy of water-pentane dimer has been determined using coupled-cluster theory with single double (triple) excitations [CCSD(T)], 2nd order Möller Plesset perturbation theory (MP2), density fitted local MP2 (DF-LMP2), as well as density functional theory using a wide variety of density functionals and several different basis sets. The M05-2X exchange correlation functionals exhibit excellent agreement with CCSD(T) and DF-LMP2 after taking into account basis set superposition error. The gas phase water-pentane interaction energy is found to be quite sensitive to the specific pentane isomer (2,2-dimethylpropane vs. n-pentane) and relative orientation of the monomeric constituents. Subsequent solution phase cluster calculations of 2,2-dimethylpropane and n-pentane solvated by water indicate a positive free energy of solvation that is in good agreement with available experimental data. Structural parameters are quite sensitive to the density functional employed and reflect differences in the two-body interaction energy calculated by each method. In contrast, cluster calculations of pentane solvation of H(2)O solute are found to be inadequate for describing the organic solvent, likely due to limitations associated with the functionals employed (B3LYP, BHandH, and M05-2X).
Kowalski, Karol; Valiev, Marat
2009-12-01
The recently introduced energy expansion based on the use of generating functional (GF) [K. Kowalski and P. D. Fan, J. Chem. Phys. 130, 084112 (2009)] provides a way of constructing size-consistent noniterative 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 wave function. Although proven to be efficient, the previously discussed form of the regularization does not lead to rigorously size-consistent corrections. In this paper we address the issue of size-consistent regularization of the GF expansion by redefining the equations for the cluster amplitudes. The performance and basic features of proposed methodology are illustrated on several gas-phase benchmark systems. Moreover, the regularized GF approaches are combined with quantum mechanical molecular mechanics module and applied to describe the SN2 reaction of CHCl3 and OH- in aqueous solution.
Directory of Open Access Journals (Sweden)
Ramin Payrovi
2007-08-01
Full Text Available Best Performace: With our Hipax Cluster PACS Server solution we are introducing the parallel computing concept as an extremely fast software system to the PACS world. In contrast to the common PACS servers, the Hipax Cluster PACS software is not only restricted to one or two computers, but can be used on a couple of servers controlling each other."nThus, the same services can be run simultaneously on different computers. The scalable system can also be expanded subsequently without lost of per-formance by adding further processors or Hipax server units, for example, if new clients or modalities are to be connected."nMaximum Failure Security: The Cluster Server concept offers high failure security. If one of the server PCs breaks down, the services can be assumed by another Hipax server unit, temporarily. If the overload of one of the server PCs is imminent, the services will be carried out by another Hipax unit (load balancing. To increase the security, e.g. against fire, the single Hipax servers can also be located separately. This concept offers maximum security, flexibility, performance, redundancy and scalability."nThe Hipax Cluster PACS Server is easy to be administrated using a web interface. In the case of a system failure (e.g. overloading, breakdown of a server PC the system administrator receives a mes-sage via Email and is so enabled to solve the problem."nFeatures"n• Based on SQL database"n• Different services running on separate PCs"n• The Hipax Server unis are coordinated and able to control each other"n• Exponentiates the power of a cluster server to the whole PACS (more processors"n• Scalable to the demands"n• Maximum performance"n• Load balancing for optimum efficiency"n• Maximum failure security because of expo-nentiated redundancy"n• Warning Email automatically sent to the system administrator in the case of failure"n• Web interface for system configuration"n• Maintenance without shut down the system
Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... A cluster headache begins as a severe, sudden headache. The headache commonly strikes 2 to 3 hours after you fall ...
Yan, Donghui; Jordan, Michael I
2011-01-01
Inspired by Random Forests (RF) in the context of classification, we propose a new clustering ensemble method---Cluster Forests (CF). Geometrically, CF randomly probes a high-dimensional data cloud to obtain "good local clusterings" and then aggregates via spectral clustering to obtain cluster assignments for the whole dataset. The search for good local clusterings is guided by a cluster quality measure $\\kappa$. CF progressively improves each local clustering in a fashion that resembles the tree growth in RF. Empirical studies on several real-world datasets under two different performance metrics show that CF compares favorably to its competitors. Theoretical analysis shows that the $\\kappa$ criterion is shown to grow each local clustering in a desirable way---it is "noise-resistant." A closed-form expression is obtained for the mis-clustering rate of spectral clustering under a perturbation model, which yields new insights into some aspects of spectral clustering.
Gieles, M.
1993-01-01
Star clusters are observed in almost every galaxy. In this thesis we address several fundamental problems concerning the formation, evolution and disruption of star clusters. From observations of (young) star clusters in the interacting galaxy M51, we found that clusters are formed in complexes of stars and star clusters. These complexes share similar properties with giant molecular clouds, from which they are formed. Many (70%) of the young clusters will not survive the fist 10 Myr, due to t...
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)
Simultaneous clustering of multiple gene expression and physical interaction datasets.
Directory of Open Access Journals (Sweden)
Manikandan Narayanan
2010-04-01
Full Text Available Many genome-wide datasets are routinely generated to study different aspects of biological systems, but integrating them to obtain a coherent view of the underlying biology remains a challenge. We propose simultaneous clustering of multiple networks as a framework to integrate large-scale datasets on the interactions among and activities of cellular components. Specifically, we develop an algorithm JointCluster that finds sets of genes that cluster well in multiple networks of interest, such as coexpression networks summarizing correlations among the expression profiles of genes and physical networks describing protein-protein and protein-DNA interactions among genes or gene-products. Our algorithm provides an efficient solution to a well-defined problem of jointly clustering networks, using techniques that permit certain theoretical guarantees on the quality of the detected clustering relative to the optimal clustering. These guarantees coupled with an effective scaling heuristic and the flexibility to handle multiple heterogeneous networks make our method JointCluster an advance over earlier approaches. Simulation results showed JointCluster to be more robust than alternate methods in recovering clusters implanted in networks with high false positive rates. In systematic evaluation of JointCluster and some earlier approaches for combined analysis of the yeast physical network and two gene expression datasets under glucose and ethanol growth conditions, JointCluster discovers clusters that are more consistently enriched for various reference classes capturing different aspects of yeast biology or yield better coverage of the analysed genes. These robust clusters, which are supported across multiple genomic datasets and diverse reference classes, agree with known biology of yeast under these growth conditions, elucidate the genetic control of coordinated transcription, and enable functional predictions for a number of uncharacterized genes.
Wang, Wei; Bao, Ting; Zeng, Xi; Xiong, Huayu; Wen, Wei; Zhang, Xiuhua; Wang, Shengfu
2017-05-15
In this work, a novel and ultrasensitive electrochemical biosensor was constructed for DNA detection based on functionalized gold clusters/graphene nanohybrids (AuNCs/GR nanobybrids) and exonuclease III (Exo III)-aided cascade target recycling. By utilizing the capacity of GR as universal template, different metal nanoclusters including AuNCs/GR nanobybrids and PtNCs/GR nanohybrids were synthesized through convenient ultrasonic method. Exo III-aided cascade recycling was initiated by target DNA, generating the final cleavage product (S2), which acted as a linkage between capture probe and the functionalized metal nanoclusters/GR conjugates in the construction of the biosensor. The AuNCs/GR-DNA-enzyme conjugates acted as interfaces of enzyme-catalyzed silver deposition reaction, achieving DNA detection ranging from 0.02 fM to 20 pM with a detection limit of 0.057 fM. In addition, PtNCs/GR-DNA conjugates presented peroxidase-like activity and the functionalized PtNCs/GR nanohybrids-based electrochemical biosensor also realized DNA detection by catalyzing the 3,3',5,5'-tetramethylbenzidine-hydrogen peroxide (TMB-H2O2) system to produce electrochemical signal. This metal clusters/GR-based multiple-amplified electrochemical biosensor provided an universal method for DNA detection. Copyright © 2016 Elsevier B.V. All rights reserved.
DEFF Research Database (Denmark)
Ackerman, Margareta; Ben-David, Shai; Branzei, Simina
2012-01-01
We investigate a natural generalization of the classical clustering problem, considering clustering tasks in which different instances may have different weights.We conduct the first extensive theoretical analysis on the influence of weighted data on standard clustering algorithms in both...... the partitional and hierarchical settings, characterizing the conditions under which algorithms react to weights. Extending a recent framework for clustering algorithm selection, we propose intuitive properties that would allow users to choose between clustering algorithms in the weighted setting and classify...
CLEAN: CLustering Enrichment ANalysis
Directory of Open Access Journals (Sweden)
Medvedovic Mario
2009-07-01
Full Text Available Abstract Background Integration of biological knowledge encoded in various lists of functionally related genes has become one of the most important aspects of analyzing genome-wide functional genomics data. In the context of cluster analysis, functional coherence of clusters established through such analyses have been used to identify biologically meaningful clusters, compare clustering algorithms and identify biological pathways associated with the biological process under investigation. Results We developed a computational framework for analytically and visually integrating knowledge-based functional categories with the cluster analysis of genomics data. The framework is based on the simple, conceptually appealing, and biologically interpretable gene-specific functional coherence score (CLEAN score. The score is derived by correlating the clustering structure as a whole with functional categories of interest. We directly demonstrate that integrating biological knowledge in this way improves the reproducibility of conclusions derived from cluster analysis. The CLEAN score differentiates between the levels of functional coherence for genes within the same cluster based on their membership in enriched functional categories. We show that this aspect results in higher reproducibility across independent datasets and produces more informative genes for distinguishing different sample types than the scores based on the traditional cluster-wide analysis. We also demonstrate the utility of the CLEAN framework in comparing clusterings produced by different algorithms. CLEAN was implemented as an add-on R package and can be downloaded at http://Clusteranalysis.org. The package integrates routines for calculating gene specific functional coherence scores and the open source interactive Java-based viewer Functional TreeView (FTreeView. Conclusion Our results indicate that using the gene-specific functional coherence score improves the reproducibility of the
On the ionospheric coupling of auroral electric fields
Directory of Open Access Journals (Sweden)
G. T. Marklund
2009-04-01
Full Text Available The quasi-static coupling of high-altitude potential structures and electric fields to the ionosphere is discussed with particular focus on the downward field-aligned current (FAC region. Results are presented from a preliminary analysis of a selection of electric field events observed by Cluster above the acceleration region. The degree of coupling is here estimated as the ratio between the magnetic field-aligned potential drop, ΔΦ_{II}, as inferred from the characteristic energy of upward ion (electron beams for the upward (downward current region and the high-altitude perpendicular (to B potential, ΔΦ_{bot}, as calculated by integrating the perpendicular electric field across the structure. For upward currents, the coupling can be expressed analytically, using the linear current-voltage relation, as outlined by Weimer et al. (1985. This gives a scale size dependent coupling where structures are coupled (decoupled above (below a critical scale size. For downward currents, the current-voltage relation is highly non-linear which complicates the understanding of how the coupling works. Results from this experimental study indicate that small-scale structures are decoupled, similar to small-scale structures in the upward current region. There are, however, exceptions to this rule as illustrated by Cluster results of small-scale intense electric fields, correlated with downward currents, indicating a perfect coupling between the ionosphere and Cluster altitude.
Cluster functional renormalization group
Reuther, Johannes; Thomale, Ronny
2014-01-01
Functional renormalization group (FRG) has become a diverse and powerful tool to derive effective low-energy scattering vertices of interacting many-body systems. Starting from a free expansion point of the action, the flow of the RG parameter Λ allows us to trace the evolution of the effective one- and two-particle vertices towards low energies by taking into account the vertex corrections between all parquet channels in an unbiased fashion. In this work, we generalize the expansion point at which the diagrammatic resummation procedure is initiated from a free UV limit to a cluster product state. We formulate a cluster FRG scheme where the noninteracting building blocks (i.e., decoupled spin clusters) are treated exactly, and the intercluster couplings are addressed via RG. As a benchmark study, we apply our cluster FRG scheme to the spin-1/2 bilayer Heisenberg model (BHM) on a square lattice where the neighboring sites in the two layers form the individual two-site clusters. Comparing with existing numerical evidence for the BHM, we obtain reasonable findings for the spin susceptibility, the spin-triplet excitation energy, and quasiparticle weight even in coupling regimes close to antiferromagnetic order. The concept of cluster FRG promises applications to a large class of interacting electron systems.
Wei, Lan; Wang, Xiaobo; Mu, Shanxue; Sun, Lixin; Yu, Zhiguo
2015-06-01
A sensitive, rapid and simple ultra high performance liquid chromatography with electrospray ionization tandem mass spectrometry method was developed to determine seven constituents (umbelliferone, apigenin, triumbelletin, daphnoretin, arctigenin, genkwanin and emodin) in Wikstroemia indica (L.) C. A. Mey. The chromatographic analysis was performed on an ACQUITY UPLC® BEH C18 column (2.1 × 50 mm, 1.7 μm) by gradient elution with the mobile phase of 0.05% formic acid aqueous solution (A) and acetonitrile (B). Multiple reaction monitoring mode with positive and negative electrospray ionization interface was carried out to detect the components. This method was validated in terms of specificity, linearity, accuracy, precision and stability. Excellent linear behavior was observed over the certain concentration ranges with the correlation coefficient values higher than 0.999. The intraday and innerday precisions were within 2.0%. The recoveries of seven analytes were 99.4-101.1% with relative standard deviation less than 1.2%. The 18 Wikstroemia indica samples from different origins were classified by hierarchical clustering analysis according to the contents of seven components. The results demonstrated that the developed method could successfully be used to quantify simultaneously of seven components in Wikstroemia indica and could be a helpful tool for the detection and confirmation of the quality of traditional Chinese medicines.
Li, Xu; Gao, Min; Choi, Jong Min; Kim, Beom-Jun; Zhou, Mao-Tian; Chen, Zhen; Jain, Antrix N; Jung, Sung Yun; Yuan, Jingsong; Wang, Wenqi; Wang, Yi; Chen, Junjie
2017-04-01
Neurofibromin (NF1) is a well known tumor suppressor that is commonly mutated in cancer patients. It physically interacts with RAS and negatively regulates RAS GTPase activity. Despite the importance of NF1 in cancer, a high quality endogenous NF1 interactome has yet to be established. In this study, we combined clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene knock-out technology with affinity purification using antibodies against endogenous proteins, followed by mass spectrometry analysis, to sensitively and accurately detect NF1 protein-protein interactions in unaltered in vivo settings. Using this system, we analyzed endogenous NF1-associated protein complexes and identified 49 high-confidence candidate interaction proteins, including RAS and other functionally relevant proteins. Through functional validation, we found that NF1 negatively regulates mechanistic target of rapamycin signaling (mTOR) in a LAMTOR1-dependent manner. In addition, the cell growth and survival of NF1-deficient cells have become dependent on hyperactivation of the mTOR pathway, and the tumorigenic properties of these cells have become dependent on LAMTOR1. Taken together, our findings may provide novel insights into therapeutic approaches targeting NF1-deficient tumors. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
Two-Center Gaussian Potential Well for Studying Light Nucleus in Cluster Structure
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Nafiseh Roshanbakht
2017-01-01
Full Text Available The clustering phenomena are very important to determine structure of light nuclei and deformation of spherical shape is inevitable. Hence, we calculated the energy levels of two-center Gaussian potential well including spin-orbit coupling by solving the Schrödinger equation in the cylindrical coordinates. This model can predict the spin and parity of the light nuclei that have two identical cluster structures.
An Emerge Approach in Inter Cluster Similarity for Quality Clusters
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H. Venkateswara Reddy
2013-04-01
Full Text Available Relationship between the datasets is one most important issue in recent years. The recent methods are based mostly on the numerical data, but these methods are not suitable for real time data such as web pages, business transactions etc., which are known as Categorical data. It is difficult to find relationship in categorical data. In this paper, a new approach is proposed for finding the relationshipbetween the categorical data, hence to find relationship between the clusters. The main aim is to identify the quality clusters based on the relationship between clusters. If there is no relationship between clusters then those clusters are treated as quality clusters.
Bridges in the random-cluster model
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Eren Metin Elçi
2016-02-01
Full Text Available The random-cluster model, a correlated bond percolation model, unifies a range of important models of statistical mechanics in one description, including independent bond percolation, the Potts model and uniform spanning trees. By introducing a classification of edges based on their relevance to the connectivity we study the stability of clusters in this model. We prove several exact relations for general graphs that allow us to derive unambiguously the finite-size scaling behavior of the density of bridges and non-bridges. For percolation, we are also able to characterize the point for which clusters become maximally fragile and show that it is connected to the concept of the bridge load. Combining our exact treatment with further results from conformal field theory, we uncover a surprising behavior of the (normalized variance of the number of (non-bridges, showing that it diverges in two dimensions below the value 4cos2(π/3=0.2315891⋯ of the cluster coupling q. Finally, we show that a partial or complete pruning of bridges from clusters enables estimates of the backbone fractal dimension that are much less encumbered by finite-size corrections than more conventional approaches.
Cluster Physics with Merging Galaxy Clusters
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Sandor M. Molnar
2016-02-01
Full Text Available Collisions between galaxy clusters provide a unique opportunity to study matter in a parameter space which cannot be explored in our laboratories on Earth. In the standard LCDM model, where the total density is dominated by the cosmological constant ($Lambda$ and the matter density by cold dark matter (CDM, structure formation is hierarchical, and clusters grow mostly by merging.Mergers of two massive clusters are the most energetic events in the universe after the Big Bang,hence they provide a unique laboratory to study cluster physics.The two main mass components in clusters behave differently during collisions:the dark matter is nearly collisionless, responding only to gravity, while the gas is subject to pressure forces and dissipation, and shocks and turbulenceare developed during collisions. In the present contribution we review the different methods used to derive the physical properties of merging clusters. Different physical processes leave their signatures on different wavelengths, thusour review is based on a multifrequency analysis. In principle, the best way to analyze multifrequency observations of merging clustersis to model them using N-body/HYDRO numerical simulations. We discuss the results of such detailed analyses.New high spatial and spectral resolution ground and space based telescopeswill come online in the near future. Motivated by these new opportunities,we briefly discuss methods which will be feasible in the near future in studying merging clusters.
Institute of Scientific and Technical Information of China (English)
聂华; 杨晓君; 刘淘英
2015-01-01
The cluster architecture has played an important role in high-end computing for the past 20 years. With the advent of Internet services, big data, and cloud computing, traditional clusters face three challenges: 1) providing flexible system balance among computing, memory, and I/O capabilities;2) reducing resource pooling overheads;and 3) addressing low performance-power eﬃciency. This position paper proposes a software-defined cluster (SDC) architecture to deal with these challenges. The SDC architecture inherits two features of traditional cluster: its architecture is multicomputer and it has loosely-coupled interconnect. SDC provides two new mechanisms: global I/O space (GIO) and hardware-supported native access (HNA) to remote devices. Application software can define a virtual cluster best suited to its needs from resources pools provided by a physical cluster, and traditional cluster ecosystems need no modification. We also discuss a prototype design and implementation of a 32-processor cloud server utilizing the SDC architecture.
Energy Technology Data Exchange (ETDEWEB)
Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.
2004-05-26
We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.
Clustering Techniques in Bioinformatics
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Muhammad Ali Masood
2015-01-01
Full Text Available Dealing with data means to group information into a set of categories either in order to learn new artifacts or understand new domains. For this purpose researchers have always looked for the hidden patterns in data that can be defined and compared with other known notions based on the similarity or dissimilarity of their attributes according to well-defined rules. Data mining, having the tools of data classification and data clustering, is one of the most powerful techniques to deal with data in such a manner that it can help researchers identify the required information. As a step forward to address this challenge, experts have utilized clustering techniques as a mean of exploring hidden structure and patterns in underlying data. Improved stability, robustness and accuracy of unsupervised data classification in many fields including pattern recognition, machine learning, information retrieval, image analysis and bioinformatics, clustering has proven itself as a reliable tool. To identify the clusters in datasets algorithm are utilized to partition data set into several groups based on the similarity within a group. There is no specific clustering algorithm, but various algorithms are utilized based on domain of data that constitutes a cluster and the level of efficiency required. Clustering techniques are categorized based upon different approaches. This paper is a survey of few clustering techniques out of many in data mining. For the purpose five of the most common clustering techniques out of many have been discussed. The clustering techniques which have been surveyed are: K-medoids, K-means, Fuzzy C-means, Density-Based Spatial Clustering of Applications with Noise (DBSCAN and Self-Organizing Map (SOM clustering.
Medvedovici, Andrei; Albu, Florin; Naşcu-Briciu, Rodica Domnica; Sârbu, Costel
2014-02-01
Discrimination power evaluation of UV-Vis and (±) electrospray ionization/mass spectrometric techniques, (ESI-MS) individually considered or coupled as detectors to reversed phase liquid chromatography (RPLC) in the characterization of Ginkgo Biloba standardized extracts, is used in herbal medicines and/or dietary supplements with the help of Fuzzy hierarchical clustering (FHC). Seventeen batches of Ginkgo Biloba commercially available standardized extracts from seven manufacturers were measured during experiments. All extracts were within the criteria of the official monograph dedicated to dried refined and quantified Ginkgo extracts, in the European Pharmacopoeia. UV-Vis and (±) ESI-MS spectra of the bulk standardized extracts in methanol were acquired. Additionally, an RPLC separation based on a simple gradient elution profile was applied to the standardized extracts. Detection was made through monitoring UV absorption at 220 nm wavelength or the total ion current (TIC) produced through (±) ESI-MS analysis. FHC was applied to raw, centered and scaled data sets, for evaluating the discrimination power of the method with respect to the origins of the extracts and to the batch to batch variability. The discrimination power increases with the increase of the intrinsic selectivity of the spectral technique being used: UV-Vis
Kneib, Jean-Paul; 10.1007/s00159-011-0047-3
2012-01-01
Clusters of galaxies are the most recently assembled, massive, bound structures in the Universe. As predicted by General Relativity, given their masses, clusters strongly deform space-time in their vicinity. Clusters act as some of the most powerful gravitational lenses in the Universe. Light rays traversing through clusters from distant sources are hence deflected, and the resulting images of these distant objects therefore appear distorted and magnified. Lensing by clusters occurs in two regimes, each with unique observational signatures. The strong lensing regime is characterized by effects readily seen by eye, namely, the production of giant arcs, multiple-images, and arclets. The weak lensing regime is characterized by small deformations in the shapes of background galaxies only detectable statistically. Cluster lenses have been exploited successfully to address several important current questions in cosmology: (i) the study of the lens(es) - understanding cluster mass distributions and issues pertaining...
Institute of Scientific and Technical Information of China (English)
曾庆磊; 庄茁; 柳占立; 王涛; 高岳
2016-01-01
水平井和水力压裂是页岩气开发中的关键技术。对水力压裂中多簇裂缝同时扩展的物理过程进行了数值模拟。采用扩展有限元法(XFEM)模拟岩石中裂缝沿着任意路径扩展，采用有限体积法(FVM)模拟裂缝中流体的流动，并且考虑井筒中流体流动以及在各簇裂缝间的流量动态分配。通过牛顿迭代对全耦合物理过程进行数值求解，重点研究了初始长度不同的两条裂缝的扩展过程，证明较大的射孔摩阻能促进两条裂缝的同时扩展。并通过算例证明了本方法的精度和有效性。%Hydraulic fracturing in the horizontal wellbore is an effective technique in the development of shale gas.In this paper,the growth of multiple hydraulic fractures clusters is simulated numerically.The extended finite element method (XFEM)is adopted to model arbitrary propagation of the fractures in shale rock and the finite volume method (FVM)is used to discretize fluid flow in the fractures.The flow in horizontal wellbore and the dynamic distribution of the flow into different fracture clusters are consi-dered.The fully coupled field equations are solved by Newton iteration.Numerical examples are pre-sented to validate the accuracy and efficiency of the method.The propagation paths of two hydraulic fractures are modeled to demonstrate that the larger perforation entry friction can promote simultaneous growth of multiple fracture clusters.
Neutrosophic Hierarchical Clustering Algoritms
Directory of Open Access Journals (Sweden)
Rıdvan Şahin
2014-03-01
Full Text Available Interval neutrosophic set (INS is a generalization of interval valued intuitionistic fuzzy set (IVIFS, whose the membership and non-membership values of elements consist of fuzzy range, while single valued neutrosophic set (SVNS is regarded as extension of intuitionistic fuzzy set (IFS. In this paper, we extend the hierarchical clustering techniques proposed for IFSs and IVIFSs to SVNSs and INSs respectively. Based on the traditional hierarchical clustering procedure, the single valued neutrosophic aggregation operator, and the basic distance measures between SVNSs, we define a single valued neutrosophic hierarchical clustering algorithm for clustering SVNSs. Then we extend the algorithm to classify an interval neutrosophic data. Finally, we present some numerical examples in order to show the effectiveness and availability of the developed clustering algorithms.
Job Oriented Monitoring Clusters
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Vijayalaxmi Cigala,
2011-03-01
Full Text Available There has been a lot of development in the field of clusters and grids. Recently, the use of clusters has been on rise in every possible field. This paper proposes a system that monitors jobs onlarge computational clusters. Monitoring jobs is essential to understand how jobs are being executed. This helps us in understanding the complete life cycle of the jobs being executed on large clusters. Also, this paper describes how the information obtained by monitoring the jobs would help in increasing the overall throughput of clusters. Heuristics help in efficient job distribution among the computational nodes, thereby accomplishing fair job distribution policy. The proposed system would be capable of loadbalancing among the computational nodes, detecting failures, taking corrective actions after failure detection, job monitoring, system resource monitoring, etc.
Clustering of resting state networks.
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Megan H Lee
Full Text Available BACKGROUND: The goal of the study was to demonstrate a hierarchical structure of resting state activity in the healthy brain using a data-driven clustering algorithm. METHODOLOGY/PRINCIPAL FINDINGS: The fuzzy-c-means clustering algorithm was applied to resting state fMRI data in cortical and subcortical gray matter from two groups acquired separately, one of 17 healthy individuals and the second of 21 healthy individuals. Different numbers of clusters and different starting conditions were used. A cluster dispersion measure determined the optimal numbers of clusters. An inner product metric provided a measure of similarity between different clusters. The two cluster result found the task-negative and task-positive systems. The cluster dispersion measure was minimized with seven and eleven clusters. Each of the clusters in the seven and eleven cluster result was associated with either the task-negative or task-positive system. Applying the algorithm to find seven clusters recovered previously described resting state networks, including the default mode network, frontoparietal control network, ventral and dorsal attention networks, somatomotor, visual, and language networks. The language and ventral attention networks had significant subcortical involvement. This parcellation was consistently found in a large majority of algorithm runs under different conditions and was robust to different methods of initialization. CONCLUSIONS/SIGNIFICANCE: The clustering of resting state activity using different optimal numbers of clusters identified resting state networks comparable to previously obtained results. This work reinforces the observation that resting state networks are hierarchically organized.
Wagstaff, Kiri L.
2012-03-01
On obtaining a new data set, the researcher is immediately faced with the challenge of obtaining a high-level understanding from the observations. What does a typical item look like? What are the dominant trends? How many distinct groups are included in the data set, and how is each one characterized? Which observable values are common, and which rarely occur? Which items stand out as anomalies or outliers from the rest of the data? This challenge is exacerbated by the steady growth in data set size [11] as new instruments push into new frontiers of parameter space, via improvements in temporal, spatial, and spectral resolution, or by the desire to "fuse" observations from different modalities and instruments into a larger-picture understanding of the same underlying phenomenon. Data clustering algorithms provide a variety of solutions for this task. They can generate summaries, locate outliers, compress data, identify dense or sparse regions of feature space, and build data models. It is useful to note up front that "clusters" in this context refer to groups of items within some descriptive feature space, not (necessarily) to "galaxy clusters" which are dense regions in physical space. The goal of this chapter is to survey a variety of data clustering methods, with an eye toward their applicability to astronomical data analysis. In addition to improving the individual researcher’s understanding of a given data set, clustering has led directly to scientific advances, such as the discovery of new subclasses of stars [14] and gamma-ray bursts (GRBs) [38]. All clustering algorithms seek to identify groups within a data set that reflect some observed, quantifiable structure. Clustering is traditionally an unsupervised approach to data analysis, in the sense that it operates without any direct guidance about which items should be assigned to which clusters. There has been a recent trend in the clustering literature toward supporting semisupervised or constrained
Nanda, Kaushik D; Krylov, Anna I
2016-11-28
We present the theory and implementation for calculating static polarizabilities within the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) framework for electronically excited states and its spin-flip variant. We evaluate the second derivatives of the EOM-CCSD Lagrangian with respect to electric-field perturbations. The relaxation of reference molecular orbitals is not included. In our approach, the wave function amplitudes satisfy the 2n + 1 rule and the amplitude-response Lagrange multipliers satisfy the 2n + 2 rule. The new implementation is validated against finite-field and CCSD response-theory calculations of the excited-state polarizabilities of pyrimidine and s-tetrazine. We use the new method to compute static polarizabilities of different types of electronic states (valence, charge-transfer, singlets, and triplets) in open- and closed-shell systems (uracil, p-nitroaniline, methylene, and p-benzyne). We also present an alternative approach for calculating excited-state static polarizabilities as expectation values by using the EOM-CCSD wave functions and energies in the polarizability expression for an exact state. We find that this computationally less demanding approach may show differences up to ∼30% relative to the excited-state polarizabilities computed using the analytic-derivative formalism.
Nanda, Kaushik D; Krylov, Anna I
2015-02-14
The equation-of-motion coupled-cluster (EOM-CC) methods provide a robust description of electronically excited states and their properties. Here, we present a formalism for two-photon absorption (2PA) cross sections for the equation-of-motion for excitation energies CC with single and double substitutions (EOM-CC for electronically excited states with single and double substitutions) wave functions. Rather than the response theory formulation, we employ the expectation-value approach which is commonly used within EOM-CC, configuration interaction, and algebraic diagrammatic construction frameworks. In addition to canonical implementation, we also exploit resolution-of-the-identity (RI) and Cholesky decomposition (CD) for the electron-repulsion integrals to reduce memory requirements and to increase parallel efficiency. The new methods are benchmarked against the CCSD and CC3 response theories for several small molecules. We found that the expectation-value 2PA cross sections are within 5% from the quadratic response CCSD values. The RI and CD approximations lead to small errors relative to the canonical implementation (less than 4%) while affording computational savings. RI/CD successfully address the well-known issue of large basis set requirements for 2PA cross sections calculations. The capabilities of the new code are illustrated by calculations of the 2PA cross sections for model chromophores of the photoactive yellow and green fluorescent proteins.
Baeck, Kyoung K.; Watts, John D.; Bartlett, Rodney J.
1997-09-01
Analytic coupled-cluster (CC) and many-body perturbation theory (MBPT) energy gradient methods with restricted Hartree-Fock (RHF), unrestricted Hartree-Fock (UHF), restricted open-shell Hartree-Fock (ROHF), and quasi-RHF(QRHF) reference functions are extended to permit dopping core and excited orbitals. By using the canonical property of the semicanonical ROHF orbitals and the RHF orbitals from which the QRHF reference function is constructed, it is shown that a general procedure can be established not only for RHF and UHF, but also for ROHF and QRHF reference functions. The basic theory and implementation are reported. To provide a systematic study of the trends and magnitudes of the effects of dropped molecular orbitals (MOs) on the structures, harmonic frequencies, and ir intensities, we study HCN, C2H2, CO2, HO2, and C2H4 at increasing levels of correlation and basis sets. The effects of the dropped MOs with the largest basis sets are about 0.003 Å and 0.1° in structures and about 1% on harmonic frequencies and ir intensities. The magnitude and the direction of the drop-MO effect tend to be almost constant from MBPT(2) to CCSD(T) methods. The two isomers of S3 are studied by the drop-MO-method, yielding very accurate results.
Energy Technology Data Exchange (ETDEWEB)
Nanda, Kaushik D.; Krylov, Anna I. [Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482 (United States)
2015-02-14
The equation-of-motion coupled-cluster (EOM-CC) methods provide a robust description of electronically excited states and their properties. Here, we present a formalism for two-photon absorption (2PA) cross sections for the equation-of-motion for excitation energies CC with single and double substitutions (EOM-CC for electronically excited states with single and double substitutions) wave functions. Rather than the response theory formulation, we employ the expectation-value approach which is commonly used within EOM-CC, configuration interaction, and algebraic diagrammatic construction frameworks. In addition to canonical implementation, we also exploit resolution-of-the-identity (RI) and Cholesky decomposition (CD) for the electron-repulsion integrals to reduce memory requirements and to increase parallel efficiency. The new methods are benchmarked against the CCSD and CC3 response theories for several small molecules. We found that the expectation-value 2PA cross sections are within 5% from the quadratic response CCSD values. The RI and CD approximations lead to small errors relative to the canonical implementation (less than 4%) while affording computational savings. RI/CD successfully address the well-known issue of large basis set requirements for 2PA cross sections calculations. The capabilities of the new code are illustrated by calculations of the 2PA cross sections for model chromophores of the photoactive yellow and green fluorescent proteins.
Nanda, Kaushik D.; Krylov, Anna I.
2015-02-01
The equation-of-motion coupled-cluster (EOM-CC) methods provide a robust description of electronically excited states and their properties. Here, we present a formalism for two-photon absorption (2PA) cross sections for the equation-of-motion for excitation energies CC with single and double substitutions (EOM-CC for electronically excited states with single and double substitutions) wave functions. Rather than the response theory formulation, we employ the expectation-value approach which is commonly used within EOM-CC, configuration interaction, and algebraic diagrammatic construction frameworks. In addition to canonical implementation, we also exploit resolution-of-the-identity (RI) and Cholesky decomposition (CD) for the electron-repulsion integrals to reduce memory requirements and to increase parallel efficiency. The new methods are benchmarked against the CCSD and CC3 response theories for several small molecules. We found that the expectation-value 2PA cross sections are within 5% from the quadratic response CCSD values. The RI and CD approximations lead to small errors relative to the canonical implementation (less than 4%) while affording computational savings. RI/CD successfully address the well-known issue of large basis set requirements for 2PA cross sections calculations. The capabilities of the new code are illustrated by calculations of the 2PA cross sections for model chromophores of the photoactive yellow and green fluorescent proteins.
Nanda, Kaushik D.; Krylov, Anna I.
2017-06-01
We present static polarizabilities and two-photon absorption (2PA) cross sections for the low-lying electronic states of prototypical diradicals such as benzynes and analogues of m-xylylene and p-quinodimethane computed with the spin-flip equation-of-motion coupled-cluster singles and doubles (EOM-SF-CCSD) method. The static polarizabilities were calculated as analytic second derivatives of the EOM energies, and the 2PA cross sections were calculated using the expectation-value approach. We explain the trends in the nonlinear responses of the SF target states by constructing few-states models based on truncated sum-over-states expressions for these nonlinear properties. By using a Huckel-type treatment of the frontier molecular orbitals that host the unpaired electrons, we rationalize the trends in the dipole interactions between the SF target states relevant in the few-states models. We demonstrate the correlation between the nonlinear responses of these electronic states and the diradical character.
Nanda, Kaushik D.; Krylov, Anna I.
2016-11-01
We present the theory and implementation for calculating static polarizabilities within the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) framework for electronically excited states and its spin-flip variant. We evaluate the second derivatives of the EOM-CCSD Lagrangian with respect to electric-field perturbations. The relaxation of reference molecular orbitals is not included. In our approach, the wave function amplitudes satisfy the 2n + 1 rule and the amplitude-response Lagrange multipliers satisfy the 2n + 2 rule. The new implementation is validated against finite-field and CCSD response-theory calculations of the excited-state polarizabilities of pyrimidine and s-tetrazine. We use the new method to compute static polarizabilities of different types of electronic states (valence, charge-transfer, singlets, and triplets) in open- and closed-shell systems (uracil, p-nitroaniline, methylene, and p-benzyne). We also present an alternative approach for calculating excited-state static polarizabilities as expectation values by using the EOM-CCSD wave functions and energies in the polarizability expression for an exact state. We find that this computationally less demanding approach may show differences up to ˜30 % relative to the excited-state polarizabilities computed using the analytic-derivative formalism.
Barragán, Patricia; Pérez de Tudela, Ricardo; Qu, Chen; Prosmiti, Rita; Bowman, Joel M
2013-07-14
Diffusion Monte Carlo (DMC) and path-integral Monte Carlo computations of the vibrational ground state and 10 K equilibrium state properties of the H7 (+)/D7 (+) cations are presented, using an ab initio full-dimensional potential energy surface. The DMC zero-point energies of dissociated fragments H5 (+)(D5 (+))+H2(D2) are also calculated and from these results and the electronic dissociation energy, dissociation energies, D0, of 752 ± 15 and 980 ± 14 cm(-1) are reported for H7 (+) and D7 (+), respectively. Due to the known error in the electronic dissociation energy of the potential surface, these quantities are underestimated by roughly 65 cm(-1). These values are rigorously determined for first time, and compared with previous theoretical estimates from electronic structure calculations using standard harmonic analysis, and available experimental measurements. Probability density distributions are also computed for the ground vibrational and 10 K state of H7 (+) and D7 (+). These are qualitatively described as a central H3 (+)/D3 (+) core surrounded by "solvent" H2/D2 molecules that nearly freely rotate.
Institute of Scientific and Technical Information of China (English)
2011-01-01
@@ Cansisting of eight scientists from the State Key Laboratory of Physical Chemistry of Solid Surfaces and Xiamen University, this creative research group is devoted to the research of cluster chemistry and creation of nanomaterials.After three-year hard work, the group scored a series of encouraging progresses in synthesis of clusters with special structures, including novel fullerenes, fullerene-like metal cluster compounds as well as other related nanomaterials, and their properties study.
Directory of Open Access Journals (Sweden)
Gulcin Salıngan
2012-07-01
Full Text Available Economic development has always been a moving target. Both the national and local governments have been facing the challenge of implementing the effective and efficient economic policy and program in order to best utilize their limited resources. One of the recent approaches in this area is called cluster-based economic analysis and strategy development. This study reviews key literature and some of the cluster based economic policies adopted by different governments. Based on this review, it proposes “the cluster life cycle” as a determining factor to identify the support requirements of clusters. A survey, designed based on literature review of International Cluster support programs, was conducted with 30 participants from 3 clusters with different maturity stage. This paper discusses the results of this study conducted among the cluster members in Eskişehir- Bilecik-Kütahya Region in Turkey on the requirement of the support to foster the development of related clusters.
Clustered regression with unknown clusters
Barman, Kishor
2011-01-01
We consider a collection of prediction experiments, which are clustered in the sense that groups of experiments ex- hibit similar relationship between the predictor and response variables. The experiment clusters as well as the regres- sion relationships are unknown. The regression relation- ships define the experiment clusters, and in general, the predictor and response variables may not exhibit any clus- tering. We call this prediction problem clustered regres- sion with unknown clusters (CRUC) and in this paper we focus on linear regression. We study and compare several methods for CRUC, demonstrate their applicability to the Yahoo Learning-to-rank Challenge (YLRC) dataset, and in- vestigate an associated mathematical model. CRUC is at the crossroads of many prior works and we study several prediction algorithms with diverse origins: an adaptation of the expectation-maximization algorithm, an approach in- spired by K-means clustering, the singular value threshold- ing approach to matrix rank minimization u...
SPATIO-TEMPORAL CLUSTER ANALYSIS OF DISEASE
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M. S. Abramovich
2014-01-01
Full Text Available The robust version of the spatial scanning statistics for clustering is proposed. Spatio-temporal cluster analysis algorithms were used for the cluster detection of incidence of thyroid carcinoma. Me-thods and algorithms of detection and building clusters for disease on studying territories are consi-dered.
Formation of innovative clusters in tourism
Directory of Open Access Journals (Sweden)
Stanislav V. Koshcheev
2011-06-01
Full Text Available Modern preconditions of development innovative clusters in Russian economy are analyzed. The importance of application of cluster approach to management of innovations in tourism is shown. Necessity formation of innovative clusters in region of tourist specialization for increase of competitiveness of territory is reflected. The model of formation of innovative clusters in tourism is offered.
Subspace clustering through attribute clustering
Institute of Scientific and Technical Information of China (English)
Kun NIU; Shubo ZHANG; Junliang CHEN
2008-01-01
Many recently proposed subspace clustering methods suffer from two severe problems. First, the algorithms typically scale exponentially with the data dimensionality or the subspace dimensionality of clusters. Second, the clustering results are often sensitive to input parameters. In this paper, a fast algorithm of subspace clustering using attribute clustering is proposed to over-come these limitations. This algorithm first filters out redundant attributes by computing the Gini coefficient. To evaluate the correlation of every two non-redundant attributes, the relation matrix of non-redundant attributes is constructed based on the relation function of two dimensional united Gini coefficients. After applying an overlapping clustering algorithm on the relation matrix, the candidate of all interesting subspaces is achieved. Finally, all subspace clusters can be derived by clustering on interesting subspaces. Experiments on both synthesis and real datasets show that the new algorithm not only achieves a significant gain of runtime and quality to find subspace clusters, but also is insensitive to input parameters.
Directory of Open Access Journals (Sweden)
Ducros Anne
2008-07-01
Full Text Available Abstract Cluster headache (CH is a primary headache disease characterized by recurrent short-lasting attacks (15 to 180 minutes of excruciating unilateral periorbital pain accompanied by ipsilateral autonomic signs (lacrimation, nasal congestion, ptosis, miosis, lid edema, redness of the eye. It affects young adults, predominantly males. Prevalence is estimated at 0.5–1.0/1,000. CH has a circannual and circadian periodicity, attacks being clustered (hence the name in bouts that can occur during specific months of the year. Alcohol is the only dietary trigger of CH, strong odors (mainly solvents and cigarette smoke and napping may also trigger CH attacks. During bouts, attacks may happen at precise hours, especially during the night. During the attacks, patients tend to be restless. CH may be episodic or chronic, depending on the presence of remission periods. CH is associated with trigeminovascular activation and neuroendocrine and vegetative disturbances, however, the precise cautive mechanisms remain unknown. Involvement of the hypothalamus (a structure regulating endocrine function and sleep-wake rhythms has been confirmed, explaining, at least in part, the cyclic aspects of CH. The disease is familial in about 10% of cases. Genetic factors play a role in CH susceptibility, and a causative role has been suggested for the hypocretin receptor gene. Diagnosis is clinical. Differential diagnoses include other primary headache diseases such as migraine, paroxysmal hemicrania and SUNCT syndrome. At present, there is no curative treatment. There are efficient treatments to shorten the painful attacks (acute treatments and to reduce the number of daily attacks (prophylactic treatments. Acute treatment is based on subcutaneous administration of sumatriptan and high-flow oxygen. Verapamil, lithium, methysergide, prednisone, greater occipital nerve blocks and topiramate may be used for prophylaxis. In refractory cases, deep-brain stimulation of the
Contextual Learning Induces Dendritic Spine Clustering in Retrosplenial Cortex
Directory of Open Access Journals (Sweden)
Adam C Frank
2014-03-01
Full Text Available Molecular and electrophysiological studies find convergent evidence suggesting that plasticity within a dendritic tree is not randomly dispersed, but rather clustered into functional groups. Further, results from in silico neuronal modeling show that clustered plasticity is able to increase storage capacity 45 times compared to dispersed plasticity. Recent in vivo work utilizing chronic 2-photon microscopy tested the clustering hypothesis and showed that repetitive motor learning is able to induce clustered addition of new dendritic spines on apical dendrites of L5 neurons in primary motor cortex; moreover, clustered spines were found to be more stable than non-clustered spines, suggesting a physiological role for spine clustering. To further test this hypothesis we used in vivo 2-photon imaging in Thy1-YFP-H mice to chronically examine dendritic spine dynamics in retrosplenial cortex (RSC during spatial learning. RSC is a key component of an extended spatial learning and memory circuit that includes hippocampus and entorhinal cortex. Importantly, RSC is known from both lesion and immediate early gene studies to be critically involved in spatial learning and more specifically in contextual fear conditioning. We utilized a modified contextual fear conditioning protocol wherein animals received a mild foot shock each day for five days; this protocol induces gradual increases in context freezing over several days before the animals reach a behavioral plateau. We coupled behavioral training with four separate in vivo imaging sessions, two before training begins, one early in training, and a final session after training is complete. This allowed us to image spine dynamics before training as well as early in learning and after animals had reached behavioral asymptote. We find that this contextual learning protocol induces a statistically significant increase in the formation of clusters of new dendritic spines in trained animals when compared to home
Cao, Zhanli; Li, Zhendong; Wang, Fan; Liu, Wenjian
2017-02-01
The spin-separated exact two-component (X2C) relativistic Hamiltonian [sf-X2C+so-DKHn, J. Chem. Phys., 2012, 137, 154114] is combined with the equation-of-motion coupled-cluster method with singles and doubles (EOM-CCSD) for the treatment of spin-orbit splittings of open-shell molecular systems. Scalar relativistic effects are treated to infinite order from the outset via the spin-free part of the X2C Hamiltonian (sf-X2C), whereas the spin-orbit couplings (SOC) are handled at the CC level via the first-order Douglas-Kroll-Hess (DKH) type of spin-orbit operator (so-DKH1). Since the exponential of single excitations, i.e., exp(T1), introduces sufficient spin orbital relaxations, the inclusion of SOC at the CC level is essentially the same in accuracy as the inclusion of SOC from the outset in terms of the two-component spinors determined variationally by the sf-X2C+so-DKH1 Hamiltonian, but is computationally more efficient. Therefore, such an approach (denoted as sf-X2C-EOM-CCSD(SOC)) can achieve uniform accuracy for the spin-orbit splittings of both light and heavy elements. For light elements, the treatment of SOC can even be postponed until the EOM step (denoted as sf-X2C-EOM(SOC)-CCSD), so as to further reduce the computational cost. To reveal the efficacy of sf-X2C-EOM-CCSD(SOC) and sf-X2C-EOM(SOC)-CCSD, the spin-orbit splittings of the (2)Π states of monohydrides up to the sixth row of the periodic table are investigated. The results show that sf-X2C-EOM-CCSD(SOC) predicts very accurate results (within 5%) for elements up to the fifth row, whereas sf-X2C-EOM(SOC)-CCSD is useful only for light elements (up to the third row but with some exceptions). For comparison, the sf-X2C-S-TD-DFT-SOC approach [spin-adapted open-shell time-dependent density functional theory, Mol. Phys., 2013, 111, 3741] is applied to the same systems. The overall accuracy (1-10%) is satisfactory.
DEFF Research Database (Denmark)
Böcker, S.; Baumbach, Jan
2013-01-01
. The problem has been the inspiration for numerous algorithms in bioinformatics, aiming at clustering entities such as genes, proteins, phenotypes, or patients. In this paper, we review exact and heuristic methods that have been proposed for the Cluster Editing problem, and also applications......The Cluster Editing problem asks to transform a graph into a disjoint union of cliques using a minimum number of edge modifications. Although the problem has been proven NP-complete several times, it has nevertheless attracted much research both from the theoretical and the applied side...
Ackerman, Margareta; Branzei, Simina; Loker, David
2011-01-01
In this paper we investigate clustering in the weighted setting, in which every data point is assigned a real valued weight. We conduct a theoretical analysis on the influence of weighted data on standard clustering algorithms in each of the partitional and hierarchical settings, characterising the precise conditions under which such algorithms react to weights, and classifying clustering methods into three broad categories: weight-responsive, weight-considering, and weight-robust. Our analysis raises several interesting questions and can be directly mapped to the classical unweighted setting.
Everitt, Brian S; Leese, Morven; Stahl, Daniel
2011-01-01
Cluster analysis comprises a range of methods for classifying multivariate data into subgroups. By organizing multivariate data into such subgroups, clustering can help reveal the characteristics of any structure or patterns present. These techniques have proven useful in a wide range of areas such as medicine, psychology, market research and bioinformatics.This fifth edition of the highly successful Cluster Analysis includes coverage of the latest developments in the field and a new chapter dealing with finite mixture models for structured data.Real life examples are used throughout to demons
Clustering Methodologies for Software Engineering
Directory of Open Access Journals (Sweden)
Mark Shtern
2012-01-01
Full Text Available The size and complexity of industrial strength software systems are constantly increasing. This means that the task of managing a large software project is becoming even more challenging, especially in light of high turnover of experienced personnel. Software clustering approaches can help with the task of understanding large, complex software systems by automatically decomposing them into smaller, easier-to-manage subsystems. The main objective of this paper is to identify important research directions in the area of software clustering that require further attention in order to develop more effective and efficient clustering methodologies for software engineering. To that end, we first present the state of the art in software clustering research. We discuss the clustering methods that have received the most attention from the research community and outline their strengths and weaknesses. Our paper describes each phase of a clustering algorithm separately. We also present the most important approaches for evaluating the effectiveness of software clustering.
Continuum modeling of myxobacteria clustering
Harvey, Cameron W.; Alber, Mark; Tsimring, Lev S.; Aranson, Igor S.
2013-03-01
In this paper we develop a continuum theory of clustering in ensembles of self-propelled inelastically colliding rods with applications to collective dynamics of common gliding bacteria Myxococcus xanthus. A multi-phase hydrodynamic model that couples densities of oriented and isotropic phases is described. This model is used for the analysis of an instability that leads to spontaneous formation of directionally moving dense clusters within initially dilute isotropic ‘gas’ of myxobacteria. Numerical simulations of this model confirm the existence of stationary dense moving clusters and also elucidate the properties of their collisions. The results are shown to be in a qualitative agreement with experiments.
Coalescence in coupled Duffing oscillators
Institute of Scientific and Technical Information of China (English)
YANG Jun-Zhong
2009-01-01
The forced Duffing oscillator has a pair of symmetrical attractors in a proper parameter regime. When a lot of Duffing oscillators are coupled linearly, the system tends to form clusters in which the neighboring oscillators fall onto the same attractor. When the coupling strength is strong, all of the oscillators fall onto one attractor. In this work, we investigate coalescence in the coupled forced Duffing oscillators. Some phenomena are found and explanations are presented.
Directory of Open Access Journals (Sweden)
Paulrajpillai Xavier
2012-02-01
Full Text Available Noble metal quantum clusters (NMQCs are the missing link between isolated noble metal atoms and nanoparticles. NMQCs are sub-nanometer core sized clusters composed of a group of atoms, most often luminescent in the visible region, and possess intriguing photo-physical and chemical properties. A trend is observed in the use of ligands, ranging from phosphines to functional proteins, for the synthesis of NMQCs in the liquid phase. In this review, we briefly overview recent advancements in the synthesis of protein protected NMQCs with special emphasis on their structural and photo-physical properties. In view of the protein protection, coupled with direct synthesis and easy functionalization, this hybrid QC-protein system is expected to have numerous optical and bioimaging applications in the future, pointers in this direction are visible in the literature.
DEFF Research Database (Denmark)
Berks, G.; Keyserlingk, Diedrich Graf von; Jantzen, Jan
2000-01-01
A symptom is a condition indicating the presence of a disease, especially, when regarded as an aid in diagnosis.Symptoms are the smallest units indicating the existence of a disease. A syndrome on the other hand is an aggregate, set or cluster of concurrent symptoms which together indicate...... and clustering are the basic concerns in medicine. Classification depends on definitions of the classes and their required degree of participant of the elements in the cases' symptoms. In medicine imprecise conditions are the rule and therefore fuzzy methods are much more suitable than crisp ones. Fuzzy c......-mean clustering is an easy and well improved tool, which has been applied in many medical fields. We used c-mean fuzzy clustering after feature extraction from an aphasia database. Factor analysis was applied on a correlation matrix of 26 symptoms of language disorders and led to five factors. The factors...
Investigating Bimodal Clustering in Human Mobility
Bagrow, James P; 10.1109/CSE.2009.283
2009-01-01
We apply a simple clustering algorithm to a large dataset of cellular telecommunication records, reducing the complexity of mobile phone users' full trajectories and allowing for simple statistics to characterize their properties. For the case of two clusters, we quantify how clustered human mobility is, how much of a user's spatial dispersion is due to motion between clusters, and how spatially and temporally separated clusters are from one another.
Sammis, John; Bailey, Holly
2010-01-01
For the past couple of decades, customer relationship management has been quietly establishing itself as the way everybody does business. Migrating to the education community only in the past five years or so, it has acquired a more genteel transcription of its acronym: constituent relationship management. However one decodes the letters, CRM is…
Sammis, John; Bailey, Holly
2010-01-01
For the past couple of decades, customer relationship management has been quietly establishing itself as the way everybody does business. Migrating to the education community only in the past five years or so, it has acquired a more genteel transcription of its acronym: constituent relationship management. However one decodes the letters, CRM is…
Liew, Christina Shu Min; Li, Xiao; Lee, Hian Kee
2016-09-20
A new sample preparation approach of combining a miniscale version of liquid-liquid extraction (LLE), termed miniscale-LLE (msLLE), with automated full evaporation dynamic headspace extraction (FEDHS) was developed. Its applicability was demonstrated in the extraction of several polycyclic aromatic hydrocarbons (PAHs) (acenaphthylene, acenaphthene, fluorene, phenanthrene, anthracene, fluoranthene, and pyrene) from aqueous samples. In the first step, msLLE was conducted with 1.75 mL of n-hexane, and all of the extract was vaporized through a Tenax TA sorbent tube via a nitrogen gas flow, in the FEDHS step. Due to the stronger π-π interaction between the Tenax TA polymer and PAHs, only the latter, and not n-hexane, was adsorbed by the sorbent. This selectivity by the Tenax TA polymer allowed an effective concentration of PAHs while eliminating n-hexane by the FEDHS process. After that, thermal desorption was applied to the PAHs to channel them into a gas chromatography/mass spectrometric (GC/MS) system for analysis. Experimental parameters affecting msLLE (solvent volume and mixing duration) and FEDHS (temperature and duration) were optimized. The obtained results achieved low limits of detection (1.85-3.63 ng/L) with good linearity (r(2) > 0.9989) and high enrichment factors ranging from 4200 to 14 100. The optimized settings were applied to the analysis of canal water sampled from an industrial area and tap water, and this methodology was compared to stir-bar sorptive extraction (SBSE). This innovative combined extraction-concentration approach proved to be fast, effective, and efficient in determining low concentrations of PAHs in aqueous samples.
Anllo, Lauren; Schüpbach, Trudi
2016-06-15
Cell migration plays crucial roles during development. An excellent model to study coordinated cell movements is provided by the migration of border cell clusters within a developing Drosophila egg chamber. In a mutagenesis screen, we isolated two alleles of the gene rickets (rk) encoding a G-protein-coupled receptor. The rk alleles result in border cell migration defects in a significant fraction of egg chambers. In rk mutants, border cells are properly specified and express the marker Slbo. Yet, analysis of both fixed as well as live samples revealed that some single border cells lag behind the main border cell cluster during migration, or, in other cases, the entire border cell cluster can remain tethered to the anterior epithelium as it migrates. These defects are observed significantly more often in mosaic border cell clusters, than in full mutant clusters. Reduction of the Rk ligand, Bursicon, in the border cell cluster also resulted in migration defects, strongly suggesting that Rk signaling is utilized for communication within the border cell cluster itself. The mutant border cell clusters show defects in localization of the adhesion protein E-cadherin, and apical polarity proteins during migration. E-cadherin mislocalization occurs in mosaic clusters, but not in full mutant clusters, correlating well with the rk border cell migration phenotype. Our work has identified a receptor with a previously unknown role in border cell migration that appears to regulate detachment and polarity of the border cell cluster coordinating processes within the cells of the cluster themselves.
Directory of Open Access Journals (Sweden)
Ahmad M Mansour
2012-01-01
Full Text Available Purpose: To present the visual outcomes and ocular sequelae of victims of cluster bombs. Materials and Methods: This retrospective, multicenter case series of ocular injury due to cluster bombs was conducted for 3 years after the war in South Lebanon (July 2006. Data were gathered from the reports to the Information Management System for Mine Action. Results: There were 308 victims of clusters bombs; 36 individuals were killed, of which 2 received ocular lacerations and; 272 individuals were injured with 18 receiving ocular injury. These 18 surviving individuals were assessed by the authors. Ocular injury occurred in 6.5% (20/308 of cluster bomb victims. Trauma to multiple organs occurred in 12 of 18 cases (67% with ocular injury. Ocular findings included corneal or scleral lacerations (16 eyes, corneal foreign bodies (9 eyes, corneal decompensation (2 eyes, ruptured cataract (6 eyes, and intravitreal foreign bodies (10 eyes. The corneas of one patient had extreme attenuation of the endothelium. Conclusions: Ocular injury occurred in 6.5% of cluster bomb victims and 67% of the patients with ocular injury sustained trauma to multiple organs. Visual morbidity in civilians is an additional reason for a global ban on the use of cluster bombs.
Clustering Approach to Stock Market Prediction
Directory of Open Access Journals (Sweden)
M.Suresh Babu
2012-01-01
Full Text Available Clustering is an adaptive procedure in which objects are clustered or grouped together, based on the principle of maximizing the intra-class similarity and minimizing the inter-class similarity. Various clustering algorithms have been developed which results to a good performance on datasets for cluster formation. This paper analyze the major clustering algorithms: K-Means, Hierarchical clustering algorithm and reverse K means and compare the performance of these three major clustering algorithms on the aspect of correctly class wise cluster building ability of algorithm. An effective clustering method, HRK (Hierarchical agglomerative and Recursive K-means clustering is proposed, to predict the short-term stock price movements after the release of financial reports. The proposed method consists of three phases. First, we convert each financial report into a feature vector and use the hierarchical agglomerative clustering method to divide the converted feature vectors into clusters. Second, for each cluster, we recursively apply the K-means clustering method to partition each cluster into sub-clusters so that most feature vectors in each subcluster belong to the same class. Then, for each sub cluster, we choose its centroid as the representative feature vector. Finally, we employ the representative feature vectors to predict the stock price movements. The experimental results show the proposed method outperforms SVM in terms of accuracy and average profits.
Pancino, E.; Bellazzini, M.; Giuffrida, G.; Marinoni, S.
2017-01-01
The treatment of crowded fields in Gaia data will only be a reality in a few years from now. In particular, for globular clusters, only the end-of-mission data (public in 2022-2023) will have the necessary full crowding treatment and will reach sufficient quality for the faintest stars. As a consequence, the work on the deblending and decontamination pipelines is still ongoing. We describe the present status of the pipelines for different Gaia instruments, and we model the end-of-mission crowding errors on the basis of available information. We then apply the nominal post-launch Gaia performances, appropriately worsened by the estimated crowding errors, to a set of 18 simulated globular clusters with different concentration, distance, and field contamination. We conclude that there will be 103-104 stars with astrometric performances virtually untouched by crowding (contaminated by <1 mmag) in the majoritiy of clusters. The most limiting factor will be field crowding, not cluster crowding: the most contaminated clusters will only contain 10-100 clean stars. We also conclude that: (i) the systemic proper motions and parallaxes will be determined to 1% or better up to ≃15 kpc, and the nearby clusters will have radial velocities to a few km s-1 ; (ii) internal kinematics will be of unprecendented quality, cluster masses will be determined to ≃10% up to 15 kpc and beyond, and it will be possible to identify differences of a few km s-1 or less in the kinematics (if any) of cluster sub-populations up to 10 kpc and beyond; (iii) the brightest stars (V≃17 mag) will have space-quality, wide-field photometry (mmag errors), and all Gaia photometry will have 1-3% errors on the absolute photometric calibration.
Comparative Study of K-means and Robust Clustering
Directory of Open Access Journals (Sweden)
Shashi Sharma
2013-09-01
Full Text Available Data mining is the mechanism of implementing patterns in large amount of data sets involving methods at the intersection of artificial intelligence, machine learning, statistics, and database systems. Clustering is the very big area in which grouping of same type of objects in data mining. Clustering has divided into different categories – partitioned clustering and hierarchical clustering. In this paper we study two types of clustering first is Kmeans which is part of partitioned clustering. Kmeans clustering generates a specific number of disjoint, flat (non-hierarchical clusters. Second clustering is robust clustering which is part of hierarchical clustering. This clustering uses Jaccard coefficient instead of using the distance measures to find the similarity between the data or documents to classify the clusters. We show comparison between Kmeans clustering and robust clustering which is better for categorical data.
Cluster-based tangible programming
CSIR Research Space (South Africa)
Smith, Andrew C
2014-05-01
Full Text Available Clustering is the act of grouping items that belong together. In this paper we explore clustering as a means to construct tangible program logic, and specifically as a means to use multiple tangible objects collectively as a single tangible program...
DEFF Research Database (Denmark)
Christensen, Thomas Budde
.g. sustainability or quality of life. The purpose of this paper is to explore how and to what extent public sector interventions that aim at forcing cluster development in industries can support sustainable development as defined in the Brundtland tradition and more recently elaborated in such concepts as eco......, Portugal and New Zealand have adopted the concept. Public sector interventions that aim to support cluster development in industries most often focus upon economic policy goals such as enhanced employment and improved productivity, but rarely emphasise broader societal policy goals relating to e...... to the automotive sector in Wales. Specifically, the paper evaluates the "Accelerates" programme initiated by the Welsh Development Agency and elaborates on how and to what extent the Accelerate programme supports the development of a sustainable automotive industry cluster. The Accelerate programme was set up...
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K. Manimaran
2013-08-01
Full Text Available Using the preformation cluster model of Gupta and collaborators we have studied all the possible cluster decay modes of 127 I. The calculated half-lives are compared with recently measured lower limits of cluster decay half-lives (for the clusters like 24Ne, 28Mg, 30Mg, 32Si, 34Si, 48Ca and 49Sc of 127I. Our calculated half-life values lies well above the experimentally measured lower limits and the trend of the values also matches with experimental ones.
Clustering of noise-induced oscillations
DEFF Research Database (Denmark)
Sosnovtseva, Olga; Fomin, A I; Postnov, D E
2001-01-01
The subject of our study is clustering in a population of excitable systems driven by Gaussian white noise and with randomly distributed coupling strength. The cluster state is frequency-locked state in which all functional units run at the same noise-induced frequency. Cooperative dynamics...
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Ionel Sergiu Pirju
2014-12-01
Full Text Available This article aims at presenting the South Asian cluster composed of India, Indonesia, Iran and Malaysia, the intercultural values that characterizes it, the supported leadership style and tracing the main macroeconomic considerations which characterizes them. The research is synchronic, analysing the contemporary situation of these countries without reference to their evolution in time, by using the positivist paradigm that explains the reality at one point. It will be analysed the overall cluster with the existing interactions between the countries that composes it, while the article being one of information will avoid building recommendation, or new theories.
Directory of Open Access Journals (Sweden)
Maurizio Rosina
2010-03-01
Full Text Available Geographic ClustersOver the past decade, public alphanumeric database have been growing at exceptional rate. Most of data can be georeferenced, so that is possible gaining new knowledge from such databases. The contribution of this paper is two-fold. We first present a model of geographic clusters, which uses only geographic and functionally data properties. The model is useful to process huge amount of public/government data, even daily upgrading. After that, we merge the model into the framework GEOPOI (GEOcoding Points Of Interest, and show some graphic map results.
Directory of Open Access Journals (Sweden)
Valerio Faraoni
2013-07-01
Full Text Available A massive scalar field in a curved spacetime can propagate along the light cone, a causal pathology, which can, in principle, be eliminated only if the scalar couples conformally to the Ricci curvature of spacetime. This property mandates conformal coupling for the field driving inflation in the early universe. During slow-roll inflation, this coupling can cause super-acceleration and, as a signature, a blue spectrum of primordial gravitational waves.
FORMATION OF A INNOVATION REGIONAL CLUSTER MODEL
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G. S. Merzlikina
2015-01-01
Full Text Available Summary. As a result of investigation of science and methodical approaches related problems of building and development of innovation clusters there were some issues in functional assignments of innovation and production clusters. Because of those issues, article’s authors differ conceptions of innovation cluster and production cluster, as they explain notion of innovation-production cluster. The main goal of this article is to reveal existing organizational issues in cluster building and its successful development. Based on regional clusters building analysis carried out there was typical practical structure of cluster members interaction revealed. This structure also have its cons, as following: absence cluster orientation to marketing environment, lack of members’ prolonged relations’ building and development system, along with ineffective management of information, financial and material streams within cluster, narrow competence difference and responsibility zones between cluster members, lack of transparence of cluster’s action, low environment changes adaptivity, hard to use cluster members’ intellectual property, and commercialization of hi-tech products. When all those issues listed above come together, it reduces life activity of existing models of innovative cluster-building along with practical opportunity of cluster realization. Because of that, authors offer an upgraded innovative-productive cluster building model with more efficient business processes management system, which includes advanced innovative cluster structure, competence matrix and subcluster responsibility zone. Suggested model differs from other ones by using unified innovative product development control center, which also controls production and marketing realization.
DEFF Research Database (Denmark)
Cortsen, Rikke Platz
2014-01-01
Alan Moore and his collaborating artists often manipulate time and space by drawing upon the formal elements of comics and making alternative constellations. This article looks at an element that is used frequently in comics of all kinds – the full page – and discusses how it helps shape spatio......, something that it shares with the full page in comics. Through an analysis of several full pages from Moore titles like Swamp Thing, From Hell, Watchmen and Promethea, it is made clear why the full page provides an apt vehicle for an apocalypse in comics....
DEFF Research Database (Denmark)
Cortsen, Rikke Platz
2014-01-01
Alan Moore and his collaborating artists often manipulate time and space by drawing upon the formal elements of comics and making alternative constellations. This article looks at an element that is used frequently in comics of all kinds – the full page – and discusses how it helps shape spatio-t......, something that it shares with the full page in comics. Through an analysis of several full pages from Moore titles like Swamp Thing, From Hell, Watchmen and Promethea, it is made clear why the full page provides an apt vehicle for an apocalypse in comics....
Coupled Neural Associative Memories
Karbasi, Amin; Salavati, Amir Hesam; Shokrollahi, Amin
2013-01-01
We propose a novel architecture to design a neural associative memory that is capable of learning a large number of patterns and recalling them later in presence of noise. It is based on dividing the neurons into local clusters and parallel plains, very similar to the architecture of the visual cortex of macaque brain. The common features of our proposed architecture with those of spatially-coupled codes enable us to show that the performance of such networks in eliminating noise is drastical...
Freestart collision for full SHA-1
Stevens, M.M.J.; Karpman, P.; Peyrin, T.
2015-01-01
We present in this article a freestart collision example for SHA-1, i.e., a collision for its internal compression function. This is the first practical break of the full SHA-1, reaching all 80 out of 80 steps, while only 10 days of computation on a 64 GPU cluster were necessary to perform the attac
CLUSTER SYNCHRONIZATION IN A COMPLEX DYNAMICAL NETWORK WITH TWO NONIDENTICAL CLUSTERS
Institute of Scientific and Technical Information of China (English)
Liang CHEN; Jun'an LU
2008-01-01
This paper further investigates cluster synchronization in a complex dynamical network with two-cluster. Each cluster contains a number of identical dynamical systems, however, the sub-systems composing the two clusters can be different, i.e., the individual dynamical system in one cluster can differ from that in the other cluster. Complete synchronization within each cluster is possible only if each node from one cluster receives the same input from nodes in other cluster. In this case, the stability condition of one-cluster synchronization is known to contain two terms: the first accounts for the contribution of the inner-cluster coupling structure while the second is simply an extra linear term, which can be deduced by the "same-input" condition. Applying the connection graph stability method, the authors obtain an upper bound of input strength for one cluster if the first account is known, by which the synchronizability of cluster can be scaled. For different clusters, there are different upper bound of input strength by virtue of different dynamics and the corresponding cluster structure. Moreover, two illustrative examples are presented and the numerical simulations coincide with the theoretical analysis.
DEFF Research Database (Denmark)
Christensen, Thomas Budde
The cluster theory attributed to Michael Porter has significantly influenced industrial policies in countries across Europe and North America since the beginning of the 1990s. Institutions such as the EU, OECD and the World Bank and governments in countries such as the UK, France, The Netherlands...
Characterization of the largest effector gene cluster of Ustilago maydis.
Directory of Open Access Journals (Sweden)
Thomas Brefort
2014-07-01
Full Text Available In the genome of the biotrophic plant pathogen Ustilago maydis, many of the genes coding for secreted protein effectors modulating virulence are arranged in gene clusters. The vast majority of these genes encode novel proteins whose expression is coupled to plant colonization. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. Here we present the functional analysis of this genomic region. We show that a 19A deletion mutant behaves like an endophyte, i.e. is still able to colonize plants and complete the infection cycle. However, tumors, the most conspicuous symptoms of maize smut disease, are only rarely formed and fungal biomass in infected tissue is significantly reduced. The generation and analysis of strains carrying sub-deletions identified several genes significantly contributing to tumor formation after seedling infection. Another of the effectors could be linked specifically to anthocyanin induction in the infected tissue. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. We propose that the analysis of plant responses to effector mutant strains that lack a strong virulence phenotype may be a general way to visualize differences in effector function.
Institute of Scientific and Technical Information of China (English)
2012-01-01
<正>Centre for Agriculture and Bioscience International( CABI) is a not-for-profit international Agricultural Information Institute with headquarters in Britain. It aims to improve people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment. CABI Full-text is one of the publishing products of CABI.CABI’s full text repository is growing rapidly and has now been integrated into all our databases including CAB Abstracts,Global Health,our Internet Resources and Abstract Journals. There are currently over 60,000 full text articles available to access. These documents,made possible by agreement with third
Optical Substructures in 48 Galaxy Clusters
Girardi, M; Fadda, D; Giuricin, G; Mardirossian, F; Mezzetti, M
1996-01-01
We analyze the presence of substructures in a set of 48 galaxy clusters, by using galaxy positions and redshifts. We use a multi-scale analysis which couples kinematical estimators with the wavelet transform. 14% of our clusters are strongly substructured (i.e. they are bimodal or complex) and 24% of the remaining unimodal clusters contain substructures at small scales. Thus, in substantial agreement with previous studies, about one third of clusters show substructures. In unimodal clusters the presence of substructures does not affect the estimates of both virial masses and velocity dispersions, which are generally in good agreement with the X-ray temperatures. Thus, unimodal clusters are not too far from a status of dynamical equilibrium. On the contrary, velocity dispersions and masses for some bimodal or complex clusters strongly depend on whether they are treated as single systems or as sums of different clumps and X-ray temperatures and velocity dispersions may be very different.
Wang, Zhengxin; Duan, Zhisheng; Cao, Jinde
2012-03-01
This paper aims to investigate the synchronization problem of coupled dynamical networks with nonidentical Duffing-type oscillators without or with coupling delays. Different from cluster synchronization of nonidentical dynamical networks in the previous literature, this paper focuses on the problem of complete synchronization, which is more challenging than cluster synchronization. By applying an impulsive controller, some sufficient criteria are obtained for complete synchronization of the coupled dynamical networks of nonidentical oscillators. Furthermore, numerical simulations are given to verify the theoretical results.
Quotients of cluster categories
Jorgensen, Peter
2007-01-01
Higher cluster categories were recently introduced as a generalization of cluster categories. This paper shows that in Dynkin types A and D, half of all higher cluster categories are actually just quotients of cluster categories. The other half can be obtained as quotients of 2-cluster categories, the "lowest" type of higher cluster categories. Hence, in Dynkin types A and D, all higher cluster phenomena are implicit in cluster categories and 2-cluster categories. In contrast, the same is not...
Institute of Scientific and Technical Information of China (English)
2014-01-01
<正>Centre for Agriculture and Bioscience International(CABI)is a not-for-profit international Agricultural Information Institute with headquarters in Britain.It aims to improve people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment.CABI Full-text is one of the publishing products of CABI.CABI’s full text repository is growing rapidly
Oscillator clustering in a resource distribution chain
DEFF Research Database (Denmark)
Postnov, D.; Sosnovtseva, Olga; Mosekilde, Erik
2005-01-01
The paper investigates the special clustering phenomena that one can observe in systems of nonlinear oscillators that are coupled via a shared flow of primary resources (or a common power supply). This type of coupling, which appears to be quite frequent in nature, implies that one can no longer...
Progressive Exponential Clustering-Based Steganography
Directory of Open Access Journals (Sweden)
Li Yue
2010-01-01
Full Text Available Cluster indexing-based steganography is an important branch of data-hiding techniques. Such schemes normally achieve good balance between high embedding capacity and low embedding distortion. However, most cluster indexing-based steganographic schemes utilise less efficient clustering algorithms for embedding data, which causes redundancy and leaves room for increasing the embedding capacity further. In this paper, a new clustering algorithm, called progressive exponential clustering (PEC, is applied to increase the embedding capacity by avoiding redundancy. Meanwhile, a cluster expansion algorithm is also developed in order to further increase the capacity without sacrificing imperceptibility.
Small Business Administration — The Regional Innovation Clusters serve a diverse group of sectors and geographies. Three of the initial pilot clusters, termed Advanced Defense Technology clusters,...
Open Clusters and OB Associations: a Review
Directory of Open Access Journals (Sweden)
Anthony G. A. Brown
2001-01-01
Full Text Available In this review on open clusters and OB associations I discuss some recent developments to which Latin American astronomers have contributed. Subsequently, results from the Hipparcos mission concerning OB associations, the Hyades and other nearby open clusters will be discussed. I end with a brief discussion of current theories of star cluster formation and prospects for future research.
Workflows for Full Waveform Inversions
Boehm, Christian; Krischer, Lion; Afanasiev, Michael; van Driel, Martin; May, Dave A.; Rietmann, Max; Fichtner, Andreas
2017-04-01
Despite many theoretical advances and the increasing availability of high-performance computing clusters, full seismic waveform inversions still face considerable challenges regarding data and workflow management. While the community has access to solvers which can harness modern heterogeneous computing architectures, the computational bottleneck has fallen to these often manpower-bounded issues that need to be overcome to facilitate further progress. Modern inversions involve huge amounts of data and require a tight integration between numerical PDE solvers, data acquisition and processing systems, nonlinear optimization libraries, and job orchestration frameworks. To this end we created a set of libraries and applications revolving around Salvus (http://salvus.io), a novel software package designed to solve large-scale full waveform inverse problems. This presentation focuses on solving passive source seismic full waveform inversions from local to global scales with Salvus. We discuss (i) design choices for the aforementioned components required for full waveform modeling and inversion, (ii) their implementation in the Salvus framework, and (iii) how it is all tied together by a usable workflow system. We combine state-of-the-art algorithms ranging from high-order finite-element solutions of the wave equation to quasi-Newton optimization algorithms using trust-region methods that can handle inexact derivatives. All is steered by an automated interactive graph-based workflow framework capable of orchestrating all necessary pieces. This naturally facilitates the creation of new Earth models and hopefully sparks new scientific insights. Additionally, and even more importantly, it enhances reproducibility and reliability of the final results.
Modulated modularity clustering as an exploratory tool for functional genomic inference.
Directory of Open Access Journals (Sweden)
Eric A Stone
2009-05-01
Full Text Available In recent years, the advent of high-throughput assays, coupled with their diminishing cost, has facilitated a systems approach to biology. As a consequence, massive amounts of data are currently being generated, requiring efficient methodology aimed at the reduction of scale. Whole-genome transcriptional profiling is a standard component of systems-level analyses, and to reduce scale and improve inference clustering genes is common. Since clustering is often the first step toward generating hypotheses, cluster quality is critical. Conversely, because the validation of cluster-driven hypotheses is indirect, it is critical that quality clusters not be obtained by subjective means. In this paper, we present a new objective-based clustering method and demonstrate that it yields high-quality results. Our method, modulated modularity clustering (MMC, seeks community structure in graphical data. MMC modulates the connection strengths of edges in a weighted graph to maximize an objective function (called modularity that quantifies community structure. The result of this maximization is a clustering through which tightly-connected groups of vertices emerge. Our application is to systems genetics, and we quantitatively compare MMC both to the hierarchical clustering method most commonly employed and to three popular spectral clustering approaches. We further validate MMC through analyses of human and Drosophila melanogaster expression data, demonstrating that the clusters we obtain are biologically meaningful. We show MMC to be effective and suitable to applications of large scale. In light of these features, we advocate MMC as a standard tool for exploration and hypothesis generation.
THEORETICAL FOUNDATIONS OF FORMATION OF ENTREPRENEURIAL CLUSTER
Directory of Open Access Journals (Sweden)
Rizhikova A. M.
2015-06-01
Full Text Available This article investigates the development of entrepreneurial cluster set direction to support the creation of innovation clusters in Russia. In the face of increasing international competition, one of the most effective ways of development of small and medium-sized enterprises in the field of innovation is their clustering. We have discussed foreign experience of studying cluster initiatives and events on social development of the regions in the context of sociological knowledge about clusters. We have revealed the meaning of an innovation cluster and the difference between business and innovation clusters. The analysis has shown that a key advantage of the business cluster in relation to the network is the participation of state authorities, as well as functional and territorial factor. On the basis of the author's research we have highlighted a number of problems which solution has been carried out through the creation of business clusters
Relativistic Binaries in Globular Clusters
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Benacquista Matthew J.
2006-02-01
Full Text Available The galactic population of globular clusters are old, dense star systems, with a typical cluster containing 10^4 - 10^7 stars. As an old population of stars, globular clusters contain many collapsed and degenerate objects. As a dense population of stars, globular clusters are the scene of many interesting close dynamical interactions between stars. These dynamical interactions can alter the evolution of individual stars and can produce tight binary systems containing one or two compact objects. In this review, we discuss the theoretical models of globular cluster evolution and binary evolution, techniques for simulating this evolution which lead to relativistic binaries, and current and possible future observational evidence for this population. Globular cluster evolution will focus on the properties that boost the production of hard binary systems and on the tidal interactions of the galaxy with the cluster, which tend to alter the structure of the globular cluster with time. The interaction of the components of hard binary systems alters the evolution of both bodies and can lead to exotic objects. Direct N-body integrations and Fokker-Planck simulations of the evolution of globular clusters that incorporate tidal interactions and lead to predictions of relativistic binary populations are also discussed. We discuss the current observational evidence for cataclysmic variables, millisecond pulsars, and low-mass X-ray binaries as well as possible future detection of relativistic binaries with gravitational radiation.
Relativistic Binaries in Globular Clusters
Directory of Open Access Journals (Sweden)
Benacquista Matthew
2002-01-01
Full Text Available The galactic population of globular clusters are old, dense star systems, with a typical cluster containing $10^4 - 10^6$ stars. As an old population of stars, globular clusters contain many collapsed and degenerate objects. As a dense population of stars, globular clusters are the scene of many interesting close dynamical interactions between stars. These dynamical interactions can alter the evolution of individual stars and can produce tight binary systems containing one or two compact objects. In this review, we discuss the theoretical models of globular cluster evolution and binary evolution, techniques for simulating this evolution which lead to relativistic binaries, and current and possible future observational evidence for this population. Globular cluster evolution will focus on the properties that boost the production of hard binary systems and on the tidal interactions of the galaxy with the cluster, which tend to alter the structure of the globular cluster with time. The interaction of the components of hard binary systems alters the evolution of both bodies and can lead to exotic objects. Direct $N$-body integrations and Fokker--Planck simulations of the evolution of globular clusters that incorporate tidal interactions and lead to predictions of relativistic binary populations are also discussed. We discuss the current observational evidence for cataclysmic variables, millisecond pulsars, and low-mass X-ray binaries as well as possible future detection of relativistic binaries with gravitational radiation.
Active matter clusters at interfaces.
Directory of Open Access Journals (Sweden)
Katherine eCopenhagen
2016-03-01
Full Text Available Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor formation and metastasis, colonies of bacteria in a biofilm, or even flocks of birds and schools of fish at the macro-scale. Such clusters typically encounter very heterogeneous environments. What happens when a cluster encounters an interface between two different environments has implications for its function and fate. Here we study this problem by using a mathematical model of a cluster that treats it as a single cohesive unit that moves in two dimensions by exerting a force/torque per unit area whose magnitude depends on the nature of the local environment. We find that low speed (overdamped clusters encountering an interface with a moderate difference in properties can lead to refraction or even total internal reflection of the cluster. For large speeds (underdamped, where inertia dominates, the clusters show more complex behaviors crossing the interface multiple times and deviating from the predictable refraction and reflection for the low velocity clusters. We then present an extreme limit of the model in the absence of rotational damping where clusters can become stuck spiraling along the interface or move in large circular trajectories after leaving the interface. Our results show a wide range of behaviors that occur when collectively moving active biological matter moves across interfaces and these insights can be used to control motion by patterning environments.
Poenaru, Dorin N.; Greiner, Walter
One of the rare examples of phenomena predicted before experimental discovery, offers the opportunity to introduce fission theory based on the asymmetric two center shell model. The valleys within the potential energy surfaces are due to the shell effects and are clearly showing why cluster radioactivity was mostly detected in parent nuclei leading to a doubly magic lead daughter. Saddle point shapes can be determined by solving an integro-differential equation. Nuclear dynamics allows us to calculate the half-lives. The following cluster decay modes (or heavy particle radioactivities) have been experimentally confirmed: 14C, 20O, 23F, 22,24-26Ne, 28,30Mg, 32,34Si with half-lives in good agreement with predicted values within our analytical superasymmetric fission model. The preformation probability is calculated as the internal barrier penetrability. An universal curve is described and used as an alternative for the estimation of the half-lives. The macroscopic-microscopic method was extended to investigate two-alpha accompanied fission and true ternary fission. The methods developed in nuclear physics are also adapted to study the stability of deposited atomic clusters on the planar surfaces.
Directory of Open Access Journals (Sweden)
Moses Iten
2005-08-01
Full Text Available “hey moses full on riot in lawson st the station’s on fire! been going since 4. molotov and more. full on,” reads an SMS message received on the backseat of a Tasmanian bus. What follows is a journey through the landscape of a Gunavidji, whose brothers have all gone to the land of the dead; metallic scraping in the glass cases of the Hobart Museum; a Palestinian woman giving up on her people; land-snails exposing cultural inaccuracies; photographing Australia’s war zone; entering the St Peter’s Basilica of Rome with bulldozers - all in the name of preparing to interview prominent Israeli writer Etgar Keret.
Thakur, C P; Sharma, D
The incidence of crimes reported to three police stations in different towns (one rural, one urban, one industrial) was studied to see if it varied with the day of the lunar cycle. The period of the study covered 1978-82. The incidence of crimes committed on full moon days was much higher than on all other days, new moon days, and seventh days after the full moon and new moon. A small peak in the incidence of crimes was observed on new moon days, but this was not significant when compared with crimes committed on other days. The incidence of crimes on equinox and solstice days did not differ significantly from those on other days, suggesting that the sun probably does not influence the incidence of crime. The increased incidence of crimes on full moon days may be due to "human tidal waves" caused by the gravitational pull of the moon.
Energy Technology Data Exchange (ETDEWEB)
Kelly, K.; White, K.
1981-03-01
An important harvesting alternative in North America is the Full Tree Method, in which trees are felled and transported to roadside, intermediate or primary landings with limbs and branches intact. The acceptance of Full Tree Systems is due to many factors including: labour productivity and increased demands on the forest for ''new products''. These conditions are shaping the future look for forest Harvesting Systems, but must not be the sole determinants. All harvesting implications, such as those affecting Productivity and silviculture, should be thoroughly understood. This paper does not try to discuss every implication, nor any particular one in depth; its purpose is to highlight those areas requiring consideration and to review several current North American Full Tree Systems. (Refs. 5).
Relevance of Dynamic Clustering to Biological Networks
Kaneko, K
1993-01-01
Abstract Network of nonlinear dynamical elements often show clustering of synchronization by chaotic instability. Relevance of the clustering to ecological, immune, neural, and cellular networks is discussed, with the emphasis of partially ordered states with chaotic itinerancy. First, clustering with bit structures in a hypercubic lattice is studied. Spontaneous formation and destruction of relevant bits are found, which give self-organizing, and chaotic genetic algorithms. When spontaneous changes of effective couplings are introduced, chaotic itinerancy of clusterings is widely seen through a feedback mechanism, which supports dynamic stability allowing for complexity and diversity, known as homeochaos. Second, synaptic dynamics of couplings is studied in relation with neural dynamics. The clustering structure is formed with a balance between external inputs and internal dynamics. Last, an extension allowing for the growth of the number of elements is given, in connection with cell differentiation. Effecti...
Institute of Scientific and Technical Information of China (English)
2013-01-01
<正>Centre for Agriculture and Bioscience International(CABI)is a not-for-profit international Agricultural Information Institute with headquarters in Britain.It aims to improve people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment.CABI Full-text is one of the publishing products of CABI.CABI’s full text repository is growing rapidly and has now been integrated into all our databases including CAB Abstracts,Global Health
Compressive full waveform lidar
Yang, Weiyi; Ke, Jun
2017-05-01
To avoid high bandwidth detector, fast speed A/D converter, and large size memory disk, a compressive full waveform LIDAR system, which uses a temporally modulated laser instead of a pulsed laser, is studied in this paper. Full waveform data from NEON (National Ecological Observatory Network) are used. Random binary patterns are used to modulate the source. To achieve 0.15 m ranging resolution, a 100 MSPS A/D converter is assumed to make measurements. SPIRAL algorithm with canonical basis is employed when Poisson noise is considered in the low illuminated condition.
Institute of Scientific and Technical Information of China (English)
2013-01-01
<正>Centre for Agriculture and Bioscience International(CABI)is a not-for-profit international Agricultural Information Institute with headquarters in Britain.It aims to improve people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment.CABI Full-text is one of the publishing products of CABI.CABI’s full text repository is growing rapidly and has now been integrated into all our databases including CAB Abstracts,Global Health,our Internet Resources and Jour-
Fuzzy Clustering Using C-Means Method
Directory of Open Access Journals (Sweden)
Georgi Krastev
2015-05-01
Full Text Available The cluster analysis of fuzzy clustering according to the fuzzy c-means algorithm has been described in this paper: the problem about the fuzzy clustering has been discussed and the general formal concept of the problem of the fuzzy clustering analysis has been presented. The formulation of the problem has been specified and the algorithm for solving it has been described.
DEFF Research Database (Denmark)
Dahl, Michael S.; Van Praag, Mirjam; Thompson, Peter
2015-01-01
We study motivations for and outcomes of couples starting up a joint firm, using a sample of 1,069 Danish couples that established a joint enterprise between 2001 and 2010, while comparing them to a set of comparable firms and couples. The main motivation for joint entrepreneurship is to create...
Single-molecule atomic force microscopy reveals clustering of the yeast plasma-membrane sensor Wsc1.
Directory of Open Access Journals (Sweden)
Jürgen J Heinisch
Full Text Available Signalling is a key feature of living cells which frequently involves the local clustering of specific proteins in the plasma membrane. How such protein clustering is achieved within membrane microdomains ("rafts" is an important, yet largely unsolved problem in cell biology. The plasma membrane of yeast cells represents a good model to address this issue, since it features protein domains that are sufficiently large and stable to be observed by fluorescence microscopy. Here, we demonstrate the ability of single-molecule atomic force microscopy to resolve lateral clustering of the cell integrity sensor Wsc1 in living Saccharomyces cerevisiae cells. We first localize individual wild-type sensors on the cell surface, revealing that they form clusters of approximately 200 nm size. Analyses of three different mutants indicate that the cysteine-rich domain of Wsc1 has a crucial, not yet anticipated function in sensor clustering and signalling. Clustering of Wsc1 is strongly enhanced in deionized water or at elevated temperature, suggesting its relevance in proper stress response. Using in vivo GFP-localization, we also find that non-clustering mutant sensors accumulate in the vacuole, indicating that clustering may prevent endocytosis and sensor turnover. This study represents the first in vivo single-molecule demonstration for clustering of a transmembrane protein in S. cerevisiae. Our findings indicate that in yeast, like in higher eukaryotes, signalling is coupled to the localized enrichment of sensors and receptors within membrane patches.
Ghobadi, Roohollah
2015-01-01
Unidirectional light transport in one-dimensional nanomaterials at the quantum level is a crucial goal to achieve for upcoming computational devices. We here employ a full-quantum mechanical approach based on master equation to describe unidirectional light transport through a pair of two-level systems coupled to a one-dimensional waveguide. By comparing with published semi-classical results, we find that the nonlinearity of the system is reduced, thereby reducing also the unidirectional light transport efficiency. Albeit not fully efficient, we find that the considered quantum system can work as a light diode with an efficiency of approximately 60%. Our results may be used in quantum computation with classical and quantized light.
Institute of Scientific and Technical Information of China (English)
2013-01-01
<正>Centre for Agriculture and Bioscience International( CABI) is a not-for-profit international Agricultural Information Institute with headquarters in Britain. It aims to improve people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment. CABI Full-text is one of the publishing products of CABI.
Institute of Scientific and Technical Information of China (English)
2013-01-01
<正>Centre for Agriculture and Bioscience International(CABI) is a not-for-profit international Agricultural Information Institute with headquarters in Britain. It aims to improve people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment. CABI Full-text is one of the publishing products of CABI.
Institute of Scientific and Technical Information of China (English)
2011-01-01
<正>Centre for Agriculture and Bioscience International(CABI)is a not-for-profit international Agricultural Information Institute with headquarters in Britain. It aims to improve people s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment. CABI Full-text is one of the publishing products of CABI.
A GMBCG galaxy cluster catalog of 55,880 rich clusters from SDSS DR7
Energy Technology Data Exchange (ETDEWEB)
Hao, Jiangang; McKay, Timothy A.; Koester, Benjamin P.; Rykoff, Eli S.; Rozo, Eduardo; Annis, James; Wechsler, Risa H.; Evrard, August; Siegel, Seth R.; Becker, Matthew; Busha, Michael; /Fermilab /Michigan U. /Chicago U., Astron. Astrophys. Ctr. /UC, Santa Barbara /KICP, Chicago /KIPAC, Menlo Park /SLAC /Caltech /Brookhaven
2010-08-01
We present a large catalog of optically selected galaxy clusters from the application of a new Gaussian Mixture Brightest Cluster Galaxy (GMBCG) algorithm to SDSS Data Release 7 data. The algorithm detects clusters by identifying the red sequence plus Brightest Cluster Galaxy (BCG) feature, which is unique for galaxy clusters and does not exist among field galaxies. Red sequence clustering in color space is detected using an Error Corrected Gaussian Mixture Model. We run GMBCG on 8240 square degrees of photometric data from SDSS DR7 to assemble the largest ever optical galaxy cluster catalog, consisting of over 55,000 rich clusters across the redshift range from 0.1 < z < 0.55. We present Monte Carlo tests of completeness and purity and perform cross-matching with X-ray clusters and with the maxBCG sample at low redshift. These tests indicate high completeness and purity across the full redshift range for clusters with 15 or more members.
A GMBCG Galaxy Cluster Catalog of 55,424 Rich Clusters from SDSS DR7
Energy Technology Data Exchange (ETDEWEB)
Hao, Jiangang; /Fermilab; McKay, Timothy A.; /Michigan U.; Koester, Benjamin P.; /Chicago U.; Rykoff, Eli S.; /UC, Santa Barbara /LBL, Berkeley; Rozo, Eduardo; /Chicago U.; Annis, James; /Fermilab; Wechsler, Risa H.; /SLAC; Evrard, August; /Michigan U.; Siegel, Seth R.; /Michigan U.; Becker, Matthew; /Chicago U.; Busha, Michael; /SLAC; Gerdes, David; /Michigan U.; Johnston, David E.; /Fermilab; Sheldon, Erin; /Brookhaven
2011-08-22
We present a large catalog of optically selected galaxy clusters from the application of a new Gaussian Mixture Brightest Cluster Galaxy (GMBCG) algorithm to SDSS Data Release 7 data. The algorithm detects clusters by identifying the red sequence plus Brightest Cluster Galaxy (BCG) feature, which is unique for galaxy clusters and does not exist among field galaxies. Red sequence clustering in color space is detected using an Error Corrected Gaussian Mixture Model. We run GMBCG on 8240 square degrees of photometric data from SDSS DR7 to assemble the largest ever optical galaxy cluster catalog, consisting of over 55,000 rich clusters across the redshift range from 0.1 < z < 0.55. We present Monte Carlo tests of completeness and purity and perform cross-matching with X-ray clusters and with the maxBCG sample at low redshift. These tests indicate high completeness and purity across the full redshift range for clusters with 15 or more members.
Clustering in Redshift Space Linear Theory
Zaroubi, S; Zaroubi, Saleem; Hoffman, Yehuda
1993-01-01
The clustering in redshift space is studied here to first order within the framework of gravitational instability. The distortion introduced by the peculiar velocities of galaxies results in anisotropy in the galaxy distribution and mode-mode coupling when analyzed in Fourier space. An exact linear calculation of the full covariance matrix in both the real and Fourier space is presented here. The explicit dependence on $\\Omeg$ and the biasing parameter is calculated and its potential use as a probe of these parameters is analyzed. It is shown that Kaiser's formalism can be applied only to a data set that subtends a small solid angle on the sky, and therefore cannot be used in the case of all sky surveys. The covariance matrix in the real space is calculated explicitly for {\\it CDM} model, where the behavior along and perpendicular to the line of sight is shown.
The inner Galactic globular clusters
Directory of Open Access Journals (Sweden)
Mateo M.
2013-03-01
Full Text Available Galactic globular clusters located towards the inner regions of the Milky Way have been historically neglected, mainly due to the difficulties caused by the presence of an elevated extinction by foreground dust, and high field star densities along the lines of sight where most of them lie. To overcome these difficulties we have developed a new method to map the differential extinction suffered by these clusters, which was successfully applied to a sample of moderately-extincted, luminous, extended, inner Galactic globular clusters observed in the optical, for which we have been able to determine more accurate physical parameters. For the most extincted inner Galactic globular clusters, near-infrared wavelengths provide a more suitable window for their study. The VVV survey, which is currently observing the central regions of the Milky Way at these wavelengths, will provide a comprehensive view, from the inner regions out to their tidal radii and beyond, of most of these globular clusters.
DEFF Research Database (Denmark)
Bregnbæk, Susanne; Bunkenborg, Mikkel
As critical voices question the quality, authenticity, and value of people, goods, and words in post-Mao China, accusations of emptiness render things open to new investments of meaning, substance, and value. Exploring the production of lack and desire through fine-grained ethnography, this volume......, there is a pervasive concern with states of lack and emptiness and the contributions suggest that this play of emptiness and fullness is crucial to ongoing constructions of quality, value, and subjectivity in China....
Single-cluster dynamics for the random-cluster model
Deng, Youjin; Qian, Xiaofeng; Blöte, Henk W. J.
2009-09-01
We formulate a single-cluster Monte Carlo algorithm for the simulation of the random-cluster model. This algorithm is a generalization of the Wolff single-cluster method for the q -state Potts model to noninteger values q>1 . Its results for static quantities are in a satisfactory agreement with those of the existing Swendsen-Wang-Chayes-Machta (SWCM) algorithm, which involves a full-cluster decomposition of random-cluster configurations. We explore the critical dynamics of this algorithm for several two-dimensional Potts and random-cluster models. For integer q , the single-cluster algorithm can be reduced to the Wolff algorithm, for which case we find that the autocorrelation functions decay almost purely exponentially, with dynamic exponents zexp=0.07 (1), 0.521 (7), and 1.007 (9) for q=2 , 3, and 4, respectively. For noninteger q , the dynamical behavior of the single-cluster algorithm appears to be very dissimilar to that of the SWCM algorithm. For large critical systems, the autocorrelation function displays a range of power-law behavior as a function of time. The dynamic exponents are relatively large. We provide an explanation for this peculiar dynamic behavior.
Directory of Open Access Journals (Sweden)
Jocelyn H Bolin
2014-04-01
Full Text Available Although traditional clustering methods (e.g., K-means have been shown to be useful in the social sciences it is often difficult for such methods to handle situations where clusters in the population overlap or are ambiguous. Fuzzy clustering, a method already recognized in many disciplines, provides a more flexible alternative to these traditional clustering methods. Fuzzy clustering differs from other traditional clustering methods in that it allows for a case to belong to multiple clusters simultaneously. Unfortunately, fuzzy clustering techniques remain relatively unused in the social and behavioral sciences. The purpose of this paper is to introduce fuzzy clustering to these audiences who are currently relatively unfamiliar with the technique. In order to demonstrate the advantages associated with this method, cluster solutions of a common perfectionism measure were created using both fuzzy clustering and K-means clustering, and the results compared. Results of these analyses reveal that different cluster solutions are found by the two methods, and the similarity between the different clustering solutions depends on the amount of cluster overlap allowed for in fuzzy clustering.
Synchronization in a ring of mutually coupled electromechanical devices
Energy Technology Data Exchange (ETDEWEB)
Yolong, V Y Taffoti [Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34100 Trieste (Italy); Woafo, P [Laboratory of Mechanics, Faculty of Sciences, P O Box 812, Yaounde (Cameroon)
2006-11-15
We study the synchronization in a ring of mutually coupled electromechanical devices. Each device consists of an electrical Duffing oscillator coupled magnetically with a linear mechanical oscillator. By varying the coupling coefficient, we find the ranges for cluster and complete synchronization, either in the regular state or in the chaotic one. Effects of this coupling parameter show various types of bifurcation sequences.
Directory of Open Access Journals (Sweden)
Nan Lin
Full Text Available Due to the advancement in sensor technology, the growing large medical image data have the ability to visualize the anatomical changes in biological tissues. As a consequence, the medical images have the potential to enhance the diagnosis of disease, the prediction of clinical outcomes and the characterization of disease progression. But in the meantime, the growing data dimensions pose great methodological and computational challenges for the representation and selection of features in image cluster analysis. To address these challenges, we first extend the functional principal component analysis (FPCA from one dimension to two dimensions to fully capture the space variation of image the signals. The image signals contain a large number of redundant features which provide no additional information for clustering analysis. The widely used methods for removing the irrelevant features are sparse clustering algorithms using a lasso-type penalty to select the features. However, the accuracy of clustering using a lasso-type penalty depends on the selection of the penalty parameters and the threshold value. In practice, they are difficult to determine. Recently, randomized algorithms have received a great deal of attentions in big data analysis. This paper presents a randomized algorithm for accurate feature selection in image clustering analysis. The proposed method is applied to both the liver and kidney cancer histology image data from the TCGA database. The results demonstrate that the randomized feature selection method coupled with functional principal component analysis substantially outperforms the current sparse clustering algorithms in image cluster analysis.
Non-lithographic SERS substrates: tailoring surface chemistry for Au nanoparticle cluster assembly.
Adams, Sarah M; Campione, Salvatore; Caldwell, Joshua D; Bezares, Francisco J; Culbertson, James C; Capolino, Filippo; Ragan, Regina
2012-07-23
Near-field plasmonic coupling and local field enhancement in metal nanoarchitectures, such as arrangements of nanoparticle clusters, have application in many technologies from medical diagnostics, solar cells, to sensors. Although nanoparticle-based cluster assemblies have exhibited signal enhancements in surface-enhanced Raman scattering (SERS) sensors, it is challenging to achieve high reproducibility in SERS response using low-cost fabrication methods. Here an innovative method is developed for fabricating self-organized clusters of metal nanoparticles on diblock copolymer thin films as SERS-active structures. Monodisperse, colloidal gold nanoparticles are attached via a crosslinking reaction on self-organized chemically functionalized poly(methyl methacrylate) domains on polystyrene-block-poly(methyl methacrylate) templates. Thereby nanoparticle clusters with sub-10-nanometer interparticle spacing are achieved. Varying the molar concentration of functional chemical groups and crosslinking agent during the assembly process is found to affect the agglomeration of Au nanoparticles into clusters. Samples with a high surface coverage of nanoparticle cluster assemblies yield relative enhancement factors on the order of 10⁹ while simultaneously producing uniform signal enhancements in point-to-point measurements across each sample. High enhancement factors are associated with the narrow gap between nanoparticles assembled in clusters in full-wave electromagnetic simulations. Reusability for small-molecule detection is also demonstrated. Thus it is shown that the combination of high signal enhancement and reproducibility is achievable using a completely non-lithographic fabrication process, thereby producing SERS substrates having high performance at low cost.