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Sample records for clusters quantum methods

  1. Quantum Monte Carlo methods and lithium cluster properties. [Atomic clusters

    SciTech Connect

    Owen, R.K.

    1990-12-01

    Properties of small lithium clusters with sizes ranging from n = 1 to 5 atoms were investigated using quantum Monte Carlo (QMC) methods. Cluster geometries were found from complete active space self consistent field (CASSCF) calculations. A detailed development of the QMC method leading to the variational QMC (V-QMC) and diffusion QMC (D-QMC) methods is shown. The many-body aspect of electron correlation is introduced into the QMC importance sampling electron-electron correlation functions by using density dependent parameters, and are shown to increase the amount of correlation energy obtained in V-QMC calculations. A detailed analysis of D-QMC time-step bias is made and is found to be at least linear with respect to the time-step. The D-QMC calculations determined the lithium cluster ionization potentials to be 0.1982(14) (0.1981), 0.1895(9) (0.1874(4)), 0.1530(34) (0.1599(73)), 0.1664(37) (0.1724(110)), 0.1613(43) (0.1675(110)) Hartrees for lithium clusters n = 1 through 5, respectively; in good agreement with experimental results shown in the brackets. Also, the binding energies per atom was computed to be 0.0177(8) (0.0203(12)), 0.0188(10) (0.0220(21)), 0.0247(8) (0.0310(12)), 0.0253(8) (0.0351(8)) Hartrees for lithium clusters n = 2 through 5, respectively. The lithium cluster one-electron density is shown to have charge concentrations corresponding to nonnuclear attractors. The overall shape of the electronic charge density also bears a remarkable similarity with the anisotropic harmonic oscillator model shape for the given number of valence electrons.

  2. Quantum Monte Carlo methods and lithium cluster properties

    SciTech Connect

    Owen, R.K.

    1990-12-01

    Properties of small lithium clusters with sizes ranging from n = 1 to 5 atoms were investigated using quantum Monte Carlo (QMC) methods. Cluster geometries were found from complete active space self consistent field (CASSCF) calculations. A detailed development of the QMC method leading to the variational QMC (V-QMC) and diffusion QMC (D-QMC) methods is shown. The many-body aspect of electron correlation is introduced into the QMC importance sampling electron-electron correlation functions by using density dependent parameters, and are shown to increase the amount of correlation energy obtained in V-QMC calculations. A detailed analysis of D-QMC time-step bias is made and is found to be at least linear with respect to the time-step. The D-QMC calculations determined the lithium cluster ionization potentials to be 0.1982(14) [0.1981], 0.1895(9) [0.1874(4)], 0.1530(34) [0.1599(73)], 0.1664(37) [0.1724(110)], 0.1613(43) [0.1675(110)] Hartrees for lithium clusters n = 1 through 5, respectively; in good agreement with experimental results shown in the brackets. Also, the binding energies per atom was computed to be 0.0177(8) [0.0203(12)], 0.0188(10) [0.0220(21)], 0.0247(8) [0.0310(12)], 0.0253(8) [0.0351(8)] Hartrees for lithium clusters n = 2 through 5, respectively. The lithium cluster one-electron density is shown to have charge concentrations corresponding to nonnuclear attractors. The overall shape of the electronic charge density also bears a remarkable similarity with the anisotropic harmonic oscillator model shape for the given number of valence electrons.

  3. Method for discovering relationships in data by dynamic quantum clustering

    DOEpatents

    Weinstein, Marvin; Horn, David

    2014-10-28

    Data clustering is provided according to a dynamical framework based on quantum mechanical time evolution of states corresponding to data points. To expedite computations, we can approximate the time-dependent Hamiltonian formalism by a truncated calculation within a set of Gaussian wave-functions (coherent states) centered around the original points. This allows for analytic evaluation of the time evolution of all such states, opening up the possibility of exploration of relationships among data-points through observation of varying dynamical-distances among points and convergence of points into clusters. This formalism may be further supplemented by preprocessing, such as dimensional reduction through singular value decomposition and/or feature filtering.

  4. ATOMIC AND MOLECULAR PHYSICS: Quantum Impurity Models with Coupled Cluster Method

    NASA Astrophysics Data System (ADS)

    Liang, Jin-Jun; Emary, Clive; Brandes, Tobias

    2010-09-01

    We investigate the ground-state properties of the Anderson single impurity model (finite Coulomb impurity repulsion) with the Coupled Cluster Method. We consider different CCM reference states and approximation schemes and make comparison with exact Green's function results for the non-interacting model and with Brillouin-Wigner perturbation theory for the full interacting model. Our results show that coupled cluster techniques are well suited to quantum impurity problems.

  5. Monodisperse cluster crystals: Classical and quantum dynamics.

    PubMed

    Díaz-Méndez, Rogelio; Mezzacapo, Fabio; Cinti, Fabio; Lechner, Wolfgang; Pupillo, Guido

    2015-11-01

    We study the phases and dynamics of a gas of monodisperse particles interacting via soft-core potentials in two spatial dimensions, which is of interest for soft-matter colloidal systems and quantum atomic gases. Using exact theoretical methods, we demonstrate that the equilibrium low-temperature classical phase simultaneously breaks continuous translational symmetry and dynamic space-time homogeneity, whose absence is usually associated with out-of-equilibrium glassy phenomena. This results in an exotic self-assembled cluster crystal with coexisting liquidlike long-time dynamical properties, which corresponds to a classical analog of supersolid behavior. We demonstrate that the effects of quantum fluctuations and bosonic statistics on cluster-glassy crystals are separate and competing: Zero-point motion tends to destabilize crystalline order, which can be restored by bosonic statistics. PMID:26651695

  6. Unconventional methods for clustering

    NASA Astrophysics Data System (ADS)

    Kotyrba, Martin

    2016-06-01

    Cluster analysis or clustering is a task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense or another) to each other than to those in other groups (clusters). It is the main task of exploratory data mining and a common technique for statistical data analysis used in many fields, including machine learning, pattern recognition, image analysis, information retrieval, and bioinformatics. The topic of this paper is one of the modern methods of clustering namely SOM (Self Organising Map). The paper describes the theory needed to understand the principle of clustering and descriptions of algorithm used with clustering in our experiments.

  7. Generalized Clustered Quantum Hall States

    NASA Astrophysics Data System (ADS)

    Simon, Steven H.; Cooper, Nigel R.; Rezayi, Ed

    2005-03-01

    The Read-Rezayi (parafermion) quantum Hall states[1] for bosons can be defined as states where the wavefunction does not vanish when g bosons come together to the same point, but does vanish as z^2 as a g+1st particle approaches that point. These states can equivalently be defined as the unique ground state of a point contact g+1 particle interaction Hamiltonian. Interestingly, the series of Read-Rezayi states appears to describe well the groundstates of rotating Bose condensates with point-contact two body interactions at a series of filling fractions [2]. If one attaches a Jastrow factor to such bose wavefunctions, one obtains fermion wavefunctions that may occur in electronic quantum Hall systems including the (g=2) Pfaffian [3] and the (g=3) ν=13/5 Read-Rezayi state [1]. In this work, we consider generalized cluster wavefunctions defined by the algebraic manner in which a wavefunction vanishes as g+1 particles coalesce. We find Hamiltonians that generate these wavefunctions as their exact ground state. Among this series of states is the previously studied Haffnian wavefunction[4] and a host of states not previously discussed. We catalogue and study the new states and discuss whether any of them might occur in actual physical systems. [1] N. Read and E. Rezayi, PRB59, 8084 (1999). [2] N. R. Cooper, N. K. Wilkin, and J. M. F. Gunn, PRL87, 120405 (2001) [3] G. Moore and N. Read, Nuc. Phys. B360, 362 (1991). [4] D. Green, PhD Thesis.

  8. Quantum and classical simulations of molecular clusters

    NASA Astrophysics Data System (ADS)

    Dong, Xiao

    Calcium nanoclusters are studied by several computational approaches with the goal of obtaining information about their energetic, stability and thermodynamic properties. Clusters with 32 to 84 calcium atoms are modeled by a tight-binding (TB) model and their structures are optimized with molecular dynamics simulated annealing, whereas clusters containing 14 to 34 atoms are optimized with the Adaptive Tempering Monte Carlo method (ATMC). Magic number clusters are determined to be of 15, 21, 23, 34, 37, 39, 45, 53, 57, and 82 atoms, in good agreement with experiments. These clusters range in size between 1 and 2 nm. The structures of clusters containing 15, 16, 18, 21, 23, 25, 35, 28, 43, 50, 58, 59, 62, 63, 76-84 atoms are new---not reported as minimum energy structures in the literature. In this cluster size range there is an enhanced ratio of surface to bulk atoms that favors an expansion of the surface bond lengths. Within the harmonic approximation, the calculated Helmhotz free energy indicates that the structures of the magic number clusters are maintained even at temperatures around 700 K. Based on TB molecular dynamics results of the mean-squared displacement as function of temperature, a premelting of the surface occurs around 600 K. The energy gap between occupied and empty states in the valence band is cluster-size-dependent and significantly larger for Ca15, Ca21, Ca23, Ca35, Ca 42, and Ca45. Calcium nanoclusters with more than 49 atoms display an incipient metallic character at temperatures higher than 500 K. The ATMC is a newly developed optimization method based on a multi-canonical Monte Carlo approach. This new method was designed to obtain the most ordered state of a system. In the simulation, the MC temperature is changed adaptively to sample configuration space in an efficient manner. The various canonical ensembles are connected along the simulation by a super-Markov chain, which allows for the adaptive excursion in configuration space leading

  9. Classical and quantum physics of hydrogen clusters.

    PubMed

    Mezzacapo, Fabio; Boninsegni, Massimo

    2009-04-22

    We present results of a comprehensive theoretical investigation of the low temperature (T) properties of clusters of para-hydrogen (p-H(2)), both pristine as well as doped with isotopic impurities (i.e., ortho-deuterium, o-D(2)). We study clusters comprising up to N = 40 molecules, by means of quantum simulations based on the continuous-space Worm algorithm. Pristine p-H(2) clusters are liquid-like and superfluid in the [Formula: see text] limit. The superfluid signal is uniform throughout these clusters; it is underlain by long cycles of permutation of molecules. Clusters with more than 22 molecules display solid-like, essentially classical behavior at temperatures down to T∼1 K; some of them are seen to turn liquid-like at sufficiently low T (quantum melting).

  10. Photo-induced brightening and broadening effects of gold quantum clusters

    NASA Astrophysics Data System (ADS)

    Huang, Hsiu-Ying; Lin, Chia-Hui; Lin, Cheng-An J.

    2016-04-01

    We describe the use of UV light under different radiation time induces a variety of fluorescence wavelength of gold quantum clusters. First, we synthesize blue-emitted gold quantum clusters by dissolving the gold trichloride in pure toluene. To simplify the expression, we assume that the several featured PL peak (425, 450, 470 nm) is the signal for blue-emitted gold quantum clusters. Undergo UV irradiation can brighten and broaden the PL spectra of gold quantum clusters, which are observed by the evolutional spectra versus exposure time. After UV light exposure, the major population of gold quantum clusters @425nm decreased and turned to gold quantum clusters@450nm, followed by the growing population of gold quantum clusters@470nm clusters. Until 2 hour exposure, the spectra become broad with major peak shifted to 525 nm. The tunable spectra from blue to green attributes to the induced growth of gold quantum clusters by UV irradiation. The UV energy indeed tunes and broadens the emission covering the whole visible-spectra range. Finally, we also utilize via proper selection of organic surfactant (such as: trioctyl phosphine, TOP) can coordinate the quantum yield enhancement of blue-emitted gold quantum clusters under UV irradiation. The experiment method is easily for gold quantum clusters synthesis. Thus we expect this materials can be developed for fluorescence labeling application in the future.

  11. Highly frustrated spin-lattice models of magnetism and their quantum phase transitions: A microscopic treatment via the coupled cluster method

    SciTech Connect

    Bishop, R. F.; Li, P. H. Y.; Campbell, C. E.

    2014-10-15

    We outline how the coupled cluster method of microscopic quantum many-body theory can be utilized in practice to give highly accurate results for the ground-state properties of a wide variety of highly frustrated and strongly correlated spin-lattice models of interest in quantum magnetism, including their quantum phase transitions. The method itself is described, and it is shown how it may be implemented in practice to high orders in a systematically improvable hierarchy of (so-called LSUBm) approximations, by the use of computer-algebraic techniques. The method works from the outset in the thermodynamic limit of an infinite lattice at all levels of approximation, and it is shown both how the 'raw' LSUBm results are themselves generally excellent in the sense that they converge rapidly, and how they may accurately be extrapolated to the exact limit, m → ∞, of the truncation index m, which denotes the only approximation made. All of this is illustrated via a specific application to a two-dimensional, frustrated, spin-half J{sub 1}{sup XXZ}−J{sub 2}{sup XXZ} model on a honeycomb lattice with nearest-neighbor and next-nearest-neighbor interactions with exchange couplings J{sub 1} > 0 and J{sub 2} ≡ κJ{sub 1} > 0, respectively, where both interactions are of the same anisotropic XXZ type. We show how the method can be used to determine the entire zero-temperature ground-state phase diagram of the model in the range 0 ≤ κ ≤ 1 of the frustration parameter and 0 ≤ Δ ≤ 1 of the spin-space anisotropy parameter. In particular, we identify a candidate quantum spin-liquid region in the phase space.

  12. Quantum cluster approach to the spinful Haldane-Hubbard model

    NASA Astrophysics Data System (ADS)

    Wu, Jingxiang; Faye, Jean Paul Latyr; Sénéchal, David; Maciejko, Joseph

    2016-02-01

    We study the spinful fermionic Haldane-Hubbard model at half-filling using a combination of quantum cluster methods: cluster perturbation theory, the variational cluster approximation, and cluster dynamical mean-field theory. We explore possible zero-temperature phases of the model as a function of onsite repulsive interaction strength and next-nearest-neighbor hopping amplitude and phase. Our approach allows us to access the regime of intermediate interaction strength, where charge fluctuations are significant and effective spin model descriptions may not be justified. Our approach also improves upon mean-field solutions of the Haldane-Hubbard model by retaining local quantum fluctuations and treating them nonperturbatively. We find a correlated topological Chern insulator for weak interactions and a topologically trivial Néel antiferromagnetic insulator for strong interactions. For intermediate interactions, we find that topologically nontrivial Néel antiferromagnetic insulating phases and/or a topologically nontrivial nonmagnetic insulating phase may be stabilized.

  13. High-performance dynamic quantum clustering on graphics processors

    SciTech Connect

    Wittek, Peter

    2013-01-15

    Clustering methods in machine learning may benefit from borrowing metaphors from physics. Dynamic quantum clustering associates a Gaussian wave packet with the multidimensional data points and regards them as eigenfunctions of the Schroedinger equation. The clustering structure emerges by letting the system evolve and the visual nature of the algorithm has been shown to be useful in a range of applications. Furthermore, the method only uses matrix operations, which readily lend themselves to parallelization. In this paper, we develop an implementation on graphics hardware and investigate how this approach can accelerate the computations. We achieve a speedup of up to two magnitudes over a multicore CPU implementation, which proves that quantum-like methods and acceleration by graphics processing units have a great relevance to machine learning.

  14. Arbitrated quantum signature scheme based on cluster states

    NASA Astrophysics Data System (ADS)

    Yang, Yu-Guang; Lei, He; Liu, Zhi-Chao; Zhou, Yi-Hua; Shi, Wei-Min

    2016-06-01

    Cluster states can be exploited for some tasks such as topological one-way computation, quantum error correction, teleportation and dense coding. In this paper, we investigate and propose an arbitrated quantum signature scheme with cluster states. The cluster states are used for quantum key distribution and quantum signature. The proposed scheme can achieve an efficiency of 100 %. Finally, we also discuss its security against various attacks.

  15. Quantum Theoretical Study of KCl and LiCl Clusters

    NASA Astrophysics Data System (ADS)

    Koetter, Ted; Hira, Ajit; Salazar, Justin; Jaramillo, Danelle

    2014-03-01

    This research focuses on the theoretical study of molecular clusters to examine the chemical properties of small KnClnandLinCln clusters (n = 2 - 20). The potentially important role of these molecular species in biochemical and medicinal processes is well known. This work applies the hybrid ab initio methods of quantum chemistry to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations were performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. Potential design of new medicinal drugs is explored.

  16. Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture

    DOEpatents

    Sanfilippo, Antonio; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2009-12-22

    Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture are described. In one aspect, a document clustering method includes providing a document set comprising a plurality of documents, providing a cluster comprising a subset of the documents of the document set, using a plurality of terms of the documents, providing a cluster label indicative of subject matter content of the documents of the cluster, wherein the cluster label comprises a plurality of word senses, and selecting one of the word senses of the cluster label.

  17. Gravimetry with Quantum Methods and Quantum Standards

    NASA Astrophysics Data System (ADS)

    Flury, J.

    2015-12-01

    Quantum metrology enables new methods for measuring gravitational quantities. Currently, significant progress in the development of quantum gravimeters, quantum optical clocks, and optical frequency transfer is underway. Quantum gravimeters use a variety of techniques to determine the gravity acceleration acting on clouds of atoms with coherent matter wave phase. We discuss configurations with very small and very large trajectories. Optical atomic clocks and optical frequency transfer allow the determination of gravity potential differences through the gravitational frequency redshift. Recent progress in clock development and in frequency transfer through optical fiber is leading to results with high relevance for geodesy. First experiments for long distance clock comparisons and chronometric leveling are underway. Concepts for geodetic modeling with relativistic quantities are being investigated.

  18. Cluster State Quantum Computation and the Repeat-Until Scheme

    NASA Astrophysics Data System (ADS)

    Kwek, L. C.

    Cluster state computation or the one way quantum computation (1WQC) relies on an initially highly entangled state (called a cluster state) and an appropriate sequence of single qubit measurements along different directions, together with feed-forward based on the measurement results, to realize a quantum computation process. The final result of the computation is obtained by measuring the last remaining qubits in the computational basis. In this short tutorial on cluster state quantum computation, we will also describe the basic ideas of a cluster state and proceed to describe how a single qubit operation can be done on a cluster state. Recently, we proposed a repeat-until-success (RUS) scheme that could effectively be used to realize one-way quantum computer on a hybrid system of photons and atoms. We will briefly describe this RUS scheme and show how it can be used to entangled two distant stationary qubits.

  19. Interdimensional degeneracies in van der Waals clusters and quantum Monte Carlo computation of rovibrational states.

    PubMed

    Nightingale, M P; Moodley, Mervlyn

    2005-07-01

    Quantum Monte Carlo estimates of the spectrum of rotationally invariant states of noble gas clusters suggest interdimensional degeneracy in N-1 and N+1 spatial dimensions. We derive this property by mapping the Schrodinger eigenvalue problem onto an eigenvalue equation in which D appears as a continuous variable. We discuss implications for quantum Monte Carlo and dimensional scaling methods.

  20. An investigation on the structure, spectroscopy and thermodynamic aspects of Br2((-))(H2O)n clusters using a conjunction of stochastic and quantum chemical methods.

    PubMed

    Naskar, Pulak; Chaudhury, Pinaki

    2016-06-28

    In this work we obtained global as well as local structures of Br2((-))(H2O)n clusters for n = 2 to 6 followed by the study of IR-spectral features and thermochemistry for the structures. The way adopted by us to obtain structures is not the conventional one used in most cases. Here we at first generated excellent quality pre-optimized structures by exploring the suitable empirical potential energy surface using stochastic optimizer simulated annealing. These structures are then further refined using quantum chemical calculations to obtain the final structures, and spectral and thermodynamic features. We clearly showed that our approach results in very quick and better convergence which reduces the computational cost and obviously using the strategy we are able to get one [i.e. global] or more than one [i.e. global and local(s)] energetically lower structures than those which are already reported for a given cluster size. Moreover, IR-spectral results and the evolutionary trends in interaction energy, solvation energy and vertical detachment energy for global structures of each size have also been presented to establish the utility of the procedure employed. PMID:27251059

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

    NASA Astrophysics Data System (ADS)

    Turi, László

    2016-04-01

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

  2. Flexible quantum circuits using scalable continuous-variable cluster states

    NASA Astrophysics Data System (ADS)

    Alexander, Rafael N.; Menicucci, Nicolas C.

    2016-06-01

    We show that measurement-based quantum computation on scalable continuous-variable (CV) cluster states admits more quantum-circuit flexibility and compactness than similar protocols for standard square-lattice CV cluster states. This advantage is a direct result of the macronode structure of these states—that is, a lattice structure in which each graph node actually consists of several physical modes. These extra modes provide additional measurement degrees of freedom at each graph location, which can be used to manipulate the flow and processing of quantum information more robustly and with additional flexibility that is not available on an ordinary lattice.

  3. Quantum chemistry of the minimal CdSe clusters.

    PubMed

    Yang, Ping; Tretiak, Sergei; Masunov, Artëm E; Ivanov, Sergei

    2008-08-21

    Colloidal quantum dots are semiconductor nanocrystals (NCs) which have stimulated a great deal of research and have attracted technical interest in recent years due to their chemical stability and the tunability of photophysical properties. While internal structure of large quantum dots is similar to bulk, their surface structure and passivating role of capping ligands (surfactants) are not fully understood to date. We apply ab initio wavefunction methods, density functional theory, and semiempirical approaches to study the passivation effects of substituted phosphine and amine ligands on the minimal cluster Cd(2)Se(2), which is also used to benchmark different computational methods versus high level ab initio techniques. Full geometry optimization of Cd(2)Se(2) at different theory levels and ligand coverage is used to understand the affinities of various ligands and the impact of ligands on cluster structure. Most possible bonding patterns between ligands and surface CdSe atoms are considered, including a ligand coordinated to Se atoms. The degree of passivation of Cd and Se atoms (one or two ligands attached to one atom) is also studied. The results suggest that B3LYP/LANL2DZ level of theory is appropriate for the system modeling, whereas frequently used semiempirical methods (such as AM1 and PM3) produce unphysical results. The use of hydrogen atom for modeling of the cluster passivating ligands is found to yield unphysical results as well. Hence, the surface termination of II-VI semiconductor NCs with hydrogen atoms often used in computational models should probably be avoided. Basis set superposition error, zero-point energy, and thermal corrections, as well as solvent effects simulated with polarized continuum model are found to produce minor variations on the ligand binding energies. The effects of Cd-Se complex structure on both the electronic band gap (highest occupied molecular orbital-lowest unoccupied molecular orbital energy difference) and ligand

  4. Limitations of quantum computing with Gaussian cluster states

    SciTech Connect

    Ohliger, M.; Kieling, K.; Eisert, J.

    2010-10-15

    We discuss the potential and limitations of Gaussian cluster states for measurement-based quantum computing. Using a framework of Gaussian-projected entangled pair states, we show that no matter what Gaussian local measurements are performed on systems distributed on a general graph, transport and processing of quantum information are not possible beyond a certain influence region, except for exponentially suppressed corrections. We also demonstrate that even under arbitrary non-Gaussian local measurements, slabs of Gaussian cluster states of a finite width cannot carry logical quantum information, even if sophisticated encodings of qubits in continuous-variable systems are allowed for. This is proven by suitably contracting tensor networks representing infinite-dimensional quantum systems. The result can be seen as sharpening the requirements for quantum error correction and fault tolerance for Gaussian cluster states and points toward the necessity of non-Gaussian resource states for measurement-based quantum computing. The results can equally be viewed as referring to Gaussian quantum repeater networks.

  5. Generalized quantum kinetic expansion: Time scale separation between intra-cluster and inter-cluster kinetics

    SciTech Connect

    Tang, Zhoufei; Gong, Zhihao; Wu, Jianlan

    2015-09-14

    For a general two-cluster network, a new methodology of the cluster-based generalized quantum kinetic expansion (GQKE) is developed in the matrix formalism under two initial conditions: the local cluster equilibrium and system-bath factorized states. For each initial condition, the site population evolution follows exactly a distinct closed equation, where all the four terms involved are systematically expanded over inter-cluster couplings. For the system-bath factorized initial state, the numerical investigation of the two models, a biased (2, 1)-site system and an unbiased (2, 2)-site system, verifies the reliability of the GQKE and the relevance of higher-order corrections. The time-integrated site-to-site rates and the time evolution of site population reveal the time scale separation between intra-cluster and inter-cluster kinetics. The population evolution of aggregated clusters can be quantitatively described by the approximate cluster Markovian kinetics.

  6. Deterministic photonic cluster state generation from quantum dot molecules

    NASA Astrophysics Data System (ADS)

    Economou, Sophia; Gimeno-Segovia, Mercedes; Rudolph, Terry

    2014-03-01

    Currently, the most promising approach for photon-based quantum information processing is measurement-based, or one-way, quantum computing. In this scheme, a large entangled state of photons is prepared upfront and the computation is implemented with single-qubit measurements alone. Available approaches to generating the cluster state are probabilistic, which makes scalability challenging. We propose to generate the cluster state using a quantum dot molecule with one electron spin per quantum dot. The two spins are coupled by exchange interaction and are periodically pulsed to produce photons. We show that the entanglement created by free evolution between the spins is transferred to the emitted photons, and thus a 2D photonic ladder can be created. Our scheme only utilizes single-spin gates and measurement, and is thus fully consistent with available technology.

  7. Cluster-like coordinates in supersymmetric quantum field theory

    PubMed Central

    Neitzke, Andrew

    2014-01-01

    Recently it has become apparent that N=2 supersymmetric quantum field theory has something to do with cluster algebras. I review one aspect of the connection: supersymmetric quantum field theories have associated hyperkähler moduli spaces, and these moduli spaces carry a structure that looks like an extension of the notion of cluster variety. In particular, one encounters the usual variables and mutations of the cluster story, along with more exotic extra variables and generalized mutations. I focus on a class of examples where the underlying cluster varieties are moduli spaces of flat connections on surfaces, as considered by Fock and Goncharov [Fock V, Goncharov A (2006) Publ Math Inst Hautes Études Sci 103:1–211]. The work reviewed here is largely joint with Davide Gaiotto and Greg Moore. PMID:24982190

  8. Cluster-like coordinates in supersymmetric quantum field theory.

    PubMed

    Neitzke, Andrew

    2014-07-01

    Recently it has become apparent that N = 2 supersymmetric quantum field theory has something to do with cluster algebras. I review one aspect of the connection: supersymmetric quantum field theories have associated hyperkähler moduli spaces, and these moduli spaces carry a structure that looks like an extension of the notion of cluster variety. In particular, one encounters the usual variables and mutations of the cluster story, along with more exotic extra variables and generalized mutations. I focus on a class of examples where the underlying cluster varieties are moduli spaces of flat connections on surfaces, as considered by Fock and Goncharov [Fock V, Goncharov A (2006) Publ Math Inst Hautes Études Sci 103:1-211]. The work reviewed here is largely joint with Davide Gaiotto and Greg Moore.

  9. Tripartite Quantum Controlled Teleportation via Seven-Qubit Cluster State

    NASA Astrophysics Data System (ADS)

    Li, Wei; Zha, Xin-Wei; Qi, Jian-Xia

    2016-09-01

    In this paper, a theoretical scheme for tripartite quantum controlled teleportation is presented using the entanglement property of seven-qubit cluster state. This means that Alice wants to transmit a entangled state of particle a to Bob, Charlie wants to transmit a entangled state of particle b to David and Edison wants to transmit a entangled state of particle c to Ford via the control of the supervisor. In the end, we compared the aspects of quantum resource consumption, operation complexity, classical resource consumption, quantum information bits transmitted, success probability and efficiency with other schemes.

  10. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1982-01-01

    Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

  11. The SMART CLUSTER METHOD - adaptive earthquake cluster analysis and declustering

    NASA Astrophysics Data System (ADS)

    Schaefer, Andreas; Daniell, James; Wenzel, Friedemann

    2016-04-01

    Earthquake declustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity with usual applications comprising of probabilistic seismic hazard assessments (PSHAs) and earthquake prediction methods. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation. Various methods have been developed to address this issue from other researchers. These have differing ranges of complexity ranging from rather simple statistical window methods to complex epidemic models. This study introduces the smart cluster method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal identification. Hereby, an adaptive search algorithm for data point clusters is adopted. It uses the earthquake density in the spatio-temporal neighbourhood of each event to adjust the search properties. The identified clusters are subsequently analysed to determine directional anisotropy, focussing on a strong correlation along the rupture plane and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010/2011 Darfield-Christchurch events, an adaptive classification procedure is applied to disassemble subsequent ruptures which may have been grouped into an individual cluster using near-field searches, support vector machines and temporal splitting. The steering parameters of the search behaviour are linked to local earthquake properties like magnitude of completeness, earthquake density and Gutenberg-Richter parameters. The method is capable of identifying and classifying earthquake clusters in space and time. It is tested and validated using earthquake data from California and New Zealand. As a result of the cluster identification process, each event in

  12. Bidirectional Quantum Teleportation by Using Five-qubit Cluster State

    NASA Astrophysics Data System (ADS)

    Sang, Ming-huang

    2016-03-01

    We propose a scheme for bidirectional quantum teleportation by using a five-qubit cluster state. In our scheme, Alice can transmit an arbitrary two-qubit entangled state to Bob and at the same time Bob can teleport an arbitrary single-qubit state to Alice.

  13. Graph-theoretic quantum system modelling for neuronal microtubules as hierarchical clustered quantum Hopfield networks

    NASA Astrophysics Data System (ADS)

    Srivastava, D. P.; Sahni, V.; Satsangi, P. S.

    2014-08-01

    Graph-theoretic quantum system modelling (GTQSM) is facilitated by considering the fundamental unit of quantum computation and information, viz. a quantum bit or qubit as a basic building block. Unit directional vectors "ket 0" and "ket 1" constitute two distinct fundamental quantum across variable orthonormal basis vectors, for the Hilbert space, specifying the direction of propagation of information, or computation data, while complementary fundamental quantum through, or flow rate, variables specify probability parameters, or amplitudes, as surrogates for scalar quantum information measure (von Neumann entropy). This paper applies GTQSM in continuum of protein heterodimer tubulin molecules of self-assembling polymers, viz. microtubules in the brain as a holistic system of interacting components representing hierarchical clustered quantum Hopfield network, hQHN, of networks. The quantum input/output ports of the constituent elemental interaction components, or processes, of tunnelling interactions and Coulombic bidirectional interactions are in cascade and parallel interconnections with each other, while the classical output ports of all elemental components are interconnected in parallel to accumulate micro-energy functions generated in the system as Hamiltonian, or Lyapunov, energy function. The paper presents an insight, otherwise difficult to gain, for the complex system of systems represented by clustered quantum Hopfield network, hQHN, through the application of GTQSM construct.

  14. Report of a Workshop on Parallelization of Coupled Cluster Methods

    SciTech Connect

    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.

  15. A New Elliptical Grid Clustering Method

    NASA Astrophysics Data System (ADS)

    Guansheng, Zheng

    A new base on grid clustering method is presented in this paper. This new method first does unsupervised learning on the high dimensions data. This paper proposed a grid-based approach to clustering. It maps the data onto a multi-dimensional space and applies a linear transformation to the feature space instead of to the objects themselves and then approach a grid-clustering method. Unlike the conventional methods, it uses a multidimensional hyper-eclipse grid cell. Some case studies and ideas how to use the algorithms are described. The experimental results show that EGC can discover abnormity shapes of clusters.

  16. Comparison of classical and quantum dynamics for collinear cluster scattering.

    PubMed

    Bäck, Andreas; Marković, Nikola

    2005-04-01

    The collinear dynamics of a cluster of four particles colliding with a fixed particle representing a surface is investigated using a four-dimensional wave packet approach. The properties of the system are chosen to resemble a water cluster interacting with graphite, but a deeper surface-particle potential is also considered causing significant dissociation of the cluster. Having four different product arrangement channels the system is quantum mechanically demanding but still manageable. The dynamical richness makes it a suitable benchmark system for evaluation of classical and quantum/classical schemes. The average energy transferred to the cluster and the three dissociation probabilities are presented as function of the initial state of the cluster. In addition to wave packet data, results obtained using quasiclassical as well as Wigner sampled classical trajectories are presented. The main conclusion is that classical mechanics can describe the dynamics of the system in a very satisfactory way. Including zero-point energy in the classical simulations is particularly important for a good description of dissociation but less important for energy transfer.

  17. Nuclear quantum effects on the stability of cationic neon clusters

    NASA Astrophysics Data System (ADS)

    Calvo, F.; Naumkin, F. Y.; Wales, D. J.

    2012-11-01

    The stable structures of cationic neon clusters containing up to 57 atoms have been located using a diatomic-in-molecules potential energy surface and basin-hopping hierarchical optimization. The effects of vibrational delocalization were included either in the harmonic approximation, or by performing Langevin molecular dynamics simulations coupled to a quantum thermal bath at T=0. For most clusters, zero-point motion is sufficiently high to blur the picture of a single well-defined structure. However, structural diversity of the ground state wavefunction is found to be lower at sizes 14, 21, and 56, which correspond to special stabilities in experimental mass spectra.

  18. Simple scheme for expanding photonic cluster states for quantum information

    SciTech Connect

    Kalasuwan, P.; Laing, A.; Coggins, J.; Callaway, M.; O'Brien, J. L.; Mendoza, G.; Nagata, T.; Takeuchi, S.; Stefanov, A.

    2010-06-15

    We show how an entangled cluster state encoded in the polarization of single photons can be straightforwardly expanded by deterministically entangling additional qubits encoded in the path degree of freedom of the constituent photons. This can be achieved using a polarization-path controlled-phase gate. We experimentally demonstrate a practical and stable realization of this approach by using a Sagnac interferometer to entangle a path qubit and polarization qubit on a single photon. We demonstrate precise control over phase of the path qubit to change the measurement basis and experimentally demonstrate properties of measurement-based quantum computing using a two-photon, three-qubit cluster state.

  19. Quantum Teleportation of Three and Four-Qubit State Using Multi-qubit Cluster States

    NASA Astrophysics Data System (ADS)

    Li, Yuan-hua; Li, Xiao-lan; Nie, Li-ping; Sang, Ming-huang

    2016-03-01

    We provide various schemes for quantum teleportation by using the four and five qubit cluster states. Explicit protocols for the perfect quantum teleportation of three and four qubit states are illustrated. It is found that the four-qubit cluster state can be used for perfect quantum teleportation of a special form of three-qubit state and the five-qubit cluster state can be used for perfect quantum teleportation of a special form of four-qubit state.

  20. Visual cluster analysis and pattern recognition methods

    DOEpatents

    Osbourn, Gordon Cecil; Martinez, Rubel Francisco

    2001-01-01

    A method of clustering using a novel template to define a region of influence. Using neighboring approximation methods, computation times can be significantly reduced. The template and method are applicable and improve pattern recognition techniques.

  1. Perspectives for quantum interference with biomolecules and biomolecular clusters

    NASA Astrophysics Data System (ADS)

    Geyer, P.; Sezer, U.; Rodewald, J.; Mairhofer, L.; Dörre, N.; Haslinger, P.; Eibenberger, S.; Brand, C.; Arndt, M.

    2016-06-01

    Modern quantum optics encompasses a wide field of phenomena that are either related to the discrete quantum nature of light, the quantum wave nature of matter or light–matter interactions. We here discuss new perspectives for quantum optics with biological nanoparticles. We focus in particular on the prospects of matter-wave interferometry with amino acids, nucleotides, polypeptides or DNA strands. We motivate the challenge of preparing these objects in a ‘biomimetic’ environment and argue that hydrated molecular beam sources are promising tools for quantum-assisted metrology. The method exploits the high sensitivity of matter-wave interference fringes to dephasing and shifts in the presence of external perturbations to access and determine molecular properties.

  2. Self consistency grouping: a stringent clustering method

    PubMed Central

    2012-01-01

    Background Numerous types of clustering like single linkage and K-means have been widely studied and applied to a variety of scientific problems. However, the existing methods are not readily applicable for the problems that demand high stringency. Methods Our method, self consistency grouping, i.e. SCG, yields clusters whose members are closer in rank to each other than to any member outside the cluster. We do not define a distance metric; we use the best known distance metric and presume that it measures the correct distance. SCG does not impose any restriction on the size or the number of the clusters that it finds. The boundaries of clusters are determined by the inconsistencies in the ranks. In addition to the direct implementation that finds the complete structure of the (sub)clusters we implemented two faster versions. The fastest version is guaranteed to find only the clusters that are not subclusters of any other clusters and the other version yields the same output as the direct implementation but does so more efficiently. Results Our tests have demonstrated that SCG yields very few false positives. This was accomplished by introducing errors in the distance measurement. Clustering of protein domain representatives by structural similarity showed that SCG could recover homologous groups with high precision. Conclusions SCG has potential for finding biological relationships under stringent conditions. PMID:23320864

  3. Electric field for tuning quantum entanglement in supported clusters.

    PubMed

    Brovko, Oleg O; Farberovich, Oleg V; Stepanyuk, Valeri S

    2014-08-01

    We show that quantum entanglement, nowadays so widely observed and used in a multitude of systems, can be traced in the atomic spins of metal clusters supported on metal surfaces. Most importantly, we show that it can be voluntarily altered with external electric fields. We use a combination of ab initio and model Heisenberg-Dirac-Van Vleck quantum spin Hamiltonian calculations to show, with the example of a prototype system (Mn dimers on Ag(0 0 1) surface), that, in an inherently unentangled system an electric field can 'switch on' the entanglement and significantly change its critical temperature parameter. The physical mechanism allowing such rigorous control of entanglement by an electric field is the field-induced change in the internal magnetic coupling of the supported nanostructure.

  4. Molecular Limits to the Quantum Confinement Model in Diamond Clusters

    SciTech Connect

    Willey, T M; Bostedt, C; van Buuren, T; Dahl, J E; Liu, S E; Carlson, R K; Terminello, L J; Moller, T

    2005-04-07

    The electronic structure of monodisperse, hydrogen-passivated diamond clusters in the gas phase has been studied with x-ray absorption spectroscopy. The data show that the bulk-related unoccupied states do not exhibit any quantum confinement. Additionally, density of states below the bulk absorption edge appears, consisting of features correlated to CH and CH{sub 2} hydrogen surface termination, resulting in an effective red shift of the lowest unoccupied states. The results contradict the commonly used and very successful quantum confinement model for semiconductors which predicts increasing band edge blue shifts with decreasing particle size. Our findings indicate that in the ultimate size limit for nanocrystals a more molecular description is necessary.

  5. Quantum cluster equilibrium model of N-methylformamide-water binary mixtures

    NASA Astrophysics Data System (ADS)

    von Domaros, Michael; Jähnigen, Sascha; Friedrich, Joachim; Kirchner, Barbara

    2016-02-01

    The established quantum cluster equilibrium (QCE) approach is refined and applied to N-methylformamide (NMF) and its aqueous solution. The QCE method is split into two iterative cycles: one which converges to the liquid phase solution of the QCE equations and another which yields the gas phase. By comparing Gibbs energies, the thermodynamically stable phase at a given temperature and pressure is then chosen. The new methodology avoids metastable solutions and allows a different treatment of the mean-field interactions within the gas and liquid phases. These changes are of crucial importance for the treatment of binary mixtures. For the first time in a QCE study, the cis-trans-isomerism of a species (NMF) is explicitly considered. Cluster geometries and frequencies are calculated using density functional theory (DFT) and complementary coupled cluster single point energies are used to benchmark the DFT results. Independent of the selected quantum-chemical method, a large set of clusters is required for an accurate thermodynamic description of the binary mixture. The liquid phase of neat NMF is found to be dominated by the cyclic trans-NMF pentamer, which can be interpreted as a linear trimer that is stabilized by explicit solvation of two further NMF molecules. This cluster reflects the known hydrogen bond network preferences of neat NMF.

  6. Universal clusters as building blocks of stable quantum matter

    NASA Astrophysics Data System (ADS)

    Endo, Shimpei; García-García, Antonio M.; Naidon, Pascal

    2016-05-01

    We present an exploratory study that suggests that Efimov physics, a leading research theme in few-body quantum physics, can also induce stable many-body ground states whose building blocks are universal clusters. We identify a range of parameters in a mass-and-density-imbalanced two-species fermionic mixture for which the ground state is a gas of Efimov-related universal trimers. An explicit calculation of the trimer-trimer interaction reveals that the trimer phase is an SU(3) Fermi liquid stable against recombination losses. We propose to experimentally observe this phase in a fermionic 53Cr-6Li mixture.

  7. Quantum fluctuations and dynamic clustering of fluctuating Cooper pairs.

    SciTech Connect

    Glatz, A.; Varlamov, A. A.; Vinokur, V. M.

    2011-05-01

    We derive the complete expression for the fluctuation conductivity in two-dimensional superconductors as a function of the temperature and the magnetic field in the whole fluctuation region above the upper critical field H{sub c2}(T). Focusing on the vicinity of the quantum phase transition near zero temperature, we propose that as the magnetic field approaches the line near H{sub c2}(0) from above, a peculiar dynamic state consisting of clusters of coherently rotating fluctuation Cooper pairs forms and estimate the characteristic size and lifetime of such clusters. We find the zero-temperature magnetic-field dependence of the transverse magnetoconductivity above H{sub c2}(0) in layered superconductors.

  8. Method for assaying clustered DNA damages

    DOEpatents

    Sutherland, Betsy M.

    2004-09-07

    Disclosed is a method for detecting and quantifying clustered damages in DNA. In this method, a first aliquot of the DNA to be tested for clustered damages with one or more lesion-specific cleaving reagents under conditions appropriate for cleavage of the DNA to produce single-strand nicks in the DNA at sites of damage lesions. The number average molecular length (Ln) of double stranded DNA is then quantitatively determined for the treated DNA. The number average molecular length (Ln) of double stranded DNA is also quantitatively determined for a second, untreated aliquot of the DNA. The frequency of clustered damages (.PHI..sub.c) in the DNA is then calculated.

  9. Symplectic method in quantum cosmology

    NASA Astrophysics Data System (ADS)

    Silva, E. V. Corrêa; Monerat, G. A.; Oliveira-Neto, G.; Neves, C.; Filho, L. G. Ferreira

    2009-08-01

    In the present work, we study the quantum cosmology description of Friedmann-Robertson-Walker models in the presence of a generic perfect fluid and a cosmological constant, which may be positive or negative. We work in Schutz’s variational formalism and the three-dimensional spatial sections may have positive, negative, or zero constant curvature. If one uses the scale factor and its canonically conjugated momentum as the phase space variables that describe the geometrical sector of these models, one obtains Wheeler-DeWitt equations with operator ordering ambiguities. In order to avoid those ambiguities and simplify the quantum treatment of the models, we follow references [Edésio M. Barbosa, Jr. and Nivaldo A. Lemos, Gen. Relativ. Gravit. 38, 1609 (2006).GRGVA80001-770110.1007/s10714-006-0333-y][Edésio M. Barbosa, Jr. and Nivaldo A. Lemos, Phys. Rev. DPRVDAQ1550-7998 78, 023504 (2008).10.1103/PhysRevD.78.023504] and introduce new phase space variables. We explicitly demonstrate, using the symplectic method, that the transformation leading from the old set of variables to the new one is canonical.

  10. Symplectic method in quantum cosmology

    SciTech Connect

    Silva, E. V. Correa; Monerat, G. A.; Oliveira-Neto, G.; Neves, C.; Ferreira Filho, L. G.

    2009-08-15

    In the present work, we study the quantum cosmology description of Friedmann-Robertson-Walker models in the presence of a generic perfect fluid and a cosmological constant, which may be positive or negative. We work in Schutz's variational formalism and the three-dimensional spatial sections may have positive, negative, or zero constant curvature. If one uses the scale factor and its canonically conjugated momentum as the phase space variables that describe the geometrical sector of these models, one obtains Wheeler-DeWitt equations with operator ordering ambiguities. In order to avoid those ambiguities and simplify the quantum treatment of the models, we follow references [Edesio M. Barbosa, Jr. and Nivaldo A. Lemos, Gen. Relativ. Gravit. 38, 1609 (2006).][Edesio M. Barbosa, Jr. and Nivaldo A. Lemos, Phys. Rev. D 78, 023504 (2008).] and introduce new phase space variables. We explicitly demonstrate, using the symplectic method, that the transformation leading from the old set of variables to the new one is canonical.

  11. Protein-protected luminescent noble metal quantum clusters: an emerging trend in atomic cluster nanoscience

    PubMed Central

    Xavier, Paulrajpillai Lourdu; Chaudhari, Kamalesh; Baksi, Ananya; Pradeep, Thalappil

    2012-01-01

    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. PMID:22312454

  12. Using Dynamic Quantum Clustering to Analyze Hierarchically Heterogeneous Samples on the Nanoscale

    SciTech Connect

    Hume, Allison; /Princeton U. /SLAC

    2012-09-07

    Dynamic Quantum Clustering (DQC) is an unsupervised, high visual data mining technique. DQC was tested as an analysis method for X-ray Absorption Near Edge Structure (XANES) data from the Transmission X-ray Microscopy (TXM) group. The TXM group images hierarchically heterogeneous materials with nanoscale resolution and large field of view. XANES data consists of energy spectra for each pixel of an image. It was determined that DQC successfully identifies structure in data of this type without prior knowledge of the components in the sample. Clusters and sub-clusters clearly reflected features of the spectra that identified chemical component, chemical environment, and density in the image. DQC can also be used in conjunction with the established data analysis technique, which does require knowledge of components present.

  13. Comparing the performance of biomedical clustering methods.

    PubMed

    Wiwie, Christian; Baumbach, Jan; Röttger, Richard

    2015-11-01

    Identifying groups of similar objects is a popular first step in biomedical data analysis, but it is error-prone and impossible to perform manually. Many computational methods have been developed to tackle this problem. Here we assessed 13 well-known methods using 24 data sets ranging from gene expression to protein domains. Performance was judged on the basis of 13 common cluster validity indices. We developed a clustering analysis platform, ClustEval (http://clusteval.mpi-inf.mpg.de), to promote streamlined evaluation, comparison and reproducibility of clustering results in the future. This allowed us to objectively evaluate the performance of all tools on all data sets with up to 1,000 different parameter sets each, resulting in a total of more than 4 million calculated cluster validity indices. We observed that there was no universal best performer, but on the basis of this wide-ranging comparison we were able to develop a short guideline for biomedical clustering tasks. ClustEval allows biomedical researchers to pick the appropriate tool for their data type and allows method developers to compare their tool to the state of the art. PMID:26389570

  14. Permanent excimer superstructures by supramolecular networking of metal quantum clusters

    NASA Astrophysics Data System (ADS)

    Santiago-Gonzalez, Beatriz; Monguzzi, Angelo; Azpiroz, Jon Mikel; Prato, Mirko; Erratico, Silvia; Campione, Marcello; Lorenzi, Roberto; Pedrini, Jacopo; Santambrogio, Carlo; Torrente, Yvan; De Angelis, Filippo; Meinardi, Francesco; Brovelli, Sergio

    2016-08-01

    Excimers are evanescent quasi-particles that typically form during collisional intermolecular interactions and exist exclusively for their excited-state lifetime. We exploited the distinctive structure of metal quantum clusters to fabricate permanent excimer-like colloidal superstructures made of ground-state noninteracting gold cores, held together by a network of hydrogen bonds between their capping ligands. This previously unknown aggregation state of matter, studied through spectroscopic experiments and ab initio calculations, conveys the photophysics of excimers into stable nanoparticles, which overcome the intrinsic limitation of excimers in single-particle applications—that is, their nearly zero formation probability in ultra-diluted solutions. In vitro experiments demonstrate the suitability of the superstructures as nonresonant intracellular probes and further reveal their ability to scavenge reactive oxygen species, which enhances their potential as anticytotoxic agents for biomedical applications.

  15. Quantum Private Comparison Protocol Based on Cluster States

    NASA Astrophysics Data System (ADS)

    Sun, Zhiwei; Long, Dongyang

    2013-01-01

    We present a quantum private comparison (QPC) protocol, enabling two players to compare the equality of their information without revealing any information about their respective private inputs, in which the four-particle cluster states as the information carriers are used. The presented protocol can ensure correctness, privacy, and fairness with the assistance of a semi-trusted third party (TP). Meanwhile, the participants including the TP are just required having the ability to perform single-particle measurements, which make the presented protocol more feasible in technique. Furthermore, the photon transmission is a one-way distribution; the Trojan horse attacks can be automatically avoided. The security of this protocol is also analyzed.

  16. Integrated Methods: Applications in Quantum Chemistry

    SciTech Connect

    Irle, Stephen; Morokuma, Keiji

    2004-03-31

    Authors introduce quantum chemical methods applicable to extended molecular systems or parts of them, describe in short the theory behind integrated methods, and discuss their applications to the most recognizable areas of nanochemistry (fullerenes, nanotubes, and silica- based nanosystems).

  17. A nonperturbative light-front coupled-cluster method

    NASA Astrophysics Data System (ADS)

    Hiller, J. R.

    2012-10-01

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

  18. Quantum transport through Ga2As2 cluster

    NASA Astrophysics Data System (ADS)

    Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

    2014-06-01

    The electronic transport properties of Ga2As2 cluster, which is sandwiched between two semiinfinite Au (1 0 0)-3 × 3 pyramical-shaped electrodes with the Ga-Ga axis of the cluster parallel to the transport direction and the As-As axis of the cluster parallel to the transport direction, respectively, is investigated with a combination of density functional theory and the non-equilibrium Green's function method. We have simulated the nanoscale junctions breaking process and found that the conductance of cluster decreases then increases when the contact is pulled apart in two configurations. We analyzed the difference of conductance from transmission spectra and projected density of states, and calculated the I-V characteristics of devices in this two configurations when dz = 2.0 Å. The I-V curves display a linear characteristics in the voltage range of 0 ˜ 2.2 V. The negative differential resistance appears within a small range of voltage in the junctions with As-As axis of the cluster parallel to the transport direction when bias is larger than 2.2 V.

  19. Likelihood methods for cluster dark energy surveys

    SciTech Connect

    Hu, Wayne; Cohn, J. D.

    2006-03-15

    Galaxy cluster counts at high redshift, binned into spatial pixels and binned into ranges in an observable proxy for mass, contain a wealth of information on both the dark energy equation of state and the mass selection function required to extract it. The likelihood of the number counts follows a Poisson distribution whose mean fluctuates with the large-scale structure of the universe. We develop a joint likelihood method that accounts for these distributions. Maximization of the likelihood over a theoretical model that includes both the cosmology and the observable-mass relations allows for a joint extraction of dark energy and cluster structural parameters.

  20. Growth of atmospheric clusters involving cluster-cluster collisions: comparison of different growth rate methods

    NASA Astrophysics Data System (ADS)

    Kontkanen, Jenni; Olenius, Tinja; Lehtipalo, Katrianne; Vehkamäki, Hanna; Kulmala, Markku; Lehtinen, Kari E. J.

    2016-05-01

    We simulated the time evolution of atmospheric cluster concentrations in a one-component system where not only do clusters grow by condensation of monomers, but cluster-cluster collisions also significantly contribute to the growth of the clusters. Our aim was to investigate the consistency of the growth rates of sub-3 nm clusters determined with different methods and the validity of the common approach to use them to estimate particle formation rates. We compared the growth rate corresponding to particle fluxes (FGR), the growth rate derived from the appearance times of clusters (AGR), and the growth rate calculated based on irreversible vapor condensation (CGR). We found that the relation between the different growth rates depends strongly on the external conditions and the properties of the model substance. The difference between the different growth rates was typically highest at the smallest, sub-2 nm sizes. FGR was generally lower than AGR and CGR; at the smallest sizes the difference was often very large, while at sizes larger than 2 nm the growth rates were closer to each other. AGR and CGR were in most cases close to each other at all sizes. The difference between the growth rates was generally lower in conditions where cluster concentrations were high, and evaporation and other losses were thus less significant. Furthermore, our results show that the conventional method used to determine particle formation rates from growth rates may give estimates far from the true values. Thus, care must be taken not only in how the growth rate is determined but also in how it is applied.

  1. A Survey of Quantum Lyapunov Control Methods

    PubMed Central

    2013-01-01

    The condition of a quantum Lyapunov-based control which can be well used in a closed quantum system is that the method can make the system convergent but not just stable. In the convergence study of the quantum Lyapunov control, two situations are classified: nondegenerate cases and degenerate cases. For these two situations, respectively, in this paper the target state is divided into four categories: the eigenstate, the mixed state which commutes with the internal Hamiltonian, the superposition state, and the mixed state which does not commute with the internal Hamiltonian. For these four categories, the quantum Lyapunov control methods for the closed quantum systems are summarized and analyzed. Particularly, the convergence of the control system to the different target states is reviewed, and how to make the convergence conditions be satisfied is summarized and analyzed. PMID:23766732

  2. Quantum Mechanical Methods for Enzyme Kinetics

    NASA Astrophysics Data System (ADS)

    Gao, Jiali; Truhlar, Donald G.

    2002-10-01

    This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.

  3. A new source for quantum optics with biomolecules and biomolecular clusters

    NASA Astrophysics Data System (ADS)

    Marksteiner, Markus; Haslinger, Philipp; Ulbricht, Hendrik; Arndt, Markus

    2008-03-01

    We present recent progress towards matter wave experiments with amino acids, polypeptides and large biomolecular clusters. All successful experiments on macromolecule interferometry so far, with fullerenes, fullerene derivates and large perfluoroalkyl-functionalized azobenzenes used effusive beam sources. The combination of Stark deflectometry with quantum interferometry also allowed us to create a new device for precisely measuring electric susceptibilities of large molecules in the gas phase. In order to apply quantum interference to molecules of biological interest, we have now implemented a pulsed laser desorption source. The combination of UV laser desorption into an intense noble gas jet and single-photon ionization by a VUV excimer laser (157nm) allows us to observe intense neutral jets of amino acids (e.g. Tryptophan), nucleotides (e.g. Guanin) and polypeptides ranging from tri-peptides to Gramicidin. Remarkably, we also found a new method for producing large neutral amino acid clusters, such as for instance Trp30, with masses exceeding 6000 amu: the addition of alkaline Earth salts in the desorption process leads to the inclusion of at least one metal atom per complex and is sufficient to catalyze the cluster formation process.

  4. Creating fractional quantum Hall states with atomic clusters using light-assisted insertion of angular momentum

    NASA Astrophysics Data System (ADS)

    Zhang, Junyi; Beugnon, Jérôme; Nascimbene, Sylvain

    2016-10-01

    We describe a protocol to prepare clusters of ultracold bosonic atoms in strongly interacting states reminiscent of fractional quantum Hall states. Our scheme consists in injecting a controlled amount of angular momentum to an atomic gas using Raman transitions carrying orbital angular momentum. By injecting one unit of angular momentum per atom, one realizes a single-vortex state, which is well described by mean-field theory for large enough particle numbers. We also present schemes to realize fractional quantum Hall states, namely, the bosonic Laughlin and Moore-Read states. We investigate the requirements for adiabatic nucleation of such topological states, in particular comparing linear Landau-Zener ramps and arbitrary ramps obtained from optimized control methods. We also show that this protocol requires excellent control over the isotropic character of the trapping potential.

  5. Clustering of CdSe/CdS Quantum Dot/Quantum Rods into Micelles Can Form Bright, Non-blinking, Stable, and Biocompatible Probes.

    PubMed

    Rafipoor, Mona; Schmidtke, Christian; Wolter, Christopher; Strelow, Christian; Weller, Horst; Lange, Holger

    2015-09-01

    We investigate clustered CdSe/CdS quantum dots/quantum rods, ranging from single to multiple encapsulated rods within amphiphilic diblock copolymer micelles, by time-resolved optical spectroscopy. The effect of the clustering and the cluster size on the optical properties is addressed. The clusters are bright and stable and show no blinking while retaining the fundamental optical properties of the individual quantum dots/quantum rods. Cell studies show neither unspecific uptake nor morphological changes of the cells, despite the increased sizes of the clusters.

  6. Cluster-state quantum computing enhanced by high-fidelity generalized measurements.

    PubMed

    Biggerstaff, D N; Kaltenbaek, R; Hamel, D R; Weihs, G; Rudolph, T; Resch, K J

    2009-12-11

    We introduce and implement a technique to extend the quantum computational power of cluster states by replacing some projective measurements with generalized quantum measurements (POVMs). As an experimental demonstration we fully realize an arbitrary three-qubit cluster computation by implementing a tunable linear-optical POVM, as well as fast active feedforward, on a two-qubit photonic cluster state. Over 206 different computations, the average output fidelity is 0.9832+/-0.0002; furthermore the error contribution from our POVM device and feedforward is only of O(10(-3)), less than some recent thresholds for fault-tolerant cluster computing.

  7. Quantum correlated cluster mean-field theory applied to the transverse Ising model

    NASA Astrophysics Data System (ADS)

    Zimmer, F. M.; Schmidt, M.; Maziero, Jonas

    2016-06-01

    Mean-field theory (MFT) is one of the main available tools for analytical calculations entailed in investigations regarding many-body systems. Recently, there has been a surge of interest in ameliorating this kind of method, mainly with the aim of incorporating geometric and correlation properties of these systems. The correlated cluster MFT (CCMFT) is an improvement that succeeded quite well in doing that for classical spin systems. Nevertheless, even the CCMFT presents some deficiencies when applied to quantum systems. In this article, we address this issue by proposing the quantum CCMFT (QCCMFT), which, in contrast to its former approach, uses general quantum states in its self-consistent mean-field equations. We apply the introduced QCCMFT to the transverse Ising model in honeycomb, square, and simple cubic lattices and obtain fairly good results both for the Curie temperature of thermal phase transition and for the critical field of quantum phase transition. Actually, our results match those obtained via exact solutions, series expansions or Monte Carlo simulations.

  8. Quantum correlated cluster mean-field theory applied to the transverse Ising model.

    PubMed

    Zimmer, F M; Schmidt, M; Maziero, Jonas

    2016-06-01

    Mean-field theory (MFT) is one of the main available tools for analytical calculations entailed in investigations regarding many-body systems. Recently, there has been a surge of interest in ameliorating this kind of method, mainly with the aim of incorporating geometric and correlation properties of these systems. The correlated cluster MFT (CCMFT) is an improvement that succeeded quite well in doing that for classical spin systems. Nevertheless, even the CCMFT presents some deficiencies when applied to quantum systems. In this article, we address this issue by proposing the quantum CCMFT (QCCMFT), which, in contrast to its former approach, uses general quantum states in its self-consistent mean-field equations. We apply the introduced QCCMFT to the transverse Ising model in honeycomb, square, and simple cubic lattices and obtain fairly good results both for the Curie temperature of thermal phase transition and for the critical field of quantum phase transition. Actually, our results match those obtained via exact solutions, series expansions or Monte Carlo simulations.

  9. Quantum correlated cluster mean-field theory applied to the transverse Ising model.

    PubMed

    Zimmer, F M; Schmidt, M; Maziero, Jonas

    2016-06-01

    Mean-field theory (MFT) is one of the main available tools for analytical calculations entailed in investigations regarding many-body systems. Recently, there has been a surge of interest in ameliorating this kind of method, mainly with the aim of incorporating geometric and correlation properties of these systems. The correlated cluster MFT (CCMFT) is an improvement that succeeded quite well in doing that for classical spin systems. Nevertheless, even the CCMFT presents some deficiencies when applied to quantum systems. In this article, we address this issue by proposing the quantum CCMFT (QCCMFT), which, in contrast to its former approach, uses general quantum states in its self-consistent mean-field equations. We apply the introduced QCCMFT to the transverse Ising model in honeycomb, square, and simple cubic lattices and obtain fairly good results both for the Curie temperature of thermal phase transition and for the critical field of quantum phase transition. Actually, our results match those obtained via exact solutions, series expansions or Monte Carlo simulations. PMID:27415217

  10. Qcompiler: Quantum compilation with the CSD method

    NASA Astrophysics Data System (ADS)

    Chen, Y. G.; Wang, J. B.

    2013-03-01

    In this paper, we present a general quantum computation compiler, which maps any given quantum algorithm to a quantum circuit consisting a sequential set of elementary quantum logic gates based on recursive cosine-sine decomposition. The resulting quantum circuit diagram is provided by directly linking the package output written in LaTeX to Qcircuit.tex . We illustrate the use of the Qcompiler package through various examples with full details of the derived quantum circuits. Besides its accuracy, generality and simplicity, Qcompiler produces quantum circuits with significantly reduced number of gates when the systems under study have a high degree of symmetry. Catalogue identifier: AENX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 4321 No. of bytes in distributed program, including test data, etc.: 50943 Distribution format: tar.gz Programming language: Fortran. Computer: Any computer with a Fortran compiler. Operating system: Linux, Mac OS X 10.5 (and later). RAM: Depends on the size of the unitary matrix to be decomposed Classification: 4.15. External routines: Lapack (http://www.netlib.org/lapack/) Nature of problem: Decompose any given unitary operation into a quantum circuit with only elementary quantum logic gates. Solution method: This package decomposes an arbitrary unitary matrix, by applying the CSD algorithm recursively, into a series of block-diagonal matrices, which can then be readily associated with elementary quantum gates to form a quantum circuit. Restrictions: The only limitation is imposed by the available memory on the user's computer. Additional comments: This package is applicable for any arbitrary unitary matrices, both real and complex. If the

  11. Quantum Teleportation of A Four-qubit State by Using Six-qubit Cluster State

    NASA Astrophysics Data System (ADS)

    Li, Yuan-hua; Sang, Ming-huang; Wang, Xian-ping; Nie, Yi-you

    2016-08-01

    We propose a scheme for perfect quantum teleportation of a special form of four-qubit state by using a six-qubit cluster state as quantum channel. In our scheme, the sender only needs six-qubit von-Neumann projective measurements, and the receiver can reconstruct the original four-qubit state by applying the appropriate unitary operation.

  12. Scalable method for demonstrating the Deutsch-Jozsa and Bernstein-Vazirani algorithms using cluster states

    SciTech Connect

    Tame, M. S.; Kim, M. S.

    2010-09-15

    We show that fundamental versions of the Deutsch-Jozsa and Bernstein-Vazirani quantum algorithms can be performed using a small entangled cluster state resource of only six qubits. We then investigate the minimal resource states needed to demonstrate general n-qubit versions and a scalable method to produce them. For this purpose, we propose a versatile photonic on-chip setup.

  13. A Bidirectional Quantum Secure Direct Communication Protocol Based on Five-Particle Cluster State

    NASA Astrophysics Data System (ADS)

    Chang, Yan; Zhang, Shi-Bin; Yan, Li-Li

    2013-09-01

    To transmit a message safely, five-particle cluster state particles are used to construct a bidirectional quantum secure direct communication protocol. Five-particle cluster state particles are used for both detecting eavesdroppers and transmitting secret messages. All of the five-particle cluster states' photons for detection are mixed to the sending sequence to detect eavesdroppers. The detection rate approaches 88% per qubit. The five-particle cluster states needed are only one fifth of the photons in the sending sequence. In this protocol, there is no photon carrying secret information transmitting in quantum channel, and the classical XOR operation which serves as a one-time-pad is used to ensure the security of the protocol. Compared with three photons of each five-particle cluster state as detection photons, the five photons in this study will decrease the five-particle cluster states needed for detection greatly.

  14. A Novel Quantum Blind Signature Scheme with Four-Particle Cluster States

    NASA Astrophysics Data System (ADS)

    Fan, Ling

    2016-03-01

    In an arbitrated quantum signature scheme, the signer signs the message and the receiver verifies the signature's validity with the assistance of the arbitrator. We present an arbitrated quantum blind signature scheme by measuring four-particle cluster states and coding. By using the special relationship of four-particle cluster states, we cannot only support the security of quantum signature, but also guarantee the anonymity of the message owner. It has a wide application to E-payment system, E-government, E-business, and etc.

  15. Fault-tolerant measurement-based quantum computing with continuous-variable cluster states.

    PubMed

    Menicucci, Nicolas C

    2014-03-28

    A long-standing open question about Gaussian continuous-variable cluster states is whether they enable fault-tolerant measurement-based quantum computation. The answer is yes. Initial squeezing in the cluster above a threshold value of 20.5 dB ensures that errors from finite squeezing acting on encoded qubits are below the fault-tolerance threshold of known qubit-based error-correcting codes. By concatenating with one of these codes and using ancilla-based error correction, fault-tolerant measurement-based quantum computation of theoretically indefinite length is possible with finitely squeezed cluster states.

  16. Clustering properties and model wave functions for non-Abelian fractional quantum Hall quasielectrons.

    PubMed

    Bernevig, B Andrei; Haldane, F D M

    2009-02-13

    We present model wave functions for quasielectron (as opposed to quasihole) excitations of the unitary Z_{k} parafermion sequence (Laughlin, Moore-Read, or Read-Rezayi) of fractional quantum Hall states. We uniquely define these states through two generalized clustering conditions: they vanish when either a cluster of k+2 electrons is put together or when two clusters of k+1 electrons are formed at different positions. For Abelian fractional quantum Hall states (k=1), our construction reproduces the Jain quasielectron wave function and elucidates the difference between the Jain and Laughlin quasielectrons. PMID:19257618

  17. Clustering Properties and Model Wave Functions for Non-Abelian Fractional Quantum Hall Quasielectrons

    NASA Astrophysics Data System (ADS)

    Bernevig, B. Andrei; Haldane, F. D. M.

    2009-02-01

    We present model wave functions for quasielectron (as opposed to quasihole) excitations of the unitary Zk parafermion sequence (Laughlin, Moore-Read, or Read-Rezayi) of fractional quantum Hall states. We uniquely define these states through two generalized clustering conditions: they vanish when either a cluster of k+2 electrons is put together or when two clusters of k+1 electrons are formed at different positions. For Abelian fractional quantum Hall states (k=1), our construction reproduces the Jain quasielectron wave function and elucidates the difference between the Jain and Laughlin quasielectrons.

  18. Treatment of dilute clusters of methanol and water by ab initio quantum mechanical calculations.

    PubMed

    Ruckenstein, Eli; Shulgin, Ivan L; Tilson, Jeffrey L

    2005-02-10

    Large molecular clusters can be considered as intermediate states between gas and condensed phases, and information about them can help us understand condensed phases. In this paper, ab initio quantum mechanical methods have been used to examine clusters formed of methanol and water molecules. The main goal was to obtain information about the intermolecular interactions and the structure of methanol/water clusters at the molecular level. The large clusters (CH(4)O...(H(2)O)(12) and H(2)O...(CH(4)O)(10)) containing one molecule of one component (methanol or water) and many (12, 10) molecules of the other component were considered. Møller-Plesset perturbation theory (MP2) was used in the calculations. Several representative cluster geometries were optimized, and nearest-neighbor interaction energies were calculated for the geometries obtained in the first step. The results of the calculations were compared to the available experimental information regarding the liquid methanol/water mixtures and to the molecular dynamics and Monte Carlo simulations, and good agreement was found. For the CH(4)O...(H(2)O)(12) cluster, it was shown that the molecules of water can be subdivided into two classes: (i) H bonded to the central methanol molecule and (ii) not H bonded to the central methanol molecule. As expected, these two classes exhibited striking energy differences. Although they are located almost the same distance from the carbon atom of the central methanol molecule, they possess very different intermolecular interaction energies with the central molecule. The H bonding constitutes a dominant factor in the hydration of methanol in dilute aqueous solutions. For the H(2)O...(CH(4)O)(10) cluster, it was shown that the central molecule of water has almost three H bonds with the methanol molecules; this result differs from those in the literature that concluded that the average number of H bonds between a central water molecule and methanol molecules in dilute solutions of

  19. Two Ways of Robust Quantum Dialogue by Using Four-Qubit Cluster State

    NASA Astrophysics Data System (ADS)

    Wang, Rui-jin; Li, Dong-fen; Liu, Yao; Qin, Zhi-guang; Baagyere, Edward

    2016-04-01

    In this paper, we present a scheme for quantum dialogue by using a four-qubit cluster state as quantum channel.The scheme has two cases: Case 1, Sender Alice and receiver Bob share information using an orderly sequence of entangled state as quantum channel which was prepared by Alice. This case is achieved as follows: The two sides agreed to encode quantum state information, then Alice perform a bell state measurement for quantum information which has been encoded. This will convey the information to Bob, then Bob measuring his own qubits, through the analysis of the measurement results of Alice and Bob, Bob can obtain quantum information. For case 2, four-qubit cluster state and quantum state information is transmitted to form a total quantum system. In the Case 2 scenario, Alice and Bob perform bell state measurements for part of the qubits, and tell the measurement result to each other through the classical channel. Finally, according to the measurement result, Alice and Bob operate an appropriate unitary transformation, as a result, Alice's qubit will be renewed upon Bob's measurements, and also, Bob's qubit will be renewed upon Alice's measurements. Thus, a bidirectional quantum dialogue is achieved. After analysis, this scheme has high security by taking certain eavesdropping attacks into account. There is therefore a certain reference value to the realization of quantum dialogue.

  20. Five-wave-packet quantum error correction based on continuous-variable cluster entanglement.

    PubMed

    Hao, Shuhong; Su, Xiaolong; Tian, Caixing; Xie, Changde; Peng, Kunchi

    2015-10-26

    Quantum error correction protects the quantum state against noise and decoherence in quantum communication and quantum computation, which enables one to perform fault-torrent quantum information processing. We experimentally demonstrate a quantum error correction scheme with a five-wave-packet code against a single stochastic error, the original theoretical model of which was firstly proposed by S. L. Braunstein and T. A. Walker. Five submodes of a continuous variable cluster entangled state of light are used for five encoding channels. Especially, in our encoding scheme the information of the input state is only distributed on three of the five channels and thus any error appearing in the remained two channels never affects the output state, i.e. the output quantum state is immune from the error in the two channels. The stochastic error on a single channel is corrected for both vacuum and squeezed input states and the achieved fidelities of the output states are beyond the corresponding classical limit.

  1. Perspective: Quantum mechanical methods in biochemistry and biophysics

    NASA Astrophysics Data System (ADS)

    Cui, Qiang

    2016-10-01

    In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.

  2. Perspective: Quantum mechanical methods in biochemistry and biophysics

    PubMed Central

    Cui, Qiang

    2016-01-01

    In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies. PMID:27782516

  3. Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

    NASA Technical Reports Server (NTRS)

    Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash; Biegel, Bryan (Technical Monitor)

    2002-01-01

    A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.

  4. A comparison of clustering methods for biogeography with fossil datasets

    PubMed Central

    2016-01-01

    Cluster analysis is one of the most commonly used methods in palaeoecological studies, particularly in studies investigating biogeographic patterns. Although a number of different clustering methods are widely used, the approach and underlying assumptions of many of these methods are quite different. For example, methods may be hierarchical or non-hierarchical in their approaches, and may use Euclidean distance or non-Euclidean indices to cluster the data. In order to assess the effectiveness of the different clustering methods as compared to one another, a simulation was designed that could assess each method over a range of both cluster distinctiveness and sampling intensity. Additionally, a non-hierarchical, non-Euclidean, iterative clustering method implemented in the R Statistical Language is described. This method, Non-Euclidean Relational Clustering (NERC), creates distinct clusters by dividing the data set in order to maximize the average similarity within each cluster, identifying clusters in which each data point is on average more similar to those within its own group than to those in any other group. While all the methods performed well with clearly differentiated and well-sampled datasets, when data are less than ideal the linkage methods perform poorly compared to non-Euclidean based k-means and the NERC method. Based on this analysis, Unweighted Pair Group Method with Arithmetic Mean and neighbor joining methods are less reliable with incomplete datasets like those found in palaeobiological analyses, and the k-means and NERC methods should be used in their place. PMID:26966658

  5. Novel systems and methods for quantum communication, quantum computation, and quantum simulation

    NASA Astrophysics Data System (ADS)

    Gorshkov, Alexey Vyacheslavovich

    Precise control over quantum systems can enable the realization of fascinating applications such as powerful computers, secure communication devices, and simulators that can elucidate the physics of complex condensed matter systems. However, the fragility of quantum effects makes it very difficult to harness the power of quantum mechanics. In this thesis, we present novel systems and tools for gaining fundamental insights into the complex quantum world and for bringing practical applications of quantum mechanics closer to reality. We first optimize and show equivalence between a wide range of techniques for storage of photons in atomic ensembles. We describe experiments demonstrating the potential of our optimization algorithms for quantum communication and computation applications. Next, we combine the technique of photon storage with strong atom-atom interactions to propose a robust protocol for implementing the two-qubit photonic phase gate, which is an important ingredient in many quantum computation and communication tasks. In contrast to photon storage, many quantum computation and simulation applications require individual addressing of closely-spaced atoms, ions, quantum dots, or solid state defects. To meet this requirement, we propose a method for coherent optical far-field manipulation of quantum systems with a resolution that is not limited by the wavelength of radiation. While alkali atoms are currently the system of choice for photon storage and many other applications, we develop new methods for quantum information processing and quantum simulation with ultracold alkaline-earth atoms in optical lattices. We show how multiple qubits can be encoded in individual alkaline-earth atoms and harnessed for quantum computing and precision measurements applications. We also demonstrate that alkaline-earth atoms can be used to simulate highly symmetric systems exhibiting spin-orbital interactions and capable of providing valuable insights into strongly

  6. Discrete range clustering using Monte Carlo methods

    NASA Technical Reports Server (NTRS)

    Chatterji, G. B.; Sridhar, B.

    1993-01-01

    For automatic obstacle avoidance guidance during rotorcraft low altitude flight, a reliable model of the nearby environment is needed. Such a model may be constructed by applying surface fitting techniques to the dense range map obtained by active sensing using radars. However, for covertness, passive sensing techniques using electro-optic sensors are desirable. As opposed to the dense range map obtained via active sensing, passive sensing algorithms produce reliable range at sparse locations, and therefore, surface fitting techniques to fill the gaps in the range measurement are not directly applicable. Both for automatic guidance and as a display for aiding the pilot, these discrete ranges need to be grouped into sets which correspond to objects in the nearby environment. The focus of this paper is on using Monte Carlo methods for clustering range points into meaningful groups. One of the aims of the paper is to explore whether simulated annealing methods offer significant advantage over the basic Monte Carlo method for this class of problems. We compare three different approaches and present application results of these algorithms to a laboratory image sequence and a helicopter flight sequence.

  7. Hall effect in quantum critical charge-cluster glass

    NASA Astrophysics Data System (ADS)

    Wu, Jie; Bollinger, Anthony T.; Sun, Yujie

    2016-04-01

    Upon doping, cuprates undergo a quantum phase transition from an insulator to a d-wave superconductor. The nature of this transition and of the insulating state is vividly debated. Here, we study the Hall effect in La2-xSrxCuO4 (LSCO) samples doped near the quantum critical point at x ˜ 0.06. Dramatic fluctuations in the Hall resistance appear below TCG ˜ 1.5 K and increase as the sample is cooled down further, signaling quantum critical behavior. We explore the doping dependence of this effect in detail, by studying a combinatorial LSCO library in which the Sr content is varied in extremely fine steps, Δx ˜ 0.00008. We observe that quantum charge fluctuations wash out when superconductivity emerges but can be restored when the latter is suppressed by applying a magnetic field, showing that the two instabilities compete for the ground state.

  8. Hall effect in quantum critical charge-cluster glass.

    PubMed

    Wu, Jie; Bollinger, Anthony T; Sun, Yujie; Božović, Ivan

    2016-04-19

    Upon doping, cuprates undergo a quantum phase transition from an insulator to a d-wave superconductor. The nature of this transition and of the insulating state is vividly debated. Here, we study the Hall effect in La2-xSrxCuO4(LSCO) samples doped near the quantum critical point atx∼ 0.06. Dramatic fluctuations in the Hall resistance appear belowTCG∼ 1.5 K and increase as the sample is cooled down further, signaling quantum critical behavior. We explore the doping dependence of this effect in detail, by studying a combinatorial LSCO library in which the Sr content is varied in extremely fine steps,Δx∼ 0.00008. We observe that quantum charge fluctuations wash out when superconductivity emerges but can be restored when the latter is suppressed by applying a magnetic field, showing that the two instabilities compete for the ground state. PMID:27044081

  9. Hall effect in quantum critical charge-cluster glass

    PubMed Central

    Wu, Jie; Bollinger, Anthony T.; Sun, Yujie; Božović, Ivan

    2016-01-01

    Upon doping, cuprates undergo a quantum phase transition from an insulator to a d-wave superconductor. The nature of this transition and of the insulating state is vividly debated. Here, we study the Hall effect in La2-xSrxCuO4 (LSCO) samples doped near the quantum critical point at x ∼ 0.06. Dramatic fluctuations in the Hall resistance appear below TCG ∼ 1.5 K and increase as the sample is cooled down further, signaling quantum critical behavior. We explore the doping dependence of this effect in detail, by studying a combinatorial LSCO library in which the Sr content is varied in extremely fine steps, Δx ∼ 0.00008. We observe that quantum charge fluctuations wash out when superconductivity emerges but can be restored when the latter is suppressed by applying a magnetic field, showing that the two instabilities compete for the ground state. PMID:27044081

  10. Hall effect in quantum critical charge-cluster glass.

    PubMed

    Wu, Jie; Bollinger, Anthony T; Sun, Yujie; Božović, Ivan

    2016-04-19

    Upon doping, cuprates undergo a quantum phase transition from an insulator to a d-wave superconductor. The nature of this transition and of the insulating state is vividly debated. Here, we study the Hall effect in La2-xSrxCuO4(LSCO) samples doped near the quantum critical point atx∼ 0.06. Dramatic fluctuations in the Hall resistance appear belowTCG∼ 1.5 K and increase as the sample is cooled down further, signaling quantum critical behavior. We explore the doping dependence of this effect in detail, by studying a combinatorial LSCO library in which the Sr content is varied in extremely fine steps,Δx∼ 0.00008. We observe that quantum charge fluctuations wash out when superconductivity emerges but can be restored when the latter is suppressed by applying a magnetic field, showing that the two instabilities compete for the ground state.

  11. Projection methods for quantum channel construction

    NASA Astrophysics Data System (ADS)

    Drusvyatskiy, Dmitriy; Li, Chi-Kwong; Pelejo, Diane Christine; Voronin, Yuen-Lam; Wolkowicz, Henry

    2015-08-01

    We consider the problem of constructing quantum channels, if they exist, that transform a given set of quantum states to another such set . In other words, we must find a completely positive linear map, if it exists, that maps a given set of density matrices to another given set of density matrices, possibly of different dimension. Using the theory of completely positive linear maps, one can formulate the problem as an instance of a positive semidefinite feasibility problem with highly structured constraints. The nature of the constraints makes projection-based algorithms very appealing when the number of variables is huge and standard interior-point methods for semidefinite programming are not applicable. We provide empirical evidence to this effect. We moreover present heuristics for finding both high-rank and low-rank solutions. Our experiments are based on the method of alternating projections and the Douglas-Rachford reflection method.

  12. Coronene molecules in helium clusters: Quantum and classical studies of energies and configurations

    SciTech Connect

    Rodríguez-Cantano, Rocío; Pérez de Tudela, Ricardo; Bartolomei, Massimiliano; Hernández, Marta I.; Campos-Martínez, José; González-Lezana, Tomás Villarreal, Pablo; Hernández-Rojas, Javier; Bretón, José

    2015-12-14

    Coronene-doped helium clusters have been studied by means of classical and quantum mechanical (QM) methods using a recently developed He–C{sub 24}H{sub 12} global potential based on the use of optimized atom-bond improved Lennard-Jones functions. Equilibrium energies and geometries at global and local minima for systems with up to 69 He atoms were calculated by means of an evolutive algorithm and a basin-hopping approach and compared with results from path integral Monte Carlo (PIMC) calculations at 2 K. A detailed analysis performed for the smallest sizes shows that the precise localization of the He atoms forming the first solvation layer over the molecular substrate is affected by differences between relative potential minima. The comparison of the PIMC results with the predictions from the classical approaches and with diffusion Monte Carlo results allows to examine the importance of both the QM and thermal effects.

  13. Quantum cluster algorithm for frustrated Ising models in a transverse field

    NASA Astrophysics Data System (ADS)

    Biswas, Sounak; Rakala, Geet; Damle, Kedar

    2016-06-01

    Working within the stochastic series expansion framework, we introduce and characterize a plaquette-based quantum cluster algorithm for quantum Monte Carlo simulations of transverse field Ising models with frustrated Ising exchange interactions. As a demonstration of the capabilities of this algorithm, we show that a relatively small ferromagnetic next-nearest-neighbor coupling drives the transverse field Ising antiferromagnet on the triangular lattice from an antiferromagnetic three-sublattice ordered state at low temperature to a ferrimagnetic three-sublattice ordered state.

  14. Multiple-quantum NMR studies of spin clusters in liquid crystals and zeolites

    SciTech Connect

    Pearson, J. . Dept. of Chemistry Lawrence Berkeley Lab., CA )

    1991-07-01

    This work will describe the use of MQ NMR to study spin clusters in anisotropic materials. A technique known as multiple-quantum spin counting was used to determine average spin cluster sizes liquid crystalline materials and in faujacitic zeolites containing aromatic hydrocarbons. The first half of the thesis will describe MQ NMR and the MQ spin counting technique, and the second half of the thesis will describe the actual experiments and their results.

  15. Hall effect in quantum critical charge-cluster glass

    DOE PAGES

    Bozovic, Ivan; Wu, Jie; Bollinger, Anthony T.; Sun, Yujie

    2016-04-04

    Upon doping, cuprates undergo a quantum phase transition from an insulator to a d-wave superconductor. The nature of this transition and of the insulating state is vividly debated. Here, we study the Hall effect in La2-xSrxCuO4 (LSCO) samples doped near the quantum critical point at x ≈ 0.06. Dramatic fluctuations in the Hall resistance appear below TCG ≈ 1.5 K and increase as the sample is cooled down further, signaling quantum critical behavior. We explore the doping dependence of this effect in detail, by studying a combinatorial LSCO library in which the Sr content is varied in extremely fine steps,more » Δx ≈ 0.00008. Furthermore, we observe that quantum charge fluctuations wash out when superconductivity emerges but can be restored when the latter is suppressed by applying a magnetic field, showing that the two instabilities compete for the ground state.« less

  16. Enhanced fluorescence intermittency of CdSe-ZnS quantum-dot clusters.

    PubMed

    Yu, Ming; Van Orden, Alan

    2006-12-01

    Fluorescence intermittency, or blinking, of individual close-packed clusters containing two or more CdSe-ZnS quantum dots (QDs) was investigated. The QD clusters exhibited rapid, intense blinking that was distinct from that of isolated QDs blinking independently. This enhanced blinking is suggested to occur when the QDs in the cluster become electronically coupled. The nature of this coupling is not known, though electrons trapped from QDs when they blink off may play a role by altering the electronic environment of neighboring QDs and enhancing their fluorescence properties.

  17. Visual cluster analysis and pattern recognition template and methods

    SciTech Connect

    Osbourn, G.C.; Martinez, R.F.

    1993-12-31

    This invention is comprised of a method of clustering using a novel template to define a region of influence. Using neighboring approximation methods, computation times can be significantly reduced. The template and method are applicable and improve pattern recognition techniques.

  18. Visual cluster analysis and pattern recognition template and methods

    DOEpatents

    Osbourn, Gordon Cecil; Martinez, Rubel Francisco

    1999-01-01

    A method of clustering using a novel template to define a region of influence. Using neighboring approximation methods, computation times can be significantly reduced. The template and method are applicable and improve pattern recognition techniques.

  19. Visual cluster analysis and pattern recognition template and methods

    DOEpatents

    Osbourn, G.C.; Martinez, R.F.

    1999-05-04

    A method of clustering using a novel template to define a region of influence is disclosed. Using neighboring approximation methods, computation times can be significantly reduced. The template and method are applicable and improve pattern recognition techniques. 30 figs.

  20. Research on Palmprint Identification Method Based on Quantum Algorithms

    PubMed Central

    Zhang, Zhanzhan

    2014-01-01

    Quantum image recognition is a technology by using quantum algorithm to process the image information. It can obtain better effect than classical algorithm. In this paper, four different quantum algorithms are used in the three stages of palmprint recognition. First, quantum adaptive median filtering algorithm is presented in palmprint filtering processing. Quantum filtering algorithm can get a better filtering result than classical algorithm through the comparison. Next, quantum Fourier transform (QFT) is used to extract pattern features by only one operation due to quantum parallelism. The proposed algorithm exhibits an exponential speed-up compared with discrete Fourier transform in the feature extraction. Finally, quantum set operations and Grover algorithm are used in palmprint matching. According to the experimental results, quantum algorithm only needs to apply square of N operations to find out the target palmprint, but the traditional method needs N times of calculation. At the same time, the matching accuracy of quantum algorithm is almost 100%. PMID:25105165

  1. Horizon entropy with loop quantum gravity methods

    NASA Astrophysics Data System (ADS)

    Pranzetti, Daniele; Sahlmann, Hanno

    2015-06-01

    We show that the spherically symmetric isolated horizon can be described in terms of an SU (2) connection and an su (2)-valued one-form, obeying certain constraints. The horizon symplectic structure is precisely the one of 3d gravity in a first order formulation. We quantize the horizon degrees of freedom in the framework of loop quantum gravity, with methods recently developed for 3d gravity with non-vanishing cosmological constant. Bulk excitations ending on the horizon act very similarly to particles in 3d gravity. The Bekenstein-Hawking law is recovered in the limit of imaginary Barbero-Immirzi parameter. Alternative methods of quantization are also discussed.

  2. Quantum Teleportation of a Three-qubit State using a Five-qubit Cluster State

    NASA Astrophysics Data System (ADS)

    Liu, Zhong-min; Zhou, Lin

    2014-12-01

    Recently Muralidharan and Panigrahi (Phys. Rev. A 78, 062333 2008) had shown that using a five-qubit cluster state as quantum channel, it is possible to teleport an arbitrary single-qubit state and an arbitrary two-qubit state. In this paper, we investigate this channel for the teleportation of a special form of three-qubit state.

  3. Bond additivity corrections for quantum chemistry methods

    SciTech Connect

    C. F. Melius; M. D. Allendorf

    1999-04-01

    In the 1980's, the authors developed a bond-additivity correction procedure for quantum chemical calculations called BAC-MP4, which has proven reliable in calculating the thermochemical properties of molecular species, including radicals as well as stable closed-shell species. New Bond Additivity Correction (BAC) methods have been developed for the G2 method, BAC-G2, as well as for a hybrid DFT/MP2 method, BAC-Hybrid. These BAC methods use a new form of BAC corrections, involving atomic, molecular, and bond-wise additive terms. These terms enable one to treat positive and negative ions as well as neutrals. The BAC-G2 method reduces errors in the G2 method due to nearest-neighbor bonds. The parameters within the BAC-G2 method only depend on atom types. Thus the BAC-G2 method can be used to determine the parameters needed by BAC methods involving lower levels of theory, such as BAC-Hybrid and BAC-MP4. The BAC-Hybrid method should scale well for large molecules. The BAC-Hybrid method uses the differences between the DFT and MP2 as an indicator of the method's accuracy, while the BAC-G2 method uses its internal methods (G1 and G2MP2) to provide an indicator of its accuracy. Indications of the average error as well as worst cases are provided for each of the BAC methods.

  4. An analytic method to compute star cluster luminosity statistics

    NASA Astrophysics Data System (ADS)

    da Silva, Robert L.; Krumholz, Mark R.; Fumagalli, Michele; Fall, S. Michael

    2014-03-01

    The luminosity distribution of the brightest star clusters in a population of galaxies encodes critical pieces of information about how clusters form, evolve and disperse, and whether and how these processes depend on the large-scale galactic environment. However, extracting constraints on models from these data is challenging, in part because comparisons between theory and observation have traditionally required computationally intensive Monte Carlo methods to generate mock data that can be compared to observations. We introduce a new method that circumvents this limitation by allowing analytic computation of cluster order statistics, i.e. the luminosity distribution of the Nth most luminous cluster in a population. Our method is flexible and requires few assumptions, allowing for parametrized variations in the initial cluster mass function and its upper and lower cutoffs, variations in the cluster age distribution, stellar evolution and dust extinction, as well as observational uncertainties in both the properties of star clusters and their underlying host galaxies. The method is fast enough to make it feasible for the first time to use Markov chain Monte Carlo methods to search parameter space to find best-fitting values for the parameters describing cluster formation and disruption, and to obtain rigorous confidence intervals on the inferred values. We implement our method in a software package called the Cluster Luminosity Order-Statistic Code, which we have made publicly available.

  5. Luminescent, bimetallic AuAg alloy quantum clusters in protein templates.

    PubMed

    Mohanty, Jyoti Sarita; Xavier, P Lourdu; Chaudhari, Kamalesh; Bootharaju, M S; Goswami, N; Pal, S K; Pradeep, T

    2012-07-21

    We report the synthesis of luminescent AuAg alloy quantum clusters (QCs) in bovine serum albumin (BSA), for the first time, with experimentally determined atomic composition. Mixing of the as-synthesized protein-protected Au and Ag clusters resulted in the formation of alloy AuAg clusters within the BSA. Mass spectrometric analysis of the product of a 1 : 1 molar ratio reaction mixture of Au(QC)@BSA and Ag(QC)@BSA suggested that the alloy clusters could be Au(38-x)Ag(x)@BSA. Further analyses by standard techniques revealed that the alloy cluster core of ∼1.2 nm diameter is composed of nearly zero valent Au and Ag atoms that exhibit distinctly different steady state and time resolved excited state luminescence profiles compared to the parent clusters. Tuning of the alloy composition was achieved by varying the molar ratio of the parent species in the reaction mixture and compositional changes were observed by mass spectrometry. In another approach, mixing of Au(3+) ions with the as-synthesized Ag(QC)@BSA also resulted in the formation of alloy clusters through galvanic exchange reactions. We believe that alloy clusters with the combined properties of the constituents in versatile protein templates would have potential applications in the future. The work presents interesting aspects of the reactivity of the protein-protected clusters. PMID:22684267

  6. Prediction of Solvent Physical Properties using the Hierarchical Clustering Method

    EPA Science Inventory

    Recently a QSAR (Quantitative Structure Activity Relationship) method, the hierarchical clustering method, was developed to estimate acute toxicity values for large, diverse datasets. This methodology has now been applied to the estimate solvent physical properties including sur...

  7. Quantum Monte Carlo methods for nuclear physics

    DOE PAGES

    Carlson, J.; Gandolfi, S.; Pederiva, F.; Pieper, Steven C.; Schiavilla, R.; Schmidt, K. E.; Wiringa, R. B.

    2015-09-09

    Quantum Monte Carlo methods have proved valuable to study the structure and reactions of light nuclei and nucleonic matter starting from realistic nuclear interactions and currents. These ab-initio calculations reproduce many low-lying states, moments, and transitions in light nuclei, and simultaneously predict many properties of light nuclei and neutron matter over a rather wide range of energy and momenta. The nuclear interactions and currents are reviewed along with a description of the continuum quantum Monte Carlo methods used in nuclear physics. These methods are similar to those used in condensed matter and electronic structure but naturally include spin-isospin, tensor, spin-orbit,more » and three-body interactions. A variety of results are presented, including the low-lying spectra of light nuclei, nuclear form factors, and transition matrix elements. Low-energy scattering techniques, studies of the electroweak response of nuclei relevant in electron and neutrino scattering, and the properties of dense nucleonic matter as found in neutron stars are also described. Furthermore, a coherent picture of nuclear structure and dynamics emerges based upon rather simple but realistic interactions and currents.« less

  8. Quantum Monte Carlo methods for nuclear physics

    DOE PAGES

    Carlson, Joseph A.; Gandolfi, Stefano; Pederiva, Francesco; Pieper, Steven C.; Schiavilla, Rocco; Schmidt, K. E,; Wiringa, Robert B.

    2014-10-19

    Quantum Monte Carlo methods have proved very valuable to study the structure and reactions of light nuclei and nucleonic matter starting from realistic nuclear interactions and currents. These ab-initio calculations reproduce many low-lying states, moments and transitions in light nuclei, and simultaneously predict many properties of light nuclei and neutron matter over a rather wide range of energy and momenta. We review the nuclear interactions and currents, and describe the continuum Quantum Monte Carlo methods used in nuclear physics. These methods are similar to those used in condensed matter and electronic structure but naturally include spin-isospin, tensor, spin-orbit, and three-bodymore » interactions. We present a variety of results including the low-lying spectra of light nuclei, nuclear form factors, and transition matrix elements. We also describe low-energy scattering techniques, studies of the electroweak response of nuclei relevant in electron and neutrino scattering, and the properties of dense nucleonic matter as found in neutron stars. A coherent picture of nuclear structure and dynamics emerges based upon rather simple but realistic interactions and currents.« less

  9. Quantum Monte Carlo methods for nuclear physics

    SciTech Connect

    Carlson, J.; Gandolfi, S.; Pederiva, F.; Pieper, Steven C.; Schiavilla, R.; Schmidt, K. E.; Wiringa, R. B.

    2015-09-09

    Quantum Monte Carlo methods have proved valuable to study the structure and reactions of light nuclei and nucleonic matter starting from realistic nuclear interactions and currents. These ab-initio calculations reproduce many low-lying states, moments, and transitions in light nuclei, and simultaneously predict many properties of light nuclei and neutron matter over a rather wide range of energy and momenta. The nuclear interactions and currents are reviewed along with a description of the continuum quantum Monte Carlo methods used in nuclear physics. These methods are similar to those used in condensed matter and electronic structure but naturally include spin-isospin, tensor, spin-orbit, and three-body interactions. A variety of results are presented, including the low-lying spectra of light nuclei, nuclear form factors, and transition matrix elements. Low-energy scattering techniques, studies of the electroweak response of nuclei relevant in electron and neutrino scattering, and the properties of dense nucleonic matter as found in neutron stars are also described. Furthermore, a coherent picture of nuclear structure and dynamics emerges based upon rather simple but realistic interactions and currents.

  10. Progeny Clustering: A Method to Identify Biological Phenotypes.

    PubMed

    Hu, Chenyue W; Kornblau, Steven M; Slater, John H; Qutub, Amina A

    2015-01-01

    Estimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the ten-dimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset. PMID:26267476

  11. Enhanced quantum coherence in graphene caused by Pd cluster deposition

    SciTech Connect

    Qin, Yuyuan; Han, Junhao; Du, Yongping; Li, Zhaoguo; Wan, Xiangang; Han, Min; Song, Fengqi; Guo, Guoping; Song, You; Pi, Li; Wang, Xuefeng

    2015-01-12

    We report on the unexpected increase in the dephasing lengths of a graphene sheet caused by the deposition of Pd nanoclusters, as demonstrated by weak localization measurements. The dephasing lengths reached saturated values at low temperatures. Theoretical calculations indicate the p-type charge transfer from the Pd clusters, which contributes more carriers. The saturated values of dephasing lengths often depend on both the carrier concentration and mean free path. Although some impurities are increased as revealed by decreased mobilities, the intense charge transfer leads to the improved saturated values and subsequent improved dephasing lengths.

  12. Spectral-luminescence characteristics of lead sulfide molecular clusters and quantum dots in fluorophosphate glasses

    NASA Astrophysics Data System (ADS)

    Lipatova, Zh. O.; Kolobkova, E. V.; Nikonorov, N. V.

    2015-12-01

    PbS molecular clusters and quantum dots (QDs) have been formed by heat treatment in fluorophosphate glasses of the Na2O3-P2O5-Ga2O3-ALF3-ZnO(S)-PbF2 system, and their spectral-luminescence characteristics have been investigated. It is experimentally shown that the transition from molecular clusters to QDs is accompanied by a stepwise change in the spectrum and luminescence quantum yield. Molecular PbS clusters luminesce in the visible spectral range (1.5-3.5 eV) and QDs luminesce in the IR region (0.6-1.4 eV). The luminescence of molecular PbS clusters is characterized by low quantum yield, which decreases from 10 to 1% with an increase in excitation energy. An increase in nanoparticle size leads to a decrease in the Stokes shift from 80 to 50 meV. The QD luminescence spectrum contains two bands, which are due to transitions from two lower excited states.

  13. Cluster growth processes by direct simulation monte carlo method

    NASA Astrophysics Data System (ADS)

    Mizuseki, H.; Jin, Y.; Kawazoe, Y.; Wille, L. T.

    Thin films obtained by cluster deposition have attracted strong attention both as a new manufacturing technique to realize high-density magnetic recording media and to create systems with unique magnetic properties. Because the film's features are influenced by the cluster properties during the flight path, the relevant physical scale to be studied is as large as centimeters. In this paper, a new model of cluster growth processes based on a combination of the Direct Simulation Monte Carlo (DSMC) method and the cluster growth model is introduced to examine the effects of experimental conditions on cluster growth by an adiabatic expansion process. From the macroscopic viewpoint, we simulate the behavior of clusters and inert gas in the flight path under different experimental conditions. The internal energy of the cluster, which consists of rotational and vibrational energies, is limited by the binding energy which depends on the cluster size. These internal and binding energies are used as criteria of the cluster growth. The binding energy is estimated by surface and volume terms. Several types of size distribution of generated clusters under various conditions are obtained by the present model. The results of the present numerical simulations reveal that the size distribution is strongly related to the experimental conditions and can be controlled.

  14. Correlating structure and fluorescence dynamics of quantum dot clusters using super-resolution imaging

    NASA Astrophysics Data System (ADS)

    Ryan, Duncan P.; Goodwin, Peter M.; Sheehan, Chris J.; Whitcomb, Kevin J.; Gelfand, Martin P.; Van Orden, Alan

    2016-02-01

    Clusters of quantum dots exhibit fluorescent behavior that differs from that of individual particles. Bulk measurements involving a large number of particles obscure these dynamics. Synthesizing clusters with 5-10 particles enables the study of collective behavior where single-molecule fluorescence techniques can be applied. Super-resolution microscopy of these clusters correlated with SEM imaging reveals the influence of geometry and structure on emission dynamics. Signatures of energy transfer can be seen in the form of enhanced blinking. Motion of the emission center of the cluster is tracked, made possible by the independent blinking events of the individual particles. Discrete steps in the localization are observed as random switching between various on/off configurations moves the location of the emission center.

  15. Experimental realization of one-way quantum computing with two-photon four-qubit cluster states.

    PubMed

    Chen, Kai; Li, Che-Ming; Zhang, Qiang; Chen, Yu-Ao; Goebel, Alexander; Chen, Shuai; Mair, Alois; Pan, Jian-Wei

    2007-09-21

    We report an experimental realization of one-way quantum computing on a two-photon four-qubit cluster state. This is accomplished by developing a two-photon cluster state source entangled both in polarization and spatial modes. With this special source, we implemented a highly efficient Grover's search algorithm and high-fidelity two-qubit quantum gates. Our experiment demonstrates that such cluster states could serve as an ideal source and a building block for rapid and precise optical quantum computation.

  16. Tuned oscillatory behavior in discrete quantum walks on star clusters

    NASA Astrophysics Data System (ADS)

    Andrade, R. F. S.; Souza, A. M. C.

    2015-10-01

    A discrete time quantum walk on the star network is considered, on which the walker has a waiting probability at any time step and for any of the N nodes. This contrasts with a previous continuous time analysis, in which the walker in any of the N -1 leaf nodes is forced to jump back to the central hub. The model amounts to considering two coin operators, one for the hub (with N possible states) and another one for all leaf nodes (with two possible states). The solution depends on N and θ , an angle gauging the action of the coin operator on the leaf nodes. Periodic solutions are identified, which can be represented as superposition of large-period branches, sharing a relative small number of shapes and displaced by a regular interval. It is shown that the large period is very sensitive to the choice of N and θ . The possibility of experimental applications of this property is briefly mentioned.

  17. New method for calculation of nuclear cluster structure of nuclei

    NASA Astrophysics Data System (ADS)

    Ibishi, A. I.

    2005-05-01

    In the calculations of the many-nucleon bound states, using the realistic nucleon-nucleon potential, and a three- and four-nucleon potential, the Exact Many-Body Nuclear Cluster Model (EMBNCM) was found to give accurate results, that converege much more rapidly, than those obtained by the Faddeev equation calculations. With the use of realistic nucleon-nucleon potentials, and many-nucleon potentials, containing strong tensor, Majorana, and repulsive core components, the many-body cluster structure of 16O, 27Al, 44Ti, and 48Ti is discussed. In 27Al(p,x)Na reactions we assume that two different nuclear cluster structures of 27Al, gives us two different isotopes of Na: 22Na and 24Na. But the most important result is the existence of two different permutations symmetries of 27Al. Using new method for calculation of nuclear cluster structure of 27Al, we have found two different nuclear cluster structures of 27Al: 24Na+3He and 25Na+d. The internal nuclear cluster wave functions of different nuclear cluster models (nuclear cluster isomers) of the same isotope are not equivalent, if we take into account Many-Body Nuclear Forces, such as 3BF and 4BF. The core clusters of 16O, 27Al, 44Ti, and 48Ti nuclei have a trigonal-pyramide Td, D2d, and C3v symmetry, while exterior clusters in 16O and 27Al[(24Na +3 He)model] nuclei have a trigonal symmetry C2v, and D3h. We have developed a new system of Jacobi coordinates for our EMBNCM model with the symmetry above. The new computer code for determination of direct nuclear cluster reactions has been written in Mathematica 5 programming language. We have found a high level of dependence of the nuclear cluster wave functions from the center of mass and cluster effects.

  18. New method for calculation of nuclear cluster structure of nuclei

    SciTech Connect

    Ibishi, A.I.

    2005-05-06

    In the calculations of the many-nucleon bound states, using the realistic nucleon-nucleon potential, and a three- and four-nucleon potential, the Exact Many-Body Nuclear Cluster Model (EMBNCM) was found to give accurate results, that converege much more rapidly, than those obtained by the Faddeev equation calculations. With the use of realistic nucleon-nucleon potentials, and many-nucleon potentials, containing strong tensor, Majorana, and repulsive core components, the many-body cluster structure of 16O, 27Al, 44Ti, and 48Ti is discussed. In 27Al(p,x)Na reactions we assume that two different nuclear cluster structures of 27Al, gives us two different isotopes of Na: 22Na and 24Na. But the most important result is the existence of two different permutations symmetries of 27Al. Using new method for calculation of nuclear cluster structure of 27Al, we have found two different nuclear cluster structures of 27Al: 24Na+3He and 25Na+d. The internal nuclear cluster wave functions of different nuclear cluster models (nuclear cluster isomers) of the same isotope are not equivalent, if we take into account Many-Body Nuclear Forces, such as 3BF and 4BF. The core clusters of 16O, 27Al, 44Ti, and 48Ti nuclei have a trigonal-pyramide Td, D2d, and C3v symmetry, while exterior clusters in 16O and 27Al[(24Na +3 He)model] nuclei have a trigonal symmetry C2v, and D3h. We have developed a new system of Jacobi coordinates for our EMBNCM model with the symmetry above. The new computer code for determination of direct nuclear cluster reactions has been written in Mathematica 5 programming language. We have found a high level of dependence of the nuclear cluster wave functions from the center of mass and cluster effects.

  19. Electron correlation in the interacting quantum atoms partition via coupled-cluster lagrangian densities.

    PubMed

    Holguín-Gallego, Fernando José; Chávez-Calvillo, Rodrigo; García-Revilla, Marco; Francisco, Evelio; Pendás, Ángel Martín; Rocha-Rinza, Tomás

    2016-07-15

    The electronic energy partition established by the Interacting Quantum Atoms (IQA) approach is an important method of wavefunction analyses which has yielded valuable insights about different phenomena in physical chemistry. Most of the IQA applications have relied upon approximations, which do not include either dynamical correlation (DC) such as Hartree-Fock (HF) or external DC like CASSCF theory. Recently, DC was included in the IQA method by means of HF/Coupled-Cluster (CC) transition densities (Chávez-Calvillo et al., Comput. Theory Chem. 2015, 1053, 90). Despite the potential utility of this approach, it has a few drawbacks, for example, it is not consistent with the calculation of CC properties different from the total electronic energy. To improve this situation, we have implemented the IQA energy partition based on CC Lagrangian one- and two-electron orbital density matrices. The development presented in this article is tested and illustrated with the H2 , LiH, H2 O, H2 S, N2 , and CO molecules for which the IQA results obtained under the consideration of (i) the CC Lagrangian, (ii) HF/CC transition densities, and (iii) HF are critically analyzed and compared. Additionally, the effect of the DC in the different components of the electronic energy in the formation of the T-shaped (H2 )2 van der Waals cluster and the bimolecular nucleophilic substitution between F(-) and CH3 F is examined. We anticipate that the approach put forward in this article will provide new understandings on subjects in physical chemistry wherein DC plays a crucial role like molecular interactions along with chemical bonding and reactivity. © 2016 Wiley Periodicals, Inc. PMID:27237084

  20. Electron correlation in the interacting quantum atoms partition via coupled-cluster lagrangian densities.

    PubMed

    Holguín-Gallego, Fernando José; Chávez-Calvillo, Rodrigo; García-Revilla, Marco; Francisco, Evelio; Pendás, Ángel Martín; Rocha-Rinza, Tomás

    2016-07-15

    The electronic energy partition established by the Interacting Quantum Atoms (IQA) approach is an important method of wavefunction analyses which has yielded valuable insights about different phenomena in physical chemistry. Most of the IQA applications have relied upon approximations, which do not include either dynamical correlation (DC) such as Hartree-Fock (HF) or external DC like CASSCF theory. Recently, DC was included in the IQA method by means of HF/Coupled-Cluster (CC) transition densities (Chávez-Calvillo et al., Comput. Theory Chem. 2015, 1053, 90). Despite the potential utility of this approach, it has a few drawbacks, for example, it is not consistent with the calculation of CC properties different from the total electronic energy. To improve this situation, we have implemented the IQA energy partition based on CC Lagrangian one- and two-electron orbital density matrices. The development presented in this article is tested and illustrated with the H2 , LiH, H2 O, H2 S, N2 , and CO molecules for which the IQA results obtained under the consideration of (i) the CC Lagrangian, (ii) HF/CC transition densities, and (iii) HF are critically analyzed and compared. Additionally, the effect of the DC in the different components of the electronic energy in the formation of the T-shaped (H2 )2 van der Waals cluster and the bimolecular nucleophilic substitution between F(-) and CH3 F is examined. We anticipate that the approach put forward in this article will provide new understandings on subjects in physical chemistry wherein DC plays a crucial role like molecular interactions along with chemical bonding and reactivity. © 2016 Wiley Periodicals, Inc.

  1. Electronic and dielectric properties of vacancy clusters as quantum dot in silicane

    SciTech Connect

    Mohan, Brij Sharma, Munish; Ahluwalia, P. K.; Kumar, Ashok

    2015-06-24

    First principal study of electronic and dielectric properties of a silicane nanostructure containing cluster of vacancies as quantum dot (QD) has been investigated within density functional theory (DFT). Electronic band structure and corresponding density of states show the decrease in band gap with increasing size of quantum dot. A band gap of 0.38 eV has been achieved for silicane containing 3QD. Electron energy loss spectra (EEL) function shows additional plasmonic features for QD containing silicane in visible region, which may have potential applications in optoelectronic devices.

  2. Electronic and dielectric properties of vacancy clusters as quantum dot in silicane

    NASA Astrophysics Data System (ADS)

    Mohan, Brij; Sharma, Munish; Kumar, Ashok; Ahluwalia, P. K.

    2015-06-01

    First principal study of electronic and dielectric properties of a silicane nanostructure containing cluster of vacancies as quantum dot (QD) has been investigated within density functional theory (DFT). Electronic band structure and corresponding density of states show the decrease in band gap with increasing size of quantum dot. A band gap of 0.38 eV has been achieved for silicane containing 3QD. Electron energy loss spectra (EEL) function shows additional plasmonic features for QD containing silicane in visible region, which may have potential applications in optoelectronic devices.

  3. Clustering PPI data by combining FA and SHC method

    PubMed Central

    2015-01-01

    Clustering is one of main methods to identify functional modules from protein-protein interaction (PPI) data. Nevertheless traditional clustering methods may not be effective for clustering PPI data. In this paper, we proposed a novel method for clustering PPI data by combining firefly algorithm (FA) and synchronization-based hierarchical clustering (SHC) algorithm. Firstly, the PPI data are preprocessed via spectral clustering (SC) which transforms the high-dimensional similarity matrix into a low dimension matrix. Then the SHC algorithm is used to perform clustering. In SHC algorithm, hierarchical clustering is achieved by enlarging the neighborhood radius of synchronized objects continuously, while the hierarchical search is very difficult to find the optimal neighborhood radius of synchronization and the efficiency is not high. So we adopt the firefly algorithm to determine the optimal threshold of the neighborhood radius of synchronization automatically. The proposed algorithm is tested on the MIPS PPI dataset. The results show that our proposed algorithm is better than the traditional algorithms in precision, recall and f-measure value. PMID:25707632

  4. Protoribosome by quantum kernel energy method.

    PubMed

    Huang, Lulu; Krupkin, Miri; Bashan, Anat; Yonath, Ada; Massa, Lou

    2013-09-10

    Experimental evidence suggests the existence of an RNA molecular prebiotic entity, called by us the "protoribosome," which may have evolved in the RNA world before evolution of the genetic code and proteins. This vestige of the RNA world, which possesses all of the capabilities required for peptide bond formation, seems to be still functioning in the heart of all of the contemporary ribosome. Within the modern ribosome this remnant includes the peptidyl transferase center. Its highly conserved nucleotide sequence is suggestive of its robustness under diverse environmental conditions, and hence on its prebiotic origin. Its twofold pseudosymmetry suggests that this entity could have been a dimer of self-folding RNA units that formed a pocket within which two activated amino acids might be accommodated, similar to the binding mode of modern tRNA molecules that carry amino acids or peptidyl moieties. Using quantum mechanics and crystal coordinates, this work studies the question of whether the putative protoribosome has properties necessary to function as an evolutionary precursor to the modern ribosome. The quantum model used in the calculations is density functional theory--B3LYP/3-21G*, implemented using the kernel energy method to make the computations practical and efficient. It occurs that the necessary conditions that would characterize a practicable protoribosome--namely (i) energetic structural stability and (ii) energetically stable attachment to substrates--are both well satisfied.

  5. Multimodal optical studies of single and clustered colloidal quantum dots for the long-term optical property evaluation of quantum dot-based molecular imaging phantoms

    PubMed Central

    Kang, HyeongGon; Clarke, Matthew L.; Lacerda, Silvia H. De Paoli; Karim, Alamgir; Pease, Leonard F.; Hwang, Jeeseong

    2012-01-01

    Understanding the optical properties of clustered quantum dots (QDs) is essential to the design of QD-based optical phantoms for molecular imaging. Single and clustered core/shell colloidal QDs of dimers, trimers, and tetramers are self-assembled, separated, and preferentially collected using electrospray differential mobility analysis (ES-DMA) with electrostatic deposition. Multimodal optical characterization and analysis of their dynamical photoluminescence (PL) properties enables the long-term evaluation of the physicochemical and optical properties of QDs in a single or a clustered state. A multimodal time-correlated spectroscopic confocal microscope capable of simultaneously measuring the time evolution of PL intensity fluctuation, PL lifetime, and emission spectra reveals the long-term dynamic optical properties of interacting QDs in individual dimeric clusters of QDs. This new method will benefit research into the quantitative interpretation of fluorescence intensity and lifetime results in QD-based molecular imaging techniques. The process of photooxidation leads to coupling of the QDs in a dimer, leading to unique optical properties when compared to an isolated QD. These results guide the design and evaluation of QD-based phantom materials for the validation of the PL measurements for quantitative molecular imaging of biological samples labeled with QD probes. PMID:22741078

  6. Coupled motion of Xe clusters and quantum vortices in He nanodroplets

    NASA Astrophysics Data System (ADS)

    Jones, Curtis F.; Bernando, Charles; Tanyag, Rico Mayro P.; Bacellar, Camila; Ferguson, Ken R.; Gomez, Luis F.; Anielski, Denis; Belkacem, Ali; Boll, Rebecca; Bozek, John; Carron, Sebastian; Cryan, James; Englert, Lars; Epp, Sascha W.; Erk, Benjamin; Foucar, Lutz; Hartmann, Robert; Neumark, Daniel M.; Rolles, Daniel; Rudenko, Artem; Siefermann, Katrin R.; Weise, Fabian; Rudek, Benedikt; Sturm, Felix P.; Ullrich, Joachim; Bostedt, Christoph; Gessner, Oliver; Vilesov, Andrey F.

    2016-05-01

    Single He nanodroplets doped with Xe atoms are studied via ultrafast coherent x-ray diffraction imaging. The diffraction images show that rotating He nanodroplets about 200 nm in diameter contain a small number of symmetrically arranged quantum vortices decorated with Xe clusters. Unexpected large distances of the vortices from the droplet center (≈0.7 -0.8 droplet radii) are explained by a significant contribution of the Xe dopants to the total angular momentum of the droplets and a stabilization of widely spaced vortex configurations by the trapped Xe clusters.

  7. Coherent resonance of quantum plasmons in the graphene-gold cluster hybrid system.

    PubMed

    Zhang, Kaibiao; Zhang, Hong; Li, Chikang

    2015-05-14

    Noble metal nanoparticles can modify the optical properties of graphene. Here we present a detailed theoretical analysis of the coherent resonance of quantum plasmons in the graphene-gold cluster hybrid system by using time dependent density functional theory (TDDFT). This plasmon coherent effect is mainly attributed to the electromagnetic field coupling between the graphene and the gold cluster. As a result, the optical response of the hybrid system exhibits a remarkably strong, selectable tuning and polarization dependent plasmon resonance enhanced in wide frequency regions. This investigation provides an improved understanding of the plasmon enhancement effect in a graphene-based photoelectric device. PMID:25874280

  8. Experimental entanglement of 60 modes of the quantum optical frequency comb and application to generating hypercubic-lattice cluster states

    NASA Astrophysics Data System (ADS)

    Pfister, Olivier; Chen, Moran; Wang, Pei; Fan, Wenjiang; Menicucci, Nicolas

    2014-05-01

    In the race to build a practical quantum computer in the laboratory, the ability to create very large quantum registers and entangle them is paramount, along with the ability to address the issue of decoherence. With particular regard to scalability, the field-based, continuous-variable (CV) flavor of quantum optics offers notable promise, in particular by enabling ``top down,'' rather than ``bottom up,'' entangling approaches of quantum field modes. It is also important to note the relevance of continuous variables to universal quantum computing, with the recent discovery of a fault tolerance threshold for quantum computing with CV cluster states and nonGaussian error correction. In 2011, some of us generated simultaneously 15 independent 4-mode cluster states over 60 modes of the quantum optical frequency comb (QOFC) of a single optical parametric oscillator (OPO). In this work, we used a single OPO to generate a 60-mode dual-rail cluster state, which is the largest entangled system to date whose subsystems are all simultaneously available. Using the exact same setup, we also generated two copies of a 30-mode dual-rail cluster state. We will then present a new proposal to ``weave'' such massively scalable continuous-variable cluster states into hypercubic-lattice quantum graphs Work supported by NSF grants PHY-0855632 and PHY-1206029.

  9. Linked-cluster expansions for quantum magnets on the hypercubic lattice

    NASA Astrophysics Data System (ADS)

    Coester, Kris; Joshi, Darshan G.; Vojta, Matthias; Schmidt, Kai Phillip

    2016-09-01

    For arbitrary space dimension d , we investigate the quantum phase transitions of two paradigmatic spin models defined on a hypercubic lattice, the coupled-dimer Heisenberg model and the transverse-field Ising model. To this end, high-order linked-cluster expansions for the ground-state energy and the one-particle gap are performed up to order 9 about the decoupled-dimer and high-field limits, respectively. Extrapolations of the high-order series yield the location of the quantum phase transition and the correlation-length exponent ν as a function of space dimension d . The results are complemented by 1 /d expansions to next-to-leading order of observables across the phase diagrams. Remarkably, our analysis of the extrapolated linked-cluster expansion allows to extract the coefficients of the full 1 /d expansion for the phase-boundary location in both models exactly in leading order and quantitatively for subleading corrections.

  10. A universal quantum key distribution method

    NASA Astrophysics Data System (ADS)

    Zhang, He-qing; Zhou, Yuan-yuan; Zhou, Xue-jun; Tian, Pei-gen

    2013-09-01

    Combining heralded pair coherent state (HPCS) with passive decoy-state idea, a new method is presented for quantum key distribution (QKD). The weak coherent source (WCS) and heralded single photon source (HSPS) are the most common photon sources for state-of-the-art QKD. However, there is a prominent crossover between the maximum secure distance and the secure key generation rate if these two sources are applied in a practical decoy-state QKD. The method in this paper does not prepare decoy states actively. Therefore, it uses the same experimental setup as the conventional protocol, and there is no need for a hardware change, so its implementation is very easy. Furthermore, the method can obtain a longer secure transmission distance, and its key generation rate is higher than that of the passive decoy-state method with WCS or HSPS in the whole secure transmission distance. Thus, the limitation of the mentioned photo sources for QKD is broken through. So the method is universal in performance and implementation.

  11. Description of an α-cluster tail in 8Be and 20Ne: Delocalization of the α cluster by quantum penetration

    NASA Astrophysics Data System (ADS)

    Kanada-En'yo, Yoshiko

    2014-10-01

    We analyze the α-cluster wave functions in cluster states of ^8Be and ^{20}Ne by comparing the exact relative wave function obtained by the generator coordinate method (GCM) with various types of trial functions. For the trial functions, we adopt the fixed range shifted Gaussian of the Brink-Bloch (BB) wave function, the spherical Gaussian with the adjustable range parameter of the spherical Tohsaki-Horiuchi-Schuck-Röpke (sTHSR), the deformed Gaussian of the deformed THSR (dTHSR), and a function with the Yukawa tail (YT). The quality of the description of the exact wave function with a trial function is judged by the squared overlap between the trial function and the GCM wave function. A better result is obtained with the sTHSR wave function than the BB wave function, and further improvement can be made with the dTHSR wave function because these wave functions can describe the outer tail better. The YT wave function gives almost an equal quality to or even better quality than the dTHSR wave function, indicating that the outer tail of α-cluster states is characterized by the Yukawa-like tail rather than the Gaussian tail. In weakly bound α-cluster states with small α separation energy and the low centrifugal and Coulomb barriers, the outer tail part is the slowly damping function described well by the quantum penetration through the effective barrier. This outer tail characterizes the almost zero-energy free α gas behavior, i.e., the delocalization of the cluster.

  12. Understanding the evolution of luminescent gold quantum clusters in protein templates.

    PubMed

    Chaudhari, Kamalesh; Xavier, Paulrajpillai Lourdu; Pradeep, Thalappil

    2011-11-22

    We show that the time-dependent biomineralization of Au(3+) by native lactoferrin (NLf) and bovine serum albumin (BSA) resulting in near-infrared (NIR) luminescent gold quantum clusters (QCs) occurs through a protein-bound Au(1+) intermediate and subsequent emergence of free protein. The evolution was probed by diverse tools, principally, using matrix-assisted laser desorption ionization mass spectrometry (MALDI MS), X-ray photoelectron spectroscopy (XPS), and photoluminescence spectroscopy (PL). The importance of alkaline pH in the formation of clusters was probed. At neutral pH, a Au(1+)-protein complex was formed (starting from Au(3+)) with the binding of 13-14 gold atoms per protein. When the pH was increased above 12, these bound gold ions were further reduced to Au(0) and nucleation and growth of cluster commenced, which was corroborated by the beginning of emission; at this point, the number of gold atoms per protein was ~25, suggesting the formation of Au(25). During the cluster evolution, at certain time intervals, for specific molar ratios of gold and protein, occurrence of free protein was noticed in the mass spectra, suggesting a mixture of products and gold ion redistribution. By providing gold ions at specific time of the reaction, monodispersed clusters with enhanced luminescence could be obtained, and the available quantity of free protein could be utilized efficiently. Monodispersed clusters would be useful in obtaining single crystals of protein-protected noble metal quantum clusters where homogeneity of the system is of primary concern.

  13. An answer checking method for quantum annealers

    NASA Astrophysics Data System (ADS)

    Perera, Dilina; Novotny, M. A.

    2016-09-01

    We present a generic approach for checking the validity of the solutions returned by quantum annealing devices to aid in the analysis of whether the solution is the true ground state of the desired problem. The underlying principle is to embed a mirrored graph G' of the original graph G, and connect the two graphs via strong ferromagnetic/antiferromagnetic couplings that span across the mirror plane. This allows one to dismiss solutions that do not agree with the underlying mirror symmetry inherent to the true ground state of the composite graph. Using a 1000 qubit D-Wave 2X device, we demonstrate this method by applying it to spin glass problems defined on the device's native Chimera architecture.

  14. QUANTUM CALCULATIONS OF ENERGETICS OF RHENIUM CLUSTERS IN TUNGSTEN

    SciTech Connect

    Setyawan, Wahyu; Nandipati, Giridhar; Roche, Kenneth J.; Kurtz, Richard J.; Wirth, Brian D.

    2015-09-22

    Density functional theory was employed to explore the energetic properties of clusters up to size 2 of Re in W. While WW<111> is the most stable intrinsic dumbbell, ReW<110> is more stable than ReW<111>. However, when they are trapped by a substitutional Re (Re_s), ReW<111> becomes more stable than ReW<110>. In this case, the most stable configuration forms a ReWRe crowdion with the W atom in between the Re atoms. Simulations of a ReW[111] (dumbbell’s vector is from Re to W) approaching a Re_s along [111] indicate that the binding energy decreases from 0.83 eV at the first nearest neighbor (NN1) to 0.10 eV at NN3 and ~0 at NN4. In addition, while ReW<111> and ReW<110> are stable near a Re_s at NN1, the ReW<100> instantaneously rotates toward ReW<111>.

  15. Toward demonstrating controlled-X operation based on continuous-variable four-partite cluster states and quantum teleporters

    SciTech Connect

    Wang Yu; Su Xiaolong; Shen Heng; Tan Aihong; Xie Changde; Peng Kunchi

    2010-02-15

    One-way quantum computation based on measurement and multipartite cluster entanglement offers the ability to perform a variety of unitary operations only through different choices of measurement bases. Here we present an experimental study toward demonstrating the controlled-X operation, a two-mode gate in which continuous variable (CV) four-partite cluster states of optical modes are utilized. Two quantum teleportation elements are used for achieving the gate operation of the quantum state transformation from input target and control states to output states. By means of the optical cluster state prepared off-line, the homodyne detection and electronic feeding forward, the information carried by the input control state is transformed to the output target state. The presented scheme of the controlled-X operation based on teleportation can be implemented nonlocally and deterministically. The distortion of the quantum information resulting from the imperfect cluster entanglement is estimated with the fidelity.

  16. Minimal Model of Quantum Kinetic Clusters for the Energy-Transfer Network of a Light-Harvesting Protein Complex.

    PubMed

    Wu, Jianlan; Tang, Zhoufei; Gong, Zhihao; Cao, Jianshu; Mukamel, Shaul

    2015-04-01

    The energy absorbed in a light-harvesting protein complex is often transferred collectively through aggregated chromophore clusters. For population evolution of chromophores, the time-integrated effective rate matrix allows us to construct quantum kinetic clusters quantitatively and determine the reduced cluster-cluster transfer rates systematically, thus defining a minimal model of energy-transfer kinetics. For Fenna-Matthews-Olson (FMO) and light-havrvesting complex II (LCHII) monomers, quantum Markovian kinetics of clusters can accurately reproduce the overall energy-transfer process in the long-time scale. The dominant energy-transfer pathways are identified in the picture of aggregated clusters. The chromophores distributed extensively in various clusters can assist a fast and long-range energy transfer.

  17. Luminescent, bimetallic AuAg alloy quantum clusters in protein templates

    NASA Astrophysics Data System (ADS)

    Mohanty, Jyoti Sarita; Xavier, P. Lourdu; Chaudhari, Kamalesh; Bootharaju, M. S.; Goswami, N.; Pal, S. K.; Pradeep, T.

    2012-06-01

    We report the synthesis of luminescent AuAg alloy quantum clusters (QCs) in bovine serum albumin (BSA), for the first time, with experimentally determined atomic composition. Mixing of the as-synthesized protein-protected Au and Ag clusters resulted in the formation of alloy AuAg clusters within the BSA. Mass spectrometric analysis of the product of a 1 : 1 molar ratio reaction mixture of AuQC@BSA and AgQC@BSA suggested that the alloy clusters could be Au38-xAgx@BSA. Further analyses by standard techniques revealed that the alloy cluster core of ~1.2 nm diameter is composed of nearly zero valent Au and Ag atoms that exhibit distinctly different steady state and time resolved excited state luminescence profiles compared to the parent clusters. Tuning of the alloy composition was achieved by varying the molar ratio of the parent species in the reaction mixture and compositional changes were observed by mass spectrometry. In another approach, mixing of Au3+ ions with the as-synthesized AgQC@BSA also resulted in the formation of alloy clusters through galvanic exchange reactions. We believe that alloy clusters with the combined properties of the constituents in versatile protein templates would have potential applications in the future. The work presents interesting aspects of the reactivity of the protein-protected clusters.We report the synthesis of luminescent AuAg alloy quantum clusters (QCs) in bovine serum albumin (BSA), for the first time, with experimentally determined atomic composition. Mixing of the as-synthesized protein-protected Au and Ag clusters resulted in the formation of alloy AuAg clusters within the BSA. Mass spectrometric analysis of the product of a 1 : 1 molar ratio reaction mixture of AuQC@BSA and AgQC@BSA suggested that the alloy clusters could be Au38-xAgx@BSA. Further analyses by standard techniques revealed that the alloy cluster core of ~1.2 nm diameter is composed of nearly zero valent Au and Ag atoms that exhibit distinctly different

  18. Absence of actual plateaus in zero-temperature magnetization curves of quantum spin clusters and chains

    NASA Astrophysics Data System (ADS)

    Ohanyan, Vadim; Rojas, Onofre; Strečka, Jozef; Bellucci, Stefano

    2015-12-01

    We examine the general features of the noncommutativity of the magnetization operator and Hamiltonian for small quantum spin clusters. The source of this noncommutativity can be a difference in the Landé g factors for different spins in the cluster, X Y anisotropy in the exchange interaction, and the presence of the Dzyaloshinskii-Moriya term in a direction different from the direction of the magnetic field. As a result, zero-temperature magnetization curves for small spin clusters mimic those for the macroscopic systems with the band(s) of magnetic excitations, i.e., for the given eigenstate of the spin cluster the corresponding magnetic moment can be an explicit function of the external magnetic field yielding the nonconstant (nonplateau) form of the magnetization curve within the given eigenstate. In addition, the X Y anisotropy makes the saturated magnetization (the eigenstate when all spins in cluster are aligned along the magnetic field) inaccessible for finite magnetic field magnitude (asymptotical saturation). We demonstrate all these features on three examples: a spin-1/2 dimer, mixed spin-(1/2,1) dimer, and a spin-1/2 ring trimer. We consider also the simplest Ising-Heisenberg chain, the Ising-X Y Z diamond chain, with four different g factors. In the chain model the magnetization curve has a more complicated and nontrivial structure than that for clusters.

  19. Quantum monte carlo study of the energetics of small hydrogenated and fluoride lithium clusters.

    PubMed

    Moreira, N L; Brito, B G A; Rabelo, J N Teixeira; Cândido, Ladir

    2016-06-30

    An investigation of the energetics of small lithium clusters doped either with a hydrogen or with a fluorine atom as a function of the number of lithium atoms using fixed-node diffusion quantum Monte Carlo (DMC) simulation is reported. It is found that the binding energy (BE) for the doped clusters increases in absolute values leading to a more stable system than for the pure ones in excellent agreement with available experimental measurements. The BE increases for pure, remains almost constant for hydrogenated, and decreases rapidly toward the bulk lithium for the fluoride as a function of the number of lithium atoms in the clusters. The BE, dissociation energy as well as the second difference in energy display a pronounced odd-even oscillation with the number of lithium atoms. The electron correlation inverts the odd-even oscillation pattern for the doped in comparison with the pure clusters and has an impact of 29%-83% to the BE being higher in the pure cluster followed by the hydrogenated and then by the fluoride. The dissociation energy and the second difference in energy indicate that the doped cluster Li3 H is the most stable whereas among the pure ones the more stable are Li2 , Li4 , and Li6 . The electron correlation energy is crucial for the stabilization of Li3 H. © 2016 Wiley Periodicals, Inc. PMID:26992447

  20. Preparation of Aun quantum clusters with catalytic activity in β-cyclodextrin polyurethane nanosponges.

    PubMed

    Vasconcelos, Diego Andrade; Kubota, Tatiana; Santos, Douglas C; Araujo, Marcia V G; Teixeira, Zaine; Gimenez, Iara F

    2016-01-20

    Here we report the use of β-cyclodextrin polyurethane nanosponges cross-linked with 1,6-hexamethylene diisocyanate as a template for the preparation of Aun quantum clusters, by the core-etching of glutathione-capped Au nanoparticles. The study of temporal evolution of the core-etching process using different Au concentrations indicated that formation of Aun clusters embedded in the nanosponge is favored by the use of lower Au concentrations, since it began at shorter times and lead to higher cluster loading. An estimation of the number of Au atoms based on the maximum photoluminescence wavelength suggested that, depending on the Au concentration and the core etching time, clusters with 11-15 atoms were formed. After excluding the possibility of an inclusion complex formation, evaluation of the catalytic activity of nanosponge-loaded Aun clusters toward the reduction of 4-nitrophenol has shown that the reaction is catalyzed by the Aun clusters with no induction time, following the Langmuir-Hinshelwood kinetic model.

  1. Preparation of Aun quantum clusters with catalytic activity in β-cyclodextrin polyurethane nanosponges.

    PubMed

    Vasconcelos, Diego Andrade; Kubota, Tatiana; Santos, Douglas C; Araujo, Marcia V G; Teixeira, Zaine; Gimenez, Iara F

    2016-01-20

    Here we report the use of β-cyclodextrin polyurethane nanosponges cross-linked with 1,6-hexamethylene diisocyanate as a template for the preparation of Aun quantum clusters, by the core-etching of glutathione-capped Au nanoparticles. The study of temporal evolution of the core-etching process using different Au concentrations indicated that formation of Aun clusters embedded in the nanosponge is favored by the use of lower Au concentrations, since it began at shorter times and lead to higher cluster loading. An estimation of the number of Au atoms based on the maximum photoluminescence wavelength suggested that, depending on the Au concentration and the core etching time, clusters with 11-15 atoms were formed. After excluding the possibility of an inclusion complex formation, evaluation of the catalytic activity of nanosponge-loaded Aun clusters toward the reduction of 4-nitrophenol has shown that the reaction is catalyzed by the Aun clusters with no induction time, following the Langmuir-Hinshelwood kinetic model. PMID:26572328

  2. Luminescent quantum clusters of gold in transferrin family protein, lactoferrin exhibiting FRET

    NASA Astrophysics Data System (ADS)

    Xavier, Paulrajpillai Lourdu; Chaudhari, Kamalesh; Verma, Pramod Kumar; Pal, Samir Kumar; Pradeep, Thalappil

    2010-12-01

    We report the synthesis of highly luminescent, water soluble quantum clusters (QCs) of gold, which are stabilized by an iron binding transferrin family protein, lactoferrin (Lf). The synthesized AuQC@Lfclusters were characterized using UV-Visiblespectroscopy, X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), photoluminescence (PL), matrix assisted laser desorption ionizationmass spectrometry (MALDI-MS), FTIR spectroscopy and circular dichroism (CD) spectroscopy along with picosecond-resolved lifetime measurements. Detailed investigations with FTIR and CD spectroscopy have revealed changes in the secondary structure of the protein in the cluster. We have also studied Förster resonance energy transfer (FRET) occurring between the protein and the cluster. The ability of the clusters to sense cupric ions selectively at ppm concentrations was tested. The stability of clusters in widely varying pH conditions and their continued luminescence make it feasible for them to be used for intracellular imaging and molecular delivery, particularly in view of Lf protection.We report the synthesis of highly luminescent, water soluble quantum clusters (QCs) of gold, which are stabilized by an iron binding transferrin family protein, lactoferrin (Lf). The synthesized AuQC@Lfclusters were characterized using UV-Visiblespectroscopy, X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), photoluminescence (PL), matrix assisted laser desorption ionizationmass spectrometry (MALDI-MS), FTIR spectroscopy and circular dichroism (CD) spectroscopy along with picosecond-resolved lifetime measurements. Detailed investigations with FTIR and CD spectroscopy have revealed changes in the secondary structure of the protein in the cluster. We have also studied Förster resonance energy transfer (FRET) occurring between the protein and the cluster. The ability of the clusters to sense cupric ions selectively at ppm concentrations was tested. The

  3. Spectral methods in quantum field theory and quantum cosmology

    NASA Astrophysics Data System (ADS)

    Esposito, Giampiero; Fucci, Guglielmo; Kamenshchik, Alexander Yu; Kirsten, Klaus

    2012-09-01

    We review the application of the spectral zeta function to the one-loop properties of quantum field theories on manifolds with boundary, with emphasis on Euclidean quantum gravity and quantum cosmology. As was shown in the literature some time ago, the only boundary conditions that are completely invariant under infinitesimal diffeomorphisms on metric perturbations suffer from a drawback, i.e. lack of strong ellipticity of the resulting boundary-value problem. Nevertheless, at least on the Euclidean 4-ball background, it remains possible to evaluate the ζ(0) value, which describes in this case a universe which, in the limit of small 3-geometry, has vanishing probability of approaching the cosmological singularity. An assessment of this result is performed here, discussing its physical and mathematical implications. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical in honour of Stuart Dowker’s 75th birthday devoted to ‘Applications of zeta functions and other spectral functions in mathematics and physics’.

  4. Lieb-Liniger-like model of quantum solvation in CO-(4)HeN clusters.

    PubMed

    Farrelly, D; Iñarrea, M; Lanchares, V; Salas, J P

    2016-05-28

    Small (4)He clusters doped with various molecules allow for the study of "quantum solvation" as a function of cluster size. A peculiarity of quantum solvation is that, as the number of (4)He atoms is increased from N = 1, the solvent appears to decouple from the molecule which, in turn, appears to undergo free rotation. This is generally taken to signify the onset of "microscopic superfluidity." Currently, little is known about the quantum mechanics of the decoupling mechanism, mainly because the system is a quantum (N + 1)-body problem in three dimensions which makes computations difficult. Here, a one-dimensional model is studied in which the (4)He atoms are confined to revolve on a ring and encircle a rotating CO molecule. The Lanczos algorithm is used to investigate the eigenvalue spectrum as the number of (4)He atoms is varied. Substantial solvent decoupling is observed for as few as N = 5 (4)He atoms. Examination of the Hamiltonian matrix, which has an almost block diagonal structure, reveals increasingly weak inter-block (solvent-molecule) coupling as the number of (4)He atoms is increased. In the absence of a dopant molecule the system is similar to a Lieb-Liniger (LL) gas and we find a relatively rapid transition to the LL limit as N is increased. In essence, the molecule initially-for very small N-provides a central, if relatively weak, attraction to organize the cluster; as more (4)He atoms are added, the repulsive interactions between the identical bosons start to dominate as the solvation ring (shell) becomes more crowded which causes the molecule to start to decouple. For low N, the molecule pins the atoms in place relative to itself; as N increases the atom-atom repulsion starts to dominate the Hamiltonian and the molecule decouples. We conclude that, while the notion of superfluidity is a useful and correct description of the decoupling process, a molecular viewpoint provides complementary insights into the quantum mechanism of the transition from a

  5. Lieb-Liniger-like model of quantum solvation in CO-4HeN clusters

    NASA Astrophysics Data System (ADS)

    Farrelly, D.; Iñarrea, M.; Lanchares, V.; Salas, J. P.

    2016-05-01

    Small 4He clusters doped with various molecules allow for the study of "quantum solvation" as a function of cluster size. A peculiarity of quantum solvation is that, as the number of 4He atoms is increased from N = 1, the solvent appears to decouple from the molecule which, in turn, appears to undergo free rotation. This is generally taken to signify the onset of "microscopic superfluidity." Currently, little is known about the quantum mechanics of the decoupling mechanism, mainly because the system is a quantum (N + 1)-body problem in three dimensions which makes computations difficult. Here, a one-dimensional model is studied in which the 4He atoms are confined to revolve on a ring and encircle a rotating CO molecule. The Lanczos algorithm is used to investigate the eigenvalue spectrum as the number of 4He atoms is varied. Substantial solvent decoupling is observed for as few as N = 5 4He atoms. Examination of the Hamiltonian matrix, which has an almost block diagonal structure, reveals increasingly weak inter-block (solvent-molecule) coupling as the number of 4He atoms is increased. In the absence of a dopant molecule the system is similar to a Lieb-Liniger (LL) gas and we find a relatively rapid transition to the LL limit as N is increased. In essence, the molecule initially—for very small N—provides a central, if relatively weak, attraction to organize the cluster; as more 4He atoms are added, the repulsive interactions between the identical bosons start to dominate as the solvation ring (shell) becomes more crowded which causes the molecule to start to decouple. For low N, the molecule pins the atoms in place relative to itself; as N increases the atom-atom repulsion starts to dominate the Hamiltonian and the molecule decouples. We conclude that, while the notion of superfluidity is a useful and correct description of the decoupling process, a molecular viewpoint provides complementary insights into the quantum mechanism of the transition from a molecular

  6. Lieb-Liniger-like model of quantum solvation in CO-(4)HeN clusters.

    PubMed

    Farrelly, D; Iñarrea, M; Lanchares, V; Salas, J P

    2016-05-28

    Small (4)He clusters doped with various molecules allow for the study of "quantum solvation" as a function of cluster size. A peculiarity of quantum solvation is that, as the number of (4)He atoms is increased from N = 1, the solvent appears to decouple from the molecule which, in turn, appears to undergo free rotation. This is generally taken to signify the onset of "microscopic superfluidity." Currently, little is known about the quantum mechanics of the decoupling mechanism, mainly because the system is a quantum (N + 1)-body problem in three dimensions which makes computations difficult. Here, a one-dimensional model is studied in which the (4)He atoms are confined to revolve on a ring and encircle a rotating CO molecule. The Lanczos algorithm is used to investigate the eigenvalue spectrum as the number of (4)He atoms is varied. Substantial solvent decoupling is observed for as few as N = 5 (4)He atoms. Examination of the Hamiltonian matrix, which has an almost block diagonal structure, reveals increasingly weak inter-block (solvent-molecule) coupling as the number of (4)He atoms is increased. In the absence of a dopant molecule the system is similar to a Lieb-Liniger (LL) gas and we find a relatively rapid transition to the LL limit as N is increased. In essence, the molecule initially-for very small N-provides a central, if relatively weak, attraction to organize the cluster; as more (4)He atoms are added, the repulsive interactions between the identical bosons start to dominate as the solvation ring (shell) becomes more crowded which causes the molecule to start to decouple. For low N, the molecule pins the atoms in place relative to itself; as N increases the atom-atom repulsion starts to dominate the Hamiltonian and the molecule decouples. We conclude that, while the notion of superfluidity is a useful and correct description of the decoupling process, a molecular viewpoint provides complementary insights into the quantum mechanism of the transition from a

  7. A liquid drop model for embedded atom method cluster energies

    NASA Technical Reports Server (NTRS)

    Finley, C. W.; Abel, P. B.; Ferrante, J.

    1996-01-01

    Minimum energy configurations for homonuclear clusters containing from two to twenty-two atoms of six metals, Ag, Au, Cu, Ni, Pd, and Pt have been calculated using the Embedded Atom Method (EAM). The average energy per atom as a function of cluster size has been fit to a liquid drop model, giving estimates of the surface and curvature energies. The liquid drop model gives a good representation of the relationship between average energy and cluster size. As a test the resulting surface energies are compared to EAM surface energy calculations for various low-index crystal faces with reasonable agreement.

  8. Spatial clustering method based on three-dimensional cloud model

    NASA Astrophysics Data System (ADS)

    Wang, Haijun; Wang, Li; Deng, Yu; Liu, Jia

    2008-12-01

    Spatial clustering is one of those major methods applying to spatial data mining and knowledge discovery. The purpose of this paper is to set forth Spatial Clustering Method Based on Multidimensional Cloud Model, which can be widely applied to the research on classification and hierarchy in realm of spatial data mining and knowledge discovery. This paper summarizes all kinds of cloud model and analyzes the optimalizing form of spatial data-three-dimensional cloud model. The limitation which sets the weighing value subjectively in traditional way and propagation of error can be avoided. The implementation procedure of this method is advanced, and the feasibility of this method is proven through experiments effectively.

  9. Method and apparatus for the production of cluster ions

    DOEpatents

    Friedman, L.; Beuhler, R.J.

    A method and apparatus for the production of cluster ions, and preferably isotopic hydrogen cluster ions is disclosed. A gas, preferably comprising a carrier gas and a substrate gas, is cooled to about its boiling point and expanded through a supersonic nozzle into a region maintained at a low pressure. Means are provided for the generation of a plasma in the gas before or just as it enters the nozzle.

  10. Method and apparatus for the production of cluster ions

    DOEpatents

    Friedman, Lewis; Beuhler, Robert J.

    1988-01-01

    A method and apparatus for the production of cluster ions, and preferably isotopic hydrogen cluster ions is disclosed. A gas, preferably comprising a carrier gas and a substrate gas, is cooled to about its boiling point and expanded through a supersonic nozzle into a region maintained at a low pressure. Means are provided for the generation of a plasma in the gas before or just as it enters the nozzle.

  11. Cluster analysis of the DrugBank chemical space using molecular quantum numbers.

    PubMed

    Awale, Mahendra; Reymond, Jean-Louis

    2012-09-15

    DrugBank (>6000 approved and experimental drugs) was analyzed using molecular quantum numbers (MQNs), which are 42 integer value descriptors of molecular structure counting atoms, bonds, polar groups and topological features. Principal component analysis of MQN-space showed that drugs differ mostly by size (PC1, 67% variance) and structural rigidity and polarity (PC2, 18% variance). Twenty-eight groups of target specific drugs were recovered by proximity sorting in MQN-space as efficiently as by substructure fingerprint (SF) similarity, but in different order allowing for lead-hopping relationships not seen in SF similarity. Clustering by MQN- or SF-similarity produced very different types of clusters. Each of the 28 drug groups spread over different clusters in both MQN- and SF-clustering, and most clusters contained drugs from different target specific groups, showing that structure-based classifications only partially overlap with bioactivity. An MQN-browsable version of DrugBank is available at www.gdb.unibe.ch. PMID:22465859

  12. Method to study highly correlated nanostructures: The logarithmic-discretization embedded-cluster approximation

    NASA Astrophysics Data System (ADS)

    Anda, E. V.; Chiappe, G.; Büsser, C. A.; Davidovich, M. A.; Martins, G. B.; Heidrich-Meisner, F.; Dagotto, E.

    2008-08-01

    This work proposes an approach to study transport properties of highly correlated local structures. The method, dubbed the logarithmic discretization embedded cluster approximation (LDECA), consists of diagonalizing a finite cluster containing the many-body terms of the Hamiltonian and embedding it into the rest of the system, combined with Wilson’s idea of a logarithmic discretization of the representation of the Hamiltonian. The physics associated with both one embedded dot and a double-dot side coupled to leads is discussed in detail. In the former case, the results perfectly agree with Bethe ansatz data, while in the latter, the physics obtained is framed in the conceptual background of a two-stage Kondo problem. A many-body formalism provides a solid theoretical foundation to the method. We argue that LDECA is well suited to study complicated problems such as transport through molecules or quantum dot structures with complex ground states.

  13. Entangled quantum electronic wavefunctions of the Mn4CaO5 cluster in photosystem II

    NASA Astrophysics Data System (ADS)

    Kurashige, Yuki; Chan, Garnet Kin-Lic; Yanai, Takeshi

    2013-08-01

    It is a long-standing goal to understand the reaction mechanisms of catalytic metalloenzymes at an entangled many-electron level, but this is hampered by the exponential complexity of quantum mechanics. Here, by exploiting the special structure of physical quantum states and using the density matrix renormalization group, we compute near-exact many-electron wavefunctions of the Mn4CaO5 cluster of photosystem II, with more than 1 × 1018 quantum degrees of freedom. This is the first treatment of photosystem II beyond the single-electron picture of density functional theory. Our calculations support recent modifications to the structure determined by X-ray crystallography. We further identify multiple low-lying energy surfaces associated with the structural distortion seen using X-ray crystallography, highlighting multistate reactivity in the chemistry of the cluster. Direct determination of Mn spin-projections from our wavefunctions suggests that current candidates that have been recently distinguished using parameterized spin models should be reassessed. Through entanglement maps, we reveal rich information contained in the wavefunctions on bonding changes in the cycle.

  14. Entangled quantum electronic wavefunctions of the Mn₄CaO₅ cluster in photosystem II.

    PubMed

    Kurashige, Yuki; Chan, Garnet Kin-Lic; Yanai, Takeshi

    2013-08-01

    It is a long-standing goal to understand the reaction mechanisms of catalytic metalloenzymes at an entangled many-electron level, but this is hampered by the exponential complexity of quantum mechanics. Here, by exploiting the special structure of physical quantum states and using the density matrix renormalization group, we compute near-exact many-electron wavefunctions of the Mn4CaO5 cluster of photosystem II, with more than 1 × 10(18) quantum degrees of freedom. This is the first treatment of photosystem II beyond the single-electron picture of density functional theory. Our calculations support recent modifications to the structure determined by X-ray crystallography. We further identify multiple low-lying energy surfaces associated with the structural distortion seen using X-ray crystallography, highlighting multistate reactivity in the chemistry of the cluster. Direct determination of Mn spin-projections from our wavefunctions suggests that current candidates that have been recently distinguished using parameterized spin models should be reassessed. Through entanglement maps, we reveal rich information contained in the wavefunctions on bonding changes in the cycle. PMID:23881496

  15. Fluorescence Imaging Assisted Photodynamic Therapy Using Photosensitizer-Linked Gold Quantum Clusters.

    PubMed

    Nair, Lakshmi V; Nazeer, Shaiju S; Jayasree, Ramapurath S; Ajayaghosh, Ayyappanpillai

    2015-06-23

    Fluorescence imaging assisted photodynamic therapy (PDT) is a viable two-in-one clinical tool for cancer treatment and follow-up. While the surface plasmon effect of gold nanorods and nanoparticles has been effective for cancer therapy, their emission properties when compared to gold nanoclusters are weak for fluorescence imaging guided PDT. In order to address the above issues, we have synthesized a near-infrared-emitting gold quantum cluster capped with lipoic acid (L-AuC with (Au)18(L)14) based nanoplatform with excellent tumor reduction property by incorporating a tumor-targeting agent (folic acid) and a photosensitizer (protoporphyrin IX), for selective PDT. The synthesized quantum cluster based photosensitizer PFL-AuC showed 80% triplet quantum yield when compared to that of the photosensitizer alone (63%). PFL-AuC having 60 μg (0.136 mM) of protoporphyrin IX was sufficient to kill 50% of the tumor cell population. Effective destruction of tumor cells was evident from the histopathology and fluorescence imaging, which confirm the in vivo PDT efficacy of PFL-AuC. PMID:25970038

  16. Measurement-based method for verifying quantum discord

    NASA Astrophysics Data System (ADS)

    Rahimi-Keshari, Saleh; Caves, Carlton M.; Ralph, Timothy C.

    2013-01-01

    We introduce a measurement-based method for verifying quantum discord of any bipartite quantum system. We show that by performing an informationally complete positive operator valued measurement (IC-POVM) on one subsystem and checking the commutativity of the conditional states of the other subsystem, quantum discord from the second subsystem to the first can be verified. This is an improvement upon previous methods, which enables us to efficiently apply our method to continuous-variable systems, as IC-POVM's are readily available from homodyne or heterodyne measurements. We show that quantum discord for Gaussian states can be verified by checking whether the peaks of the conditional Wigner functions corresponding to two different outcomes of heterodyne measurement coincide at the same point in the phase space. Using this method, we also prove that the only Gaussian states with zero discord are product states; hence, Gaussian states with Gaussian discord have nonzero quantum discord.

  17. A New Method of Open Cluster Membership Determination

    NASA Astrophysics Data System (ADS)

    Gao, Xin-hua; Chen, Li; Hou, Zhen-jie

    2014-07-01

    Membership determination is the key-important step to study open clusters, which can directly influence on the estimation of open clusters’ physical parameters. DBSCAN (Density Based Spatial Clustering of Applications with Noise) is a density-based clustering algorithm in data mining techniques. In this paper the DBSCAN algorithm has been used for the first time to make the membership determination of the open clusters NGC 6791 and M 67 (NGC 2682). Our results indicate that the DBSCAN algorithm can effectively eliminate the contamination of field stars. The obtained member stars of NGC 6791 exhibit clearly a doubled main-sequence structure in the color-magnitude diagram, implying that NGC 6791 may have a more complicated history of star formation and evolution. The clustering analysis of M67 indicates the presence of mass segregation, and the distinct relative motion between the central part and the outer part of the cluster. These results demonstrate that the DBSCAN algorithm is an effective method of membership determination, and that it has some advantages superior to the conventional kinematic method.

  18. A Cluster-Based Method for Test Construction.

    ERIC Educational Resources Information Center

    Boekkooi-Timminga, Ellen

    1990-01-01

    A new test construction model based on the Rasch model is proposed. This model, the cluster-based method, considers groups of interchangeable items rather than individual items and uses integer programing. Results for six test construction problems indicate that the method produces accurate results in small amounts of time. (SLD)

  19. Nuclear quantum effects in water clusters: the role of the molecular flexibility.

    PubMed

    González, Briesta S; Noya, Eva G; Vega, Carlos; Sesé, Luis M

    2010-02-25

    With the objective of establishing the importance of water flexibility in empirical models which explicitly include nuclear quantum effects, we have carried out path integral Monte Carlo simulations in water clusters with up to seven molecules. Two recently developed models have been used for comparison: the rigid TIP4PQ/2005 and the flexible q-TIP4P/F models, both inspired by the rigid TIP4P/2005 model. To obtain a starting configuration for our simulations, we have located the global minima for the rigid TIP4P/2005 and TIP4PQ/2005 models and for the flexible q-TIP4P/F model. All the structures are similar to those predicted by the rigid TIP4P potential showing that the charge distribution mainly determines the global minimum structure. For the flexible q-TIP4P/F model, we have studied the geometrical distortion upon isotopic substitution by studying tritiated water clusters. Our results show that tritiated water clusters exhibit an r(OT) distance shorter than the r(OH) distance in water clusters, not significant changes in the Phi(HOH) angle, and a lower average dipole moment than water clusters. We have also carried out classical simulations with the rigid TIP4PQ/2005 model showing that the rotational kinetic energy is greatly affected by quantum effects, but the translational kinetic energy is only slightly modified. The potential energy is also noticeably higher than in classical simulations. Finally, as a concluding remark, we have calculated the formation energies of water clusters using both models, finding that the formation energies predicted by the rigid TIP4PQ/2005 model are lower by roughly 0.6 kcal/mol than those of the flexible q-TIP4P/F model for clusters of moderate size, the origin of this difference coming mainly from the geometrical distortion of the water molecule in the clusters that causes an increase in the intramolecular potential energy.

  20. New clustering methods for population comparison on paternal lineages.

    PubMed

    Juhász, Z; Fehér, T; Bárány, G; Zalán, A; Németh, E; Pádár, Z; Pamjav, H

    2015-04-01

    The goal of this study is to show two new clustering and visualising techniques developed to find the most typical clusters of 18-dimensional Y chromosomal haplogroup frequency distributions of 90 Western Eurasian populations. The first technique called "self-organizing cloud (SOC)" is a vector-based self-learning method derived from the Self Organising Map and non-metric Multidimensional Scaling algorithms. The second technique is a new probabilistic method called the "maximal relation probability" (MRP) algorithm, based on a probability function having its local maximal values just in the condensation centres of the input data. This function is calculated immediately from the distance matrix of the data and can be interpreted as the probability that a given element of the database has a real genetic relation with at least one of the remaining elements. We tested these two new methods by comparing their results to both each other and the k-medoids algorithm. By means of these new algorithms, we determined 10 clusters of populations based on the similarity of haplogroup composition. The results obtained represented a genetically, geographically and historically well-interpretable picture of 10 genetic clusters of populations mirroring the early spread of populations from the Fertile Crescent to the Caucasus, Central Asia, Arabia and Southeast Europe. The results show that a parallel clustering of populations using SOC and MRP methods can be an efficient tool for studying the demographic history of populations sharing common genetic footprints.

  1. Theory of the vortex-clustering transition in a confined two-dimensional quantum fluid

    NASA Astrophysics Data System (ADS)

    Yu, Xiaoquan; Billam, Thomas P.; Nian, Jun; Reeves, Matthew T.; Bradley, Ashton S.

    2016-08-01

    Clustering of like-sign vortices in a planar bounded domain is known to occur at negative temperature, a phenomenon that Onsager demonstrated to be a consequence of bounded phase space. In a confined superfluid, quantized vortices can support such an ordered phase, provided they evolve as an almost isolated subsystem containing sufficient energy. A detailed theoretical understanding of the statistical mechanics of such states thus requires a microcanonical approach. Here we develop an analytical theory of the vortex clustering transition in a neutral system of quantum vortices confined to a two-dimensional disk geometry, within the microcanonical ensemble. The choice of ensemble is essential for identifying the correct thermodynamic limit of the system, enabling a rigorous description of clustering in the language of critical phenomena. As the system energy increases above a critical value, the system develops global order via the emergence of a macroscopic dipole structure from the homogeneous phase of vortices, spontaneously breaking the Z2 symmetry associated with invariance under vortex circulation exchange, and the rotational SO (2 ) symmetry due to the disk geometry. The dipole structure emerges characterized by the continuous growth of the macroscopic dipole moment which serves as a global order parameter, resembling a continuous phase transition. The critical temperature of the transition, and the critical exponent associated with the dipole moment, are obtained exactly within mean-field theory. The clustering transition is shown to be distinct from the final state reached at high energy, known as supercondensation. The dipole moment develops via two macroscopic vortex clusters and the cluster locations are found analytically, both near the clustering transition and in the supercondensation limit. The microcanonical theory shows excellent agreement with Monte Carlo simulations, and signatures of the transition are apparent even for a modest system of 100

  2. Accurate method of modeling cluster scaling relations in modified gravity

    NASA Astrophysics Data System (ADS)

    He, Jian-hua; Li, Baojiu

    2016-06-01

    We propose a new method to model cluster scaling relations in modified gravity. Using a suite of nonradiative hydrodynamical simulations, we show that the scaling relations of accumulated gas quantities, such as the Sunyaev-Zel'dovich effect (Compton-y parameter) and the x-ray Compton-y parameter, can be accurately predicted using the known results in the Λ CDM model with a precision of ˜3 % . This method provides a reliable way to analyze the gas physics in modified gravity using the less demanding and much more efficient pure cold dark matter simulations. Our results therefore have important theoretical and practical implications in constraining gravity using cluster surveys.

  3. Galaxy Cluster Center Detection Methods with Weak Lensing

    NASA Astrophysics Data System (ADS)

    Simet, Melanie

    2013-01-01

    The precise location of galaxy cluster centers is a persistent problem in weak lensing mass estimates and in interpretations of clusters in a cosmological context. Misidentification of centers, either because a well-defined center does not exist or because candidate centers are incorrectly identified or ranked, leads to systematic underestimates of cluster masses. Weak lensing provides a potential lever on this issue by directly probing the distribution of dark matter. We test methods of determining cluster centers directly from weak lensing data and examine the effects of such self-calibration on the measured masses. Drawing on lensing data from the Sloan Digital Sky Survey Stripe 82, a 275 square degree region of coadded data in the Southern Galactic Cap, together with a catalog of MaxBCG clusters, we show that halo substructure as well as shape noise and stochasticity in galaxy positions limit the precision of such a self-calibration (in the context of Stripe 82, to ~500 h-1 kpc or larger) and bias the mass estimates around these points to a level that is likely unacceptable for the purposes of making cosmological measurements. In cases where other center identification methods fail, however, the method may still be useful to distinguish between competing options.

  4. Agent-based method for distributed clustering of textual information

    DOEpatents

    Potok, Thomas E [Oak Ridge, TN; Reed, Joel W [Knoxville, TN; Elmore, Mark T [Oak Ridge, TN; Treadwell, Jim N [Louisville, TN

    2010-09-28

    A computer method and system for storing, retrieving and displaying information has a multiplexing agent (20) that calculates a new document vector (25) for a new document (21) to be added to the system and transmits the new document vector (25) to master cluster agents (22) and cluster agents (23) for evaluation. These agents (22, 23) perform the evaluation and return values upstream to the multiplexing agent (20) based on the similarity of the document to documents stored under their control. The multiplexing agent (20) then sends the document (21) and the document vector (25) to the master cluster agent (22), which then forwards it to a cluster agent (23) or creates a new cluster agent (23) to manage the document (21). The system also searches for stored documents according to a search query having at least one term and identifying the documents found in the search, and displays the documents in a clustering display (80) of similarity so as to indicate similarity of the documents to each other.

  5. The secret of dimethyl sulfoxide-water mixtures. A quantum chemical study of 1DMSO-nwater clusters.

    PubMed

    Kirchner, Barbara; Reiher, Markus

    2002-05-29

    DMSO-water mixtures exhibit a marked freezing point depression, reaching close to 60 K at n(DMSO) = 0.33. The phase diagram indicates that stable DMSO-water clusters may be responsible for this phenomenon. Using time-independent quantum chemical methods, we investigate possible candidates for stable supermolecules at mole fractions n(DMSO) = 0.25 and 0.33. The model clusters are built by adding various numbers of water molecules to a single DMSO molecule. Structures and interaction energetics are discussed in the light of experimental and theoretical results from the literature. A comparison with results from molecular dynamics simulations is of particular interest. Our optimized structures are spatially very different from those previously identified through MD simulations. To identify the structural patterns characterizing the clusters, we classify them on the basis of hydrogen-acceptor interactions. These are well separated on an interaction energy scale. For the hydrophobic interactions of the methyl groups with water, attractive interactions of up to 8 kJ/mol are found. In forming clusters corresponding to a range of different mole fractions, up to four water molecules are added to each DMSO molecule. This corresponds to a rough local model of solvation. Examination of the trends in the interactions indicates that the methyl-water interaction becomes more important upon solvation. Finally, we investigate how the clusters interact and attempt to explain which role is played by the various structures and their intercluster interaction modes in the freezing behavior of DMSO-water.

  6. Quantum Cloning of an Unknown 2-Atom State via Entangled Cluster States

    NASA Astrophysics Data System (ADS)

    Yu, L.-z.; Zhong, F.

    2016-06-01

    This paper presented a scheme for cloning a 2-atom state in the QED cavity with the help of Victor who is the state's preparer. The cloning scheme has two steps. In the first step, the scheme requires probabilistic teleportation of a 2-atom state that is unknown in advance, and uses a 4-atom cluster state as quantum channel. In the second step, perfect copies of the 2-atom entangled state may be realized with the assistance of Victor. The finding is that our scheme has two outstanding advantages: it is not sensitive to the cavity decay, and Bell state is easy to identify.

  7. Entanglement percolation on a quantum internet with scale-free and clustering characters

    SciTech Connect

    Wu Liang; Zhu Shiqun

    2011-11-15

    The applicability of entanglement percolation protocol to real Internet structure is investigated. If the current Internet can be used directly in the quantum regime, the protocol can provide a way to establish long-distance entanglement when the links are pure nonmaximally entangled states. This applicability is primarily due to the combination of scale-free degree distribution and a high level of clustering, both of which are widely observed in many natural and artificial networks including the current Internet. It suggests that the topology of real Internet may play an important role in entanglement establishment.

  8. Reexamining the Security of Controlled Quantum Secure Direct Communication by Using Four Particle Cluster States

    NASA Astrophysics Data System (ADS)

    Qin, Su-Juan

    2012-09-01

    A controlled quantum secure direct communication protocol (Zhang et al. in Int. J. Theor. Phys. 48:2971-2976, 2009) by using four particle cluster states was proposed recently. Yang et al. presented an attack with fake entangled particles (FEP attack) and gave an improvement (Yang et al. in Int. J. Theor. Phys. 50:395-400, 2010). In this paper, we reexamine the protocol's security and discover that, Bob can also take a different attack, disentanglement attack, to obtain Alice's secret message without controller's permission. Moreover, our attack strategy also works for Yang's improvement.

  9. Bipartite quantum channels using multipartite cluster-type entangled coherent states

    SciTech Connect

    Munhoz, P. P.; Semiao, F. L.; Roversi, J. A.; Vidiella-Barranco, A.

    2010-04-15

    We propose a particular encoding for bipartite entangled states derived from multipartite cluster-type entangled coherent states (CTECSs). We investigate the effects of amplitude damping on the entanglement content of this bipartite state, as well as its usefulness as a quantum channel for teleportation. We find interesting relationships among the amplitude of the coherent states constituting the CTECSs, the number of subsystems forming the logical qubits (redundancy), and the extent to which amplitude damping affects the entanglement of the channel. For instance, in the sense of sudden death of entanglement, given a fixed value of the initial coherent state amplitude, the entanglement life span is shortened if redundancy is increased.

  10. Solution of relativistic quantum optics problems using clusters of graphical processing units

    SciTech Connect

    Gordon, D.F. Hafizi, B.; Helle, M.H.

    2014-06-15

    Numerical solution of relativistic quantum optics problems requires high performance computing due to the rapid oscillations in a relativistic wavefunction. Clusters of graphical processing units are used to accelerate the computation of a time dependent relativistic wavefunction in an arbitrary external potential. The stationary states in a Coulomb potential and uniform magnetic field are determined analytically and numerically, so that they can used as initial conditions in fully time dependent calculations. Relativistic energy levels in extreme magnetic fields are recovered as a means of validation. The relativistic ionization rate is computed for an ion illuminated by a laser field near the usual barrier suppression threshold, and the ionizing wavefunction is displayed.

  11. Vortex clustering and universal scaling laws in two-dimensional quantum turbulence.

    PubMed

    Skaugen, Audun; Angheluta, Luiza

    2016-03-01

    We investigate numerically the statistics of quantized vortices in two-dimensional quantum turbulence using the Gross-Pitaevskii equation. We find that a universal -5/3 scaling law in the turbulent energy spectrum is intimately connected with the vortex statistics, such as number fluctuations and vortex velocity, which is also characterized by a similar scaling behavior. The -5/3 scaling law appearing in the power spectrum of vortex number fluctuations is consistent with the scenario of passive advection of isolated vortices by a turbulent superfluid velocity generated by like-signed vortex clusters. The velocity probability distribution of clustered vortices is also sensitive to spatial configurations, and exhibits a power-law tail distribution with a -5/3 exponent. PMID:27078291

  12. Low-energy spectrum of iron-sulfur clusters directly from many-particle quantum mechanics

    NASA Astrophysics Data System (ADS)

    Sharma, Sandeep; Sivalingam, Kantharuban; Neese, Frank; Chan, Garnet Kin-Lic

    2014-10-01

    Iron-sulfur clusters are a universal biological motif. They carry out electron transfer, redox chemistry and even oxygen sensing, in diverse processes including nitrogen fixation, respiration and photosynthesis. Their low-lying electronic states are key to their remarkable reactivity, but they cannot be directly observed. Here, we present the first ever quantum calculation of the electronic levels of [2Fe-2S] and [4Fe-4S] clusters free from any model assumptions. Our results highlight the limitations of long-standing models of their electronic structure. In particular, we demonstrate that the widely used Heisenberg double exchange model underestimates the number of states by one to two orders of magnitude, which can conclusively be traced to the absence of Fe dd excitations, thought to be important in these clusters. Furthermore, the electronic energy levels of even the same spin are dense on the scale of vibrational fluctuations and this provides a natural explanation for the ubiquity of these clusters in catalysis in nature.

  13. Select and Cluster: A Method for Finding Functional Networks of Clustered Voxels in fMRI

    PubMed Central

    DonGiovanni, Danilo

    2016-01-01

    Extracting functional connectivity patterns among cortical regions in fMRI datasets is a challenge stimulating the development of effective data-driven or model based techniques. Here, we present a novel data-driven method for the extraction of significantly connected functional ROIs directly from the preprocessed fMRI data without relying on a priori knowledge of the expected activations. This method finds spatially compact groups of voxels which show a homogeneous pattern of significant connectivity with other regions in the brain. The method, called Select and Cluster (S&C), consists of two steps: first, a dimensionality reduction step based on a blind multiresolution pairwise correlation by which the subset of all cortical voxels with significant mutual correlation is selected and the second step in which the selected voxels are grouped into spatially compact and functionally homogeneous ROIs by means of a Support Vector Clustering (SVC) algorithm. The S&C method is described in detail. Its performance assessed on simulated and experimental fMRI data is compared to other methods commonly used in functional connectivity analyses, such as Independent Component Analysis (ICA) or clustering. S&C method simplifies the extraction of functional networks in fMRI by identifying automatically spatially compact groups of voxels (ROIs) involved in whole brain scale activation networks.

  14. Select and Cluster: A Method for Finding Functional Networks of Clustered Voxels in fMRI

    PubMed Central

    DonGiovanni, Danilo

    2016-01-01

    Extracting functional connectivity patterns among cortical regions in fMRI datasets is a challenge stimulating the development of effective data-driven or model based techniques. Here, we present a novel data-driven method for the extraction of significantly connected functional ROIs directly from the preprocessed fMRI data without relying on a priori knowledge of the expected activations. This method finds spatially compact groups of voxels which show a homogeneous pattern of significant connectivity with other regions in the brain. The method, called Select and Cluster (S&C), consists of two steps: first, a dimensionality reduction step based on a blind multiresolution pairwise correlation by which the subset of all cortical voxels with significant mutual correlation is selected and the second step in which the selected voxels are grouped into spatially compact and functionally homogeneous ROIs by means of a Support Vector Clustering (SVC) algorithm. The S&C method is described in detail. Its performance assessed on simulated and experimental fMRI data is compared to other methods commonly used in functional connectivity analyses, such as Independent Component Analysis (ICA) or clustering. S&C method simplifies the extraction of functional networks in fMRI by identifying automatically spatially compact groups of voxels (ROIs) involved in whole brain scale activation networks. PMID:27656202

  15. A Quantum-Based Similarity Method in Virtual Screening.

    PubMed

    Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

    2015-10-02

    One of the most widely-used techniques for ligand-based virtual screening is similarity searching. This study adopted the concepts of quantum mechanics to present as state-of-the-art similarity method of molecules inspired from quantum theory. The representation of molecular compounds in mathematical quantum space plays a vital role in the development of quantum-based similarity approach. One of the key concepts of quantum theory is the use of complex numbers. Hence, this study proposed three various techniques to embed and to re-represent the molecular compounds to correspond with complex numbers format. The quantum-based similarity method that developed in this study depending on complex pure Hilbert space of molecules called Standard Quantum-Based (SQB). The recall of retrieved active molecules were at top 1% and top 5%, and significant test is used to evaluate our proposed methods. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints. Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.

  16. Clustering Methods with Qualitative Data: a Mixed-Methods Approach for Prevention Research with Small Samples.

    PubMed

    Henry, David; Dymnicki, Allison B; Mohatt, Nathaniel; Allen, James; Kelly, James G

    2015-10-01

    Qualitative methods potentially add depth to prevention research but can produce large amounts of complex data even with small samples. Studies conducted with culturally distinct samples often produce voluminous qualitative data but may lack sufficient sample sizes for sophisticated quantitative analysis. Currently lacking in mixed-methods research are methods allowing for more fully integrating qualitative and quantitative analysis techniques. Cluster analysis can be applied to coded qualitative data to clarify the findings of prevention studies by aiding efforts to reveal such things as the motives of participants for their actions and the reasons behind counterintuitive findings. By clustering groups of participants with similar profiles of codes in a quantitative analysis, cluster analysis can serve as a key component in mixed-methods research. This article reports two studies. In the first study, we conduct simulations to test the accuracy of cluster assignment using three different clustering methods with binary data as produced when coding qualitative interviews. Results indicated that hierarchical clustering, K-means clustering, and latent class analysis produced similar levels of accuracy with binary data and that the accuracy of these methods did not decrease with samples as small as 50. Whereas the first study explores the feasibility of using common clustering methods with binary data, the second study provides a "real-world" example using data from a qualitative study of community leadership connected with a drug abuse prevention project. We discuss the implications of this approach for conducting prevention research, especially with small samples and culturally distinct communities.

  17. Clustering Methods with Qualitative Data: A Mixed Methods Approach for Prevention Research with Small Samples

    PubMed Central

    Henry, David; Dymnicki, Allison B.; Mohatt, Nathaniel; Allen, James; Kelly, James G.

    2016-01-01

    Qualitative methods potentially add depth to prevention research, but can produce large amounts of complex data even with small samples. Studies conducted with culturally distinct samples often produce voluminous qualitative data, but may lack sufficient sample sizes for sophisticated quantitative analysis. Currently lacking in mixed methods research are methods allowing for more fully integrating qualitative and quantitative analysis techniques. Cluster analysis can be applied to coded qualitative data to clarify the findings of prevention studies by aiding efforts to reveal such things as the motives of participants for their actions and the reasons behind counterintuitive findings. By clustering groups of participants with similar profiles of codes in a quantitative analysis, cluster analysis can serve as a key component in mixed methods research. This article reports two studies. In the first study, we conduct simulations to test the accuracy of cluster assignment using three different clustering methods with binary data as produced when coding qualitative interviews. Results indicated that hierarchical clustering, K-Means clustering, and latent class analysis produced similar levels of accuracy with binary data, and that the accuracy of these methods did not decrease with samples as small as 50. Whereas the first study explores the feasibility of using common clustering methods with binary data, the second study provides a “real-world” example using data from a qualitative study of community leadership connected with a drug abuse prevention project. We discuss the implications of this approach for conducting prevention research, especially with small samples and culturally distinct communities. PMID:25946969

  18. New method for calculating binding energies in quantum mechanics and quantum field theories

    SciTech Connect

    Gat, G.; Rosenstein, B. Institute of Physics, Academia Sinica, Taipei, 11529 )

    1993-01-04

    We propose a systematic perturbative method for calculating the binding energy of threshold bound states---states which exist for arbitrary small coupling. The starting point is a (regularized) free theory. Explicit calculations are performed for quantum mechanics with arbitrary short-range potential in 1D and various (1+1)-dimensional quantum field theories. We check the method by comparing the results with exact formulas available in solvable models.

  19. Integrative clustering methods for high-dimensional molecular data

    PubMed Central

    Chalise, Prabhakar; Koestler, Devin C.; Bimali, Milan; Yu, Qing; Fridley, Brooke L.

    2014-01-01

    High-throughput ‘omic’ data, such as gene expression, DNA methylation, DNA copy number, has played an instrumental role in furthering our understanding of the molecular basis in states of human health and disease. As cells with similar morphological characteristics can exhibit entirely different molecular profiles and because of the potential that these discrepancies might further our understanding of patient-level variability in clinical outcomes, there is significant interest in the use of high-throughput ‘omic’ data for the identification of novel molecular subtypes of a disease. While numerous clustering methods have been proposed for identifying of molecular subtypes, most were developed for single “omic’ data types and may not be appropriate when more than one ‘omic’ data type are collected on study subjects. Given that complex diseases, such as cancer, arise as a result of genomic, epigenomic, transcriptomic, and proteomic alterations, integrative clustering methods for the simultaneous clustering of multiple ‘omic’ data types have great potential to aid in molecular subtype discovery. Traditionally, ad hoc manual data integration has been performed using the results obtained from the clustering of individual ‘omic’ data types on the same set of patient samples. However, such methods often result in inconsistent assignment of subjects to the molecular cancer subtypes. Recently, several methods have been proposed in the literature that offers a rigorous framework for the simultaneous integration of multiple ‘omic’ data types in a single comprehensive analysis. In this paper, we present a systematic review of existing integrative clustering methods. PMID:25243110

  20. Galaxy cluster center detection methods with weak lensing

    NASA Astrophysics Data System (ADS)

    Simet, Melanie

    The precise location of galaxy cluster centers is a persistent problem in weak lensing mass estimates and in interpretations of clusters in a cosmological context. In this work, we test methods of centroid determination from weak lensing data and examine the effects of such self-calibration on the measured masses. Drawing on lensing data from the Sloan Digital Sky Survey Stripe 82, a 275 square degree region of coadded data in the Southern Galactic Cap, together with a catalog of MaxBCG clusters, we show that halo substructure as well as shape noise and stochasticity in galaxy positions limit the precision of such a self-calibration (in the context of Stripe 82, to ˜ 500 h-1 kpc or larger) and bias the mass estimates around these points to a level that is likely unacceptable for the purposes of making cosmological measurements. We also project the usefulness of this technique in future surveys.

  1. Hybrid QTAIM and electrostatic potential-based quantum topology phase diagrams for water clusters.

    PubMed

    Kumar, Anmol; Gadre, Shridhar R; Chenxia, Xiao; Tianlv, Xu; Kirk, Steven Robert; Jenkins, Samantha

    2015-06-21

    The topological diversity of sets of isomers of water clusters (W = H2O)n, 7 ≤ n ≤ 10, is analyzed employing the scalar fields of total electronic charge density ρ(r) and the molecular electrostatic potential (MESP). The features uncovered by the MESP are shown to be complementary to those revealed by the theory of atoms in molecules (QTAIM) analysis. The MESP is known to exhibit the electron localizations such as lone pairs that are central to water cluster behavior. Therefore, a 'hybrid' QTAIM and MESP quantum topology phase diagram (QTPD) for Wn, 7 ≤ n ≤ 10, is introduced in addition to the QTPD. The 'spanning' QTPD with upper and lower bounds is constructed from the solutions of the Poincaré-Hopf relation involving the non-degenerate critical points. The changing subtle balance between the planar and three dimensional character of the growing water clusters Wn, 4 ≤ n ≤ 10, is revealed. Characterization of the structure of the QTPDs, possible with new tools, demonstrated the migration of the position of the global minimum on the spanning QTPD from the lower bound to upper bound as the Wn, 4 ≤ n ≤ 10, cluster grows in size. Differences in the structure of the QTPD are found between the clusters containing even versus odd monomers for Wn, n = 7-10. The energetic stability of the clusters which possess even number of monomers viz. n = 8, 10 is higher than that of the n = 7, 9 clusters due to relatively higher numbers of hydrogen-bond BCPs in the n = 8, 10 clusters, in agreement with energetic results reported in the literature. A 'hybrid' QTPD is created from a new chemical relation bHB + l ≥ 2n for Wn that relates the number of hydrogen-bond bond critical points (bHB) with the number of oxygen lone pairs exclusively specified by the negative valued MESP (3,+3) critical points (l). The topologies of the subset bHB + l = 2n for Wn, point the way to the discovery of unknown 'missing' lower energy isomers. A discussion of the relative merits and

  2. Method of preparing size-selected metal clusters

    DOEpatents

    Elam, Jeffrey W.; Pellin, Michael J.; Stair, Peter C.

    2010-05-11

    The invention provides a method for depositing catalytic clusters on a surface, the method comprising confining the surface to a controlled atmosphere; contacting the surface with catalyst containing vapor for a first period of time; removing the vapor from the controlled atmosphere; and contacting the surface with a reducing agent for a second period of time so as to produce catalyst-containing nucleation sites.

  3. Exciton photoluminescence and energy in a percolation cluster of ZnSe quantum dots as a fractal object

    SciTech Connect

    Bondar, N. V. Brodyn, M. S.

    2012-05-15

    The results of studies of samples containing ZnSe quantum dots with a density corresponding to or considerably higher than the exciton percolation threshold, at which quantum dots form conglomerates, are reported. Excitonic emission from a percolation cluster of bound quantum dots as a fractal object is observed for the first time. Analysis of the structure of the photoluminescence spectra shows that the spectra are determined by the contribution of exciton states that belong to different structural elements of the percolation cluster, specifically, to the skeleton (backbone), dangling (dead) ends, and internal hollow spaces. A qualitative model is proposed to interpret the dependence of the exciton energy in these structural elements on the concentration of quantum dots in the material.

  4. Electron density of states of Fe-based superconductors: Quantum trajectory Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Kashurnikov, V. A.; Krasavin, A. V.; Zhumagulov, Ya. V.

    2016-03-01

    The spectral and total electron densities of states in two-dimensional FeAs clusters, which simulate iron-based superconductors, have been calculated using the generalized quantum Monte Carlo algorithm within the full two-orbital model. Spectra have been reconstructed by solving the integral equation relating the Matsubara Green's function and spectral density by the method combining the gradient descent and Monte Carlo algorithms. The calculations have been performed for clusters with dimensions up to 10 × 10 FeAs cells. The profiles of the Fermi surface for the entire Brillouin zone have been presented in the quasiparticle approximation. Data for the total density of states near the Fermi level have been obtained. The effect of the interaction parameter, size of the cluster, and temperature on the spectrum of excitations has been studied.

  5. Solid oxide fuel cell anode image segmentation based on a novel quantum-inspired fuzzy clustering

    NASA Astrophysics Data System (ADS)

    Fu, Xiaowei; Xiang, Yuhan; Chen, Li; Xu, Xin; Li, Xi

    2015-12-01

    High quality microstructure modeling can optimize the design of fuel cells. For three-phase accurate identification of Solid Oxide Fuel Cell (SOFC) microstructure, this paper proposes a novel image segmentation method on YSZ/Ni anode Optical Microscopic (OM) images. According to Quantum Signal Processing (QSP), the proposed approach exploits a quantum-inspired adaptive fuzziness factor to adaptively estimate the energy function in the fuzzy system based on Markov Random Filed (MRF). Before defuzzification, a quantum-inspired probability distribution based on distance and gray correction is proposed, which can adaptively adjust the inaccurate probability estimation of uncertain points caused by noises and edge points. In this study, the proposed method improves accuracy and effectiveness of three-phase identification on the micro-investigation. It provides firm foundation to investigate the microstructural evolution and its related properties.

  6. Fast synthesize ZnO quantum dots via ultrasonic method.

    PubMed

    Yang, Weimin; Zhang, Bing; Ding, Nan; Ding, Wenhao; Wang, Lixi; Yu, Mingxun; Zhang, Qitu

    2016-05-01

    Green emission ZnO quantum dots were synthesized by an ultrasonic sol-gel method. The ZnO quantum dots were synthesized in various ultrasonic temperature and time. Photoluminescence properties of these ZnO quantum dots were measured. Time-resolved photoluminescence decay spectra were also taken to discover the change of defects amount during the reaction. Both ultrasonic temperature and time could affect the type and amount of defects in ZnO quantum dots. Total defects of ZnO quantum dots decreased with the increasing of ultrasonic temperature and time. The dangling bonds defects disappeared faster than the optical defects. Types of optical defects first changed from oxygen interstitial defects to oxygen vacancy and zinc interstitial defects. Then transformed back to oxygen interstitial defects again. The sizes of ZnO quantum dots would be controlled by both ultrasonic temperature and time as well. That is, with the increasing of ultrasonic temperature and time, the sizes of ZnO quantum dots first decreased then increased. Moreover, concentrated raw materials solution brought larger sizes and more optical defects of ZnO quantum dots.

  7. Collocation method for fractional quantum mechanics

    SciTech Connect

    Amore, Paolo; Hofmann, Christoph P.; Saenz, Ricardo A.; Fernandez, Francisco M.

    2010-12-15

    We show that it is possible to obtain numerical solutions to quantum mechanical problems involving a fractional Laplacian, using a collocation approach based on little sinc functions, which discretizes the Schroedinger equation on a uniform grid. The different boundary conditions are naturally implemented using sets of functions with the appropriate behavior. Good convergence properties are observed. A comparison with results based on a Wentzel-Kramers-Brillouin analysis is performed.

  8. Investigation of quantum confinement behavior of zinc sulphide quantum dots synthesized via various chemical methods

    SciTech Connect

    Jose, Meera Sakthivel, T. Chandran, Hrisheekesh T. Nivea, R. Gunasekaran, V.

    2014-10-15

    In this work, undoped and Ag-doped ZnS quantum dots were synthesized using various chemical methods. The products were characterized using X-ray diffraction (XRD), UV-visible spectroscopy and Photoluminescence spectroscopy. Our results revealed that the size of the as-prepared samples range from 1–6 nm in diameter and have a cubic zinc-blende structure. Also, we observed the emission of different wavelength of light from different sized quantum dots of the same material due to quantum confinement effect. The results will be presented in detail and ZnS can be a potential candidate for optical device development and applications.

  9. Methods of observation of the centrifugal quantum states of neutrons

    NASA Astrophysics Data System (ADS)

    Cubitt, R.; Nesvizhevsky, V. V.; Petukhov, A. K.; Voronin, A. Yu.; Pignol, G.; Protasov, K. V.; Gurshijants, P.

    2009-12-01

    We propose methods for observation of the quasi-stationary states of neutrons, localized near a curved mirror surface. The bounding effective well is formed by the centrifugal potential and the mirror's optical potential. This phenomenon is an example of an exactly solvable "quantum bouncer" problem that can be studied experimentally. It could provide a new tool for studying fundamental neutron-matter interactions, neutron quantum optics and surface physics effects. The feasibility of observation of such quantum states has been proven in first experiments.

  10. Unbiased methods for removing systematics from galaxy clustering measurements

    NASA Astrophysics Data System (ADS)

    Elsner, Franz; Leistedt, Boris; Peiris, Hiranya V.

    2016-02-01

    Measuring the angular clustering of galaxies as a function of redshift is a powerful method for extracting information from the three-dimensional galaxy distribution. The precision of such measurements will dramatically increase with ongoing and future wide-field galaxy surveys. However, these are also increasingly sensitive to observational and astrophysical contaminants. Here, we study the statistical properties of three methods proposed for controlling such systematics - template subtraction, basic mode projection, and extended mode projection - all of which make use of externally supplied template maps, designed to characterize and capture the spatial variations of potential systematic effects. Based on a detailed mathematical analysis, and in agreement with simulations, we find that the template subtraction method in its original formulation returns biased estimates of the galaxy angular clustering. We derive closed-form expressions that should be used to correct results for this shortcoming. Turning to the basic mode projection algorithm, we prove it to be free of any bias, whereas we conclude that results computed with extended mode projection are biased. Within a simplified setup, we derive analytical expressions for the bias and discuss the options for correcting it in more realistic configurations. Common to all three methods is an increased estimator variance induced by the cleaning process, albeit at different levels. These results enable unbiased high-precision clustering measurements in the presence of spatially varying systematics, an essential step towards realizing the full potential of current and planned galaxy surveys.

  11. Self-organized formation of quantum dots of a material on a substrate

    DOEpatents

    Zhang, Zhenyu; Wendelken, John F.; Chang, Ming-Che; Pai, Woei Wu

    2001-01-01

    Systems and methods are described for fabricating arrays of quantum dots. A method for making a quantum dot device, includes: forming clusters of atoms on a substrate; and charging the clusters of atoms such that the clusters of atoms repel one another. The systems and methods provide advantages because the quantum dots can be ordered with regard to spacing and/or size.

  12. CLUSTERING OF LARGE CELL POPULATIONS: METHOD AND APPLICATION TO THE BASAL FOREBRAIN CHOLINERGIC SYSTEM

    PubMed Central

    Nadasdy, Zoltan; Varsanyi, Peter; Zaborszky, Laszlo

    2010-01-01

    Functionally related groups of neurons spatially cluster together in the brain. To detect groups of functionally related neurons from 3D histological data, we developed an objective clustering method that provides a description of detected cell clusters that is quantitative and amenable to visual exploration. This method is based on bubble clustering (Gupta and Gosh, 2008). Our implementation consists of three steps: (i) an initial data exploration for scanning the clustering parameter space; (ii) determination of the optimal clustering parameters; (iii) final clustering. We designed this algorithm to flexibly detect clusters without assumptions about the underlying cell distribution within a cluster or the number and sizes of clusters. We implemented the clustering function as an integral part of the neuroanatomical data visualization software Virtual RatBrain (http://www.virtualratbrain.org). We applied this algorithm to the basal forebrain cholinergic system, which consists of a diffuse but inhomogeneous population of neurons (Zaborszky, 1992). With this clustering method, we confirmed the inhomogeneity in this system, defined cell clusters, quantified and localized them, and determined the cell density within clusters. Furthermore, by applying the clustering method to multiple specimens from both rat and monkey, we found that cholinergic clusters display remarkable cross-species preservation of cell density within clusters. This method is efficient not only for clustering cell body distributions but may also be used to study other distributed neuronal structural elements, including synapses, receptors, dendritic spines and molecular markers. PMID:20398701

  13. Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

    NASA Technical Reports Server (NTRS)

    Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

    2003-01-01

    Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

  14. Method to efficiently simulate the thermodynamic properties of the Fermi-Hubbard model on a quantum computer

    NASA Astrophysics Data System (ADS)

    Dallaire-Demers, Pierre-Luc; Wilhelm, Frank K.

    2016-03-01

    Many phenomena of strongly correlated materials are encapsulated in the Fermi-Hubbard model whose thermodynamic properties can be computed from its grand-canonical potential. In general, there is no closed-form expression of the grand-canonical potential for lattices of more than one spatial dimension, but solutions can be numerically approximated using cluster methods. To model long-range effects such as order parameters, a powerful method to compute the cluster's Green's function consists of finding its self-energy through a variational principle. This allows the possibility of studying various phase transitions at finite temperature in the Fermi-Hubbard model. However, a classical cluster solver quickly hits an exponential wall in the memory (or computation time) required to store the computation variables. Here it is shown theoretically that the cluster solver can be mapped to a subroutine on a quantum computer whose quantum memory usage scales linearly with the number of orbitals in the simulated cluster and the number of measurements scales quadratically. A quantum computer with a few tens of qubits could therefore simulate the thermodynamic properties of complex fermionic lattices inaccessible to classical supercomputers.

  15. A general method for selecting quantum channel for bidirectional controlled state teleportation and other schemes of controlled quantum communication

    NASA Astrophysics Data System (ADS)

    Thapliyal, Kishore; Verma, Amit; Pathak, Anirban

    2015-12-01

    Recently, a large number of protocols for bidirectional controlled state teleportation (BCST) have been proposed using n-qubit entangled states (nin {5,6,7}) as quantum channel. Here, we propose a general method of selecting multiqubit (n>4) quantum channels suitable for BCST and show that all the channels used in the existing protocols of BCST can be obtained using the proposed method. Further, it is shown that the quantum channels used in the existing protocols of BCST form only a negligibly small subset of the set of all the quantum channels that can be constructed using the proposed method to implement BCST. It is also noted that all these quantum channels are also suitable for controlled bidirectional remote state preparation. Following the same logic, methods for selecting quantum channels for other controlled quantum communication tasks, such as controlled bidirectional joint remote state preparation and controlled quantum dialogue, are also provided.

  16. Efficient method for the calculation of dissipative quantum transport in quantum cascade lasers.

    PubMed

    Greck, Peter; Birner, Stefan; Huber, Bernhard; Vogl, Peter

    2015-03-01

    We present a novel and very efficient method for calculating quantum transport in quantum cascade lasers (QCLs). It follows the nonequilibrium Green's function (NEGF) framework but sidesteps the calculation of lesser self-energies by replacing them by a quasi-equilibrium expression. This method generalizes the phenomenological Büttiker probe model by taking into account individual scattering mechanisms. It is orders of magnitude more efficient than a fully self-consistent NEGF calculation for realistic devices. We apply this method to a new THz QCL design which works up to 250 K - according to our calculations.

  17. Vertical nano superconducting quantum interference device based on Josepshon tunnel nanojunctions for small spin cluster detection

    NASA Astrophysics Data System (ADS)

    Granata, Carmine; Vettoliere, Antonio; Fretto, Matteo; Leo, Natascia De; Vincenzo, Lacquaniti

    2015-06-01

    The ultra high sensitivity exhibited by Superconducting Quantum Interference Device (SQUIDs) could be the key to explore new field of nanoscience such as the investigation of small cluster of elementary magnetic moments. In this paper, an ultra high sensitive niobium nanoSQUID based on submicron Josephson tunnel junction is presented. It has been fabricated in a vertical configuration by using a three-dimensional focused ion beam sculpting technique. In such a configuration, the nanosensor loop (area of 0.25 μm2) is perpendicular to the substrate plane allowing to drastically reduce the spurious effects of the external magnetic field employed to excite the nano-objects under investigation. Main device characteristics have been measured at T=4.2 K by using a low noise readout electronics. Due to high voltage responsivity, the nanosensor has exhibited a spectral density of the magnetic flux noise as low as 1.6 μΦ0/Hz1/2.

  18. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1981-01-01

    The application of ab initio quantum mechanical approaches in the study of metal atom clusters requires simplifying techniques that do not compromise the reliability of the calculations. Various aspects of the implementation of the effective core potential (ECP) technique for the removal of the metal atom core electrons from the calculation were examined. The ECP molecular integral formulae were modified to bring out the shell characteristics as a first step towards fulfilling the increasing need to speed up the computation of the ECP integrals. Work on the relationships among the derivatives of the molecular integrals that extends some of the techniques pioneered by Komornicki for the calculation of the gradients of the electronic energy was completed and a formulation of the ECP approach that quite naturally unifies the various state-of-the-art "shape- and Hamiltonian-consistent" techniques was discovered.

  19. Method for adding nodes to a quantum key distribution system

    DOEpatents

    Grice, Warren P

    2015-02-24

    An improved quantum key distribution (QKD) system and method are provided. The system and method introduce new clients at intermediate points along a quantum channel, where any two clients can establish a secret key without the need for a secret meeting between the clients. The new clients perform operations on photons as they pass through nodes in the quantum channel, and participate in a non-secret protocol that is amended to include the new clients. The system and method significantly increase the number of clients that can be supported by a conventional QKD system, with only a modest increase in cost. The system and method are compatible with a variety of QKD schemes, including polarization, time-bin, continuous variable and entanglement QKD.

  20. Numerical matrix method for quantum periodic potentials

    NASA Astrophysics Data System (ADS)

    Le Vot, Felipe; Meléndez, Juan J.; Yuste, Santos B.

    2016-06-01

    A numerical matrix methodology is applied to quantum problems with periodic potentials. The procedure consists essentially in replacing the true potential by an alternative one, restricted by an infinite square well, and in expressing the wave functions as finite superpositions of eigenfunctions of the infinite well. A matrix eigenvalue equation then yields the energy levels of the periodic potential within an acceptable accuracy. The methodology has been successfully used to deal with problems based on the well-known Kronig-Penney (KP) model. Besides the original model, these problems are a dimerized KP solid, a KP solid containing a surface, and a KP solid under an external field. A short list of additional problems that can be solved with this procedure is presented.

  1. Super pixel density based clustering automatic image classification method

    NASA Astrophysics Data System (ADS)

    Xu, Mingxing; Zhang, Chuan; Zhang, Tianxu

    2015-12-01

    The image classification is an important means of image segmentation and data mining, how to achieve rapid automated image classification has been the focus of research. In this paper, based on the super pixel density of cluster centers algorithm for automatic image classification and identify outlier. The use of the image pixel location coordinates and gray value computing density and distance, to achieve automatic image classification and outlier extraction. Due to the increased pixel dramatically increase the computational complexity, consider the method of ultra-pixel image preprocessing, divided into a small number of super-pixel sub-blocks after the density and distance calculations, while the design of a normalized density and distance discrimination law, to achieve automatic classification and clustering center selection, whereby the image automatically classify and identify outlier. After a lot of experiments, our method does not require human intervention, can automatically categorize images computing speed than the density clustering algorithm, the image can be effectively automated classification and outlier extraction.

  2. Electron and boson clusters in confined geometries: Symmetry breaking in quantum dots and harmonic traps

    PubMed Central

    Yannouleas, Constantine; Landman, Uzi

    2006-01-01

    We discuss the formation of crystalline electron clusters in semiconductor quantum dots and of crystalline patterns of neutral bosons in harmonic traps. In a first example, we use calculations for two electrons in an elliptic quantum dot to show that the electrons can localize and form a molecular dimer. The calculated singlet–triplet splitting (J) as a function of the magnetic field (B) agrees with cotunneling measurements with its behavior reflecting the effective dissociation of the dimer for large B. Knowledge of the dot shape and of J(B) allows determination of the degree of entanglement. In a second example, we study strongly repelling neutral bosons in two-dimensional harmonic traps. Going beyond the Gross–Pitaevskii (GP) mean-field approximation, we show that bosons can localize and form polygonal-ring-like crystalline patterns. The total energy of the crystalline phase saturates in contrast to the GP solution, and its spatial extent becomes smaller than that of the GP condensate. PMID:16740665

  3. Calculating Floquet states of large quantum systems: A parallelization strategy and its cluster implementation

    NASA Astrophysics Data System (ADS)

    Laptyeva, T. V.; Kozinov, E. A.; Meyerov, I. B.; Ivanchenko, M. V.; Denisov, S. V.; Hänggi, P.

    2016-04-01

    We present a numerical approach to calculate non-equilibrium eigenstates of a periodically time-modulated quantum system. The approach is based on the use of a chain of single-step propagating operators. Each operator is time-specific and constructed by combining the Magnus expansion of the time-dependent system Hamiltonian with the Chebyshev expansion of an operator exponent. The construction of the unitary Floquet operator, which evolves a system state over the full modulation period, is performed by propagating the identity matrix over the period. The independence of the evolution of basis vectors makes the propagation stage suitable for realization on a parallel cluster. Once the propagation stage is completed, a routine diagonalization of the Floquet matrix is performed. Finally, an additional propagation round, now involving the eigenvectors as the initial states, allows to resolve the time-dependence of the Floquet states and calculate their characteristics. We demonstrate the accuracy and scalability of the algorithm by applying it to calculate the Floquet states of two quantum models, namely (i) a synthesized random-matrix Hamiltonian and (ii) a many-body Bose-Hubbard dimer, both of the size up to 104 states.

  4. Recent Developments in Quantum Monte Carlo: Methods and Applications

    NASA Astrophysics Data System (ADS)

    Aspuru-Guzik, Alan; Austin, Brian; Domin, Dominik; Galek, Peter T. A.; Handy, Nicholas; Prasad, Rajendra; Salomon-Ferrer, Romelia; Umezawa, Naoto; Lester, William A.

    2007-12-01

    The quantum Monte Carlo method in the diffusion Monte Carlo form has become recognized for its capability of describing the electronic structure of atomic, molecular and condensed matter systems to high accuracy. This talk will briefly outline the method with emphasis on recent developments connected with trial function construction, linear scaling, and applications to selected systems.

  5. Theoretical method for analyzing quantum dynamics of correlated photons

    SciTech Connect

    Koshino, Kazuki; Nakatani, Masatoshi

    2009-05-15

    We present a theoretical method for the efficient analysis of quantum nonlinear dynamics of correlated photons. Since correlated photons can be regarded as a superposition of uncorrelated photons, semiclassical analysis can be applied to this problem. The proposed method is demonstrated for a V-type three-level atom as a nonlinear optical system.

  6. Generation of high-fidelity four-photon cluster state and quantum-domain demonstration of one-way quantum computing.

    PubMed

    Tokunaga, Yuuki; Kuwashiro, Shin; Yamamoto, Takashi; Koashi, Masato; Imoto, Nobuyuki

    2008-05-30

    We experimentally demonstrate a simple scheme for generating a four-photon entangled cluster state with fidelity over 0.860+/-0.015. We show that the fidelity is high enough to guarantee that the produced state is distinguished from Greenberger-Horne-Zeilinger, W, and Dicke types of genuine four-qubit entanglement. We also demonstrate basic operations of one-way quantum computing using the produced state and show that the output state fidelities surpass classical bounds, which indicates that the entanglement in the produced state essentially contributes to the quantum operation.

  7. The quantum bouncer by the path integral method

    NASA Astrophysics Data System (ADS)

    Goodings, D. A.; Szeredi, T.

    1991-10-01

    The path integral formulation of quantum mechanics in the semiclassical or WKB approximation provides a physically intuitive way of relating a classical system to its quantum analog. A fruitful way of studying quantum chaos is based upon applying the Gutzwiller periodic orbit sum rule, a result derived by the path integral method in the WKB approximation. This provides some motivation for learning about path integral techniques. In this paper a pedagogical example of the path integral formalism is presented in the hope of conveying the basic physical and mathematical concepts. The ``quantum bouncer'' is studied—the quantum version of a particle moving in one dimension above a perfectly reflecting surface while subject to a constant force directed toward the surface. The classical counterpart of this system is a ball bouncing on a floor in a constant gravitational field, collisions with the floor being assumed to be elastic. Path integration is used to derive the energy eigenvalues and eigenfunctions of the quantum bouncer in the WKB or semiclassical approximation. The results are shown to be the same as those obtained by solving the Schrödinger equation in the same approximation.

  8. A scanning method for detecting clustering pattern of both attribute and structure in social networks

    NASA Astrophysics Data System (ADS)

    Wang, Tai-Chi; Phoa, Frederick Kin Hing

    2016-03-01

    Community/cluster is one of the most important features in social networks. Many cluster detection methods were proposed to identify such an important pattern, but few were able to identify the statistical significance of the clusters by considering the likelihood of network structure and its attributes. Based on the definition of clustering, we propose a scanning method, originated from analyzing spatial data, for identifying clusters in social networks. Since the properties of network data are more complicated than those of spatial data, we verify our method's feasibility via simulation studies. The results show that the detection powers are affected by cluster sizes and connection probabilities. According to our simulation results, the detection accuracy of structure clusters and both structure and attribute clusters detected by our proposed method is better than that of other methods in most of our simulation cases. In addition, we apply our proposed method to some empirical data to identify statistically significant clusters.

  9. A theoretical study of water clusters: the relation between hydrogen-bond topology and interaction energy from quantum-chemical computations for clusters with up to 22 molecules.

    PubMed

    Lenz, Annika; Ojamäe, Lars

    2005-05-01

    Quantum-chemical calculations of a variety of water clusters with eight, ten and twelve molecules were performed, as well as for selected clusters with up to 22 water molecules. Geometry optimizations were carried out at the B3LYP/cc-pVDZ level and single-point energies were calculated at the B3LYP/aug-cc-pVDZ level for selected clusters. The electronic energies were studied with respect to the geometry of the oxygen arrangement and six different characteristics of the hydrogen-bond arrangement in the cluster. Especially the effect of the placement of the non-hydrogen bonding hydrogens on the interaction energy was studied. Models for the interaction energy with respect to different characteristics of the hydrogen-bond arrangement were derived through least-square fits. The results from the study of the clusters with eight, ten and twelve molecules are used to predict possible low-energy structures for various shapes of clusters with up to 22 molecules.

  10. Quantum-size effect on the electronic and optical properties of hybrid TiO{sub 2}/Au clusters

    SciTech Connect

    Liu, Chun-Sheng E-mail: yexiaojuan1980@gmail.com; Wang, Xiangfu; Yan, Xiaohong; Ye, Xiaojuan E-mail: yexiaojuan1980@gmail.com; Zeng, Zhi

    2014-08-07

    Although TiO{sub 2}/Au nanosystems exhibit high photocatalytic activities under solar radiation in the experiment, the quantum-size effect of TiO{sub 2} on the growth, electronic properties, and reactivity of Au clusters remains elusive. Using (time dependent) density functional theory, it is found that Au atoms attach to low-coordinated Ti and O atoms and serve as seeds for the growth of Au clusters, and the electronic (optical) properties of hybrid Au-TiO{sub 2} nano-clusters depend strongly upon the type of supported Au clusters. Interestingly, decorating TiO{sub 2} nano-particles with even-numbered Au clusters (Au{sub 8} or Au{sub 10}) can enhance the photocatalytic activity by: (i) spatially separating electron and hole states and (ii) balancing redox strength and visible light absorption. Furthermore, the interactions between the Au-TiO{sub 2} clusters and a single water molecule have been studied. It will open up new avenues for exploring controlled photocatalysts in semiconductor-based quantum-confined systems.

  11. A fast variational Gaussian wavepacket method: size-induced structural transitions in large neon clusters.

    PubMed

    Georgescu, Ionuţ; Mandelshtam, Vladimir A

    2011-10-21

    The variational Gaussian wavepacket (VGW) approximation provides an alternative to path integral Monte Carlo for the computation of thermodynamic properties of many-body systems at thermal equilibrium. It provides a direct access to the thermal density matrix and is particularly efficient for Monte Carlo approaches, as for an N-body system it operates in a non-inflated 3N-dimensional configuration space. Here, we greatly accelerate the VGW method by retaining only the relevant short-range correlations in the (otherwise full) 3N × 3N Gaussian width matrix without sacrificing the accuracy of the fully coupled VGW method. This results in the reduction of the original O(N(3)) scaling to O(N(2)). The fast-VGW method is then applied to quantum Lennard-Jones clusters with sizes up to N = 6500 atoms. Following Doye and Calvo [JCP 116, 8307 (2002)] we study the competition between the icosahedral and decahedral structural motifs in Ne(N) clusters as a function of N. PMID:22029296

  12. A fast variational Gaussian wavepacket method: size-induced structural transitions in large neon clusters.

    PubMed

    Georgescu, Ionuţ; Mandelshtam, Vladimir A

    2011-10-21

    The variational Gaussian wavepacket (VGW) approximation provides an alternative to path integral Monte Carlo for the computation of thermodynamic properties of many-body systems at thermal equilibrium. It provides a direct access to the thermal density matrix and is particularly efficient for Monte Carlo approaches, as for an N-body system it operates in a non-inflated 3N-dimensional configuration space. Here, we greatly accelerate the VGW method by retaining only the relevant short-range correlations in the (otherwise full) 3N × 3N Gaussian width matrix without sacrificing the accuracy of the fully coupled VGW method. This results in the reduction of the original O(N(3)) scaling to O(N(2)). The fast-VGW method is then applied to quantum Lennard-Jones clusters with sizes up to N = 6500 atoms. Following Doye and Calvo [JCP 116, 8307 (2002)] we study the competition between the icosahedral and decahedral structural motifs in Ne(N) clusters as a function of N.

  13. Tree Method for Quantum Vortex Dynamics

    NASA Astrophysics Data System (ADS)

    Baggaley, A. W.; Barenghi, C. F.

    2012-01-01

    We present a numerical method to compute the evolution of vortex filaments in superfluid helium. The method is based on a tree algorithm which considerably speeds up the calculation of Biot-Savart integrals. We show that the computational cost scales as Nlog( N) rather than N 2, where N is the number of discretization points. We test the method and its properties for a variety of vortex configurations, ranging from simple vortex rings to a counterflow vortex tangle, and compare results against the Local Induction Approximation and the exact Biot-Savart law.

  14. A multiscale quantum mechanics/electromagnetics method for device simulations.

    PubMed

    Yam, ChiYung; Meng, Lingyi; Zhang, Yu; Chen, GuanHua

    2015-04-01

    Multiscale modeling has become a popular tool for research applying to different areas including materials science, microelectronics, biology, chemistry, etc. In this tutorial review, we describe a newly developed multiscale computational method, incorporating quantum mechanics into electronic device modeling with the electromagnetic environment included through classical electrodynamics. In the quantum mechanics/electromagnetics (QM/EM) method, the regions of the system where active electron scattering processes take place are treated quantum mechanically, while the surroundings are described by Maxwell's equations and a semiclassical drift-diffusion model. The QM model and the EM model are solved, respectively, in different regions of the system in a self-consistent manner. Potential distributions and current densities at the interface between QM and EM regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. The method is illustrated in the simulation of several realistic systems. In the case of junctionless field-effect transistors, transfer characteristics are obtained and a good agreement between experiments and simulations is achieved. Optical properties of a tandem photovoltaic cell are studied and the simulations demonstrate that multiple QM regions are coupled through the classical EM model. Finally, the study of a carbon nanotube-based molecular device shows the accuracy and efficiency of the QM/EM method.

  15. Bayesian methods, maximum entropy, and quantum Monte Carlo

    SciTech Connect

    Gubernatis, J.E.; Silver, R.N. ); Jarrell, M. )

    1991-01-01

    We heuristically discuss the application of the method of maximum entropy to the extraction of dynamical information from imaginary-time, quantum Monte Carlo data. The discussion emphasizes the utility of a Bayesian approach to statistical inference and the importance of statistically well-characterized data. 14 refs.

  16. The influence of sodium nanoparticles formation on luminescent properties of fluorophosphate glasses containing molecular clusters and quantum dots of lead selenide

    NASA Astrophysics Data System (ADS)

    Lipatova, Zh. O.; Kolobkova, E. V.; Sidorov, A. I.; Nikonorov, N. V.

    2016-08-01

    The influence of sodium nanoparticles and secondary heat treatment conditions on the spectralluminescent characteristics of fluorophosphate glasses with PbSe molecular clusters and quantum dots is studied. Experiments with glasses containing no sodium nanoparticles show that their thermal treatment leads to the formation of molecular clusters with subsequent formation of quantum dots having an intense luminescence. The results of numerical simulation for glasses with sodium nanoparticles shows that heat treatment leads to formation of a sodium fluoride shell on the nanoparticles surface. It is shown that quenching of the luminescence of PbSe molecular clusters and quantum dots takes place in these glasses.

  17. Efficient hybrid-symbolic methods for quantum mechanical calculations

    NASA Astrophysics Data System (ADS)

    Scott, T. C.; Zhang, Wenxing

    2015-06-01

    We present hybrid symbolic-numerical tools to generate optimized numerical code for rapid prototyping and fast numerical computation starting from a computer algebra system (CAS) and tailored to any given quantum mechanical problem. Although a major focus concerns the quantum chemistry methods of H. Nakatsuji which has yielded successful and very accurate eigensolutions for small atoms and molecules, the tools are general and may be applied to any basis set calculation with a variational principle applied to its linear and non-linear parameters.

  18. A spatial shape constrained clustering method for mammographic mass segmentation.

    PubMed

    Lou, Jian-Yong; Yang, Xu-Lei; Cao, Ai-Ze

    2015-01-01

    A novel clustering method is proposed for mammographic mass segmentation on extracted regions of interest (ROIs) by using deterministic annealing incorporating circular shape function (DACF). The objective function reported in this study uses both intensity and spatial shape information, and the dominant dissimilarity measure is controlled by two weighting parameters. As a result, pixels having similar intensity information but located in different regions can be differentiated. Experimental results shows that, by using DACF, the mass segmentation results in digitized mammograms are improved with optimal mass boundaries, less number of noisy patches, and computational efficiency. An average probability of segmentation error of 7.18% for well-defined masses (or 8.06% for ill-defined masses) was obtained by using DACF on MiniMIAS database, with 5.86% (or 5.55%) and 6.14% (or 5.27%) improvements as compared to the standard DA and fuzzy c-means methods. PMID:25737739

  19. bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System

    PubMed Central

    Alexander, Nathan; Woetzel, Nils; Meiler, Jens

    2016-01-01

    Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

  20. An Immune Quantum Communication Model for Dephasing Noise Using Four-Qubit Cluster State

    NASA Astrophysics Data System (ADS)

    Wang, Rui-jin; Li, Dong-fen; Qin, Zhi-guang

    2016-01-01

    Quantum secure communication of dephasing in the presence of noise is a hot spot in research in the field of quantum secure communication. Quantum steganography aims is to transfer secret information in public quantum channel. But because effect of annealing phase noise, quantum states which is need to transfer easily delayed or changed. So, quantum steganography is very meaning apply to transmit secret information covertly in quantum noisy channels. The article introduced dephasing noise impact on the physics of quantum state, through the theoretical research, construct the logic of quantum states to back the phase noise immunity, and construct the decoherence free subspace, It can guarantees fidelity secret information exchange through quantum communication model in a noisy environment.

  1. Perturbative approximation to hybrid equation of motion coupled cluster/effective fragment potential method

    SciTech Connect

    Ghosh, Debashree

    2014-03-07

    Hybrid quantum mechanics/molecular mechanics (QM/MM) methods provide an attractive way to closely retain the accuracy of the QM method with the favorable computational scaling of the MM method. Therefore, it is not surprising that QM/MM methods are being increasingly used for large chemical/biological systems. Hybrid equation of motion coupled cluster singles doubles/effective fragment potential (EOM-CCSD/EFP) methods have been developed over the last few years to understand the effect of solvents and other condensed phases on the electronic spectra of chromophores. However, the computational cost of this approach is still dominated by the steep scaling of the EOM-CCSD method. In this work, we propose and implement perturbative approximations to the EOM-CCSD method in this hybrid scheme to reduce the cost of EOM-CCSD/EFP. The timings and accuracy of this hybrid approach is tested for calculation of ionization energies, excitation energies, and electron affinities of microsolvated nucleic acid bases (thymine and cytosine), phenol, and phenolate.

  2. Perturbative approximation to hybrid equation of motion coupled cluster/effective fragment potential method.

    PubMed

    Ghosh, Debashree

    2014-03-01

    Hybrid quantum mechanics/molecular mechanics (QM/MM) methods provide an attractive way to closely retain the accuracy of the QM method with the favorable computational scaling of the MM method. Therefore, it is not surprising that QM/MM methods are being increasingly used for large chemical/biological systems. Hybrid equation of motion coupled cluster singles doubles/effective fragment potential (EOM-CCSD/EFP) methods have been developed over the last few years to understand the effect of solvents and other condensed phases on the electronic spectra of chromophores. However, the computational cost of this approach is still dominated by the steep scaling of the EOM-CCSD method. In this work, we propose and implement perturbative approximations to the EOM-CCSD method in this hybrid scheme to reduce the cost of EOM-CCSD/EFP. The timings and accuracy of this hybrid approach is tested for calculation of ionization energies, excitation energies, and electron affinities of microsolvated nucleic acid bases (thymine and cytosine), phenol, and phenolate. PMID:24606347

  3. Quantum Monte Carlo methods for nuclei.

    SciTech Connect

    Wiringa, R. B.; Physics

    2008-01-01

    A major goal in nuclear physics is to understand how nuclear binding, structure, and reactions can be described from the underlying interactions between individual nucleons. We want to compute the properties of an A-nucleon system as an A-body problem with free-space nuclear interactions that describe nucleon-nucleon (NN) scattering and the two-nucleon bound-state. Properties of interest for a given nucleus include the ground-state binding energy, excitation spectrum, one- and two-nucleon density and momentum distributions, electromagnetic moments and transitions. They also wish to describe the interactions of nuclei with electrons, neutrinos, pions, nucleons, and other nuclei. Such calculations can provide a standard of comparison to test whether sub-nucleonic effects, such as explicit quark degrees of freedom, must be invoked to explain an observed phenomenon. they can also be used to evaluate nuclear matrix elements needed for some test of the standard model, and to predict reaction rates that are difficult or impossible to measure in the laboratory. For example, all the astrophysical reactions that contribute to the Big Bang or to solar energy production should be amenable to such ab initio calculations. To achieve this goal, they must both determine reasonable Hamiltonians to be used and devise reliable many-body methods to evaluate them. Significant progress has been made in the past decade on both fronts, with the development of a number of potential models that accurately reproduce NN elastic scattering data, and a variety of advanced many-body methods. In practice, to reproduce experimental energies and transitions, it appears necessary to add many-nucleon forces to the Hamiltonian and electroweak charge and current operators beyond the basic single-nucleon terms. While testing their interactions and currents against experiment, it is also important to test the many-body methods against each other to ensure that any approximations made are not biasing the

  4. The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis

    NASA Astrophysics Data System (ADS)

    Wu, Xiongwu; Chen, Yidong; Brooks, Bernard R.; Su, Yan A.

    2004-12-01

    An unsupervised data clustering method, called the local maximum clustering (LMC) method, is proposed for identifying clusters in experiment data sets based on research interest. A magnitude property is defined according to research purposes, and data sets are clustered around each local maximum of the magnitude property. By properly defining a magnitude property, this method can overcome many difficulties in microarray data clustering such as reduced projection in similarities, noises, and arbitrary gene distribution. To critically evaluate the performance of this clustering method in comparison with other methods, we designed three model data sets with known cluster distributions and applied the LMC method as well as the hierarchic clustering method, the[InlineEquation not available: see fulltext.]-mean clustering method, and the self-organized map method to these model data sets. The results show that the LMC method produces the most accurate clustering results. As an example of application, we applied the method to cluster the leukemia samples reported in the microarray study of Golub et al. (1999).

  5. Advances in methods and algorithms in a modern quantum chemistry program package.

    PubMed

    Shao, Yihan; Molnar, Laszlo Fusti; Jung, Yousung; Kussmann, Jörg; Ochsenfeld, Christian; Brown, Shawn T; Gilbert, Andrew T B; Slipchenko, Lyudmila V; Levchenko, Sergey V; O'Neill, Darragh P; DiStasio, Robert A; Lochan, Rohini C; Wang, Tao; Beran, Gregory J O; Besley, Nicholas A; Herbert, John M; Lin, Ching Yeh; Van Voorhis, Troy; Chien, Siu Hung; Sodt, Alex; Steele, Ryan P; Rassolov, Vitaly A; Maslen, Paul E; Korambath, Prakashan P; Adamson, Ross D; Austin, Brian; Baker, Jon; Byrd, Edward F C; Dachsel, Holger; Doerksen, Robert J; Dreuw, Andreas; Dunietz, Barry D; Dutoi, Anthony D; Furlani, Thomas R; Gwaltney, Steven R; Heyden, Andreas; Hirata, So; Hsu, Chao-Ping; Kedziora, Gary; Khalliulin, Rustam Z; Klunzinger, Phil; Lee, Aaron M; Lee, Michael S; Liang, Wanzhen; Lotan, Itay; Nair, Nikhil; Peters, Baron; Proynov, Emil I; Pieniazek, Piotr A; Rhee, Young Min; Ritchie, Jim; Rosta, Edina; Sherrill, C David; Simmonett, Andrew C; Subotnik, Joseph E; Woodcock, H Lee; Zhang, Weimin; Bell, Alexis T; Chakraborty, Arup K; Chipman, Daniel M; Keil, Frerich J; Warshel, Arieh; Hehre, Warren J; Schaefer, Henry F; Kong, Jing; Krylov, Anna I; Gill, Peter M W; Head-Gordon, Martin

    2006-07-21

    Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces. PMID:16902710

  6. Method and system for data clustering for very large databases

    NASA Technical Reports Server (NTRS)

    Zhang, Tian (Inventor); Ramakrishnan, Raghu (Inventor); Livny, Miron (Inventor)

    1998-01-01

    Multi-dimensional data contained in very large databases is efficiently and accurately clustered to determine patterns therein and extract useful information from such patterns. Conventional computer processors may be used which have limited memory capacity and conventional operating speed, allowing massive data sets to be processed in a reasonable time and with reasonable computer resources. The clustering process is organized using a clustering feature tree structure wherein each clustering feature comprises the number of data points in the cluster, the linear sum of the data points in the cluster, and the square sum of the data points in the cluster. A dense region of data points is treated collectively as a single cluster, and points in sparsely occupied regions can be treated as outliers and removed from the clustering feature tree. The clustering can be carried out continuously with new data points being received and processed, and with the clustering feature tree being restructured as necessary to accommodate the information from the newly received data points.

  7. Revealing Monoamine Oxidase B Catalytic Mechanisms by Means of the Quantum Chemical Cluster Approach.

    PubMed

    Zapata-Torres, Gerald; Fierro, Angélica; Barriga-González, German; Salgado, J Cristian; Celis-Barros, Cristian

    2015-07-27

    Two of the possible catalytic mechanisms for neurotransmitter oxidative deamination by monoamine oxidase B (MAO B), namely, polar nucleophilic and hydride transfer, were addressed in order to comprehend the nature of their rate-determining step. The Quantum Chemical Cluster Approach was used to obtain transition states of MAO B complexed with phenylethylamine (PEA), benzylamine (BA), and p-nitrobenzylamine (NBA). The choice of these amines relies on their importance to address MAO B catalytic mechanisms so as to help us to answer questions such as why BA is a better substrate than NBA or how para-substitution affects substrate's reactivity. Transition states were later validated by comparison with the experimental free energy barriers. From a theoretical point of view, and according to the our reported transition states, their calculated barriers and structural and orbital differences obtained by us among these compounds, we propose that good substrates such as BA and PEA might follow the hydride transfer pathway while poor substrates such as NBA prefer the polar nucleophilic mechanism, which might suggest that MAO B can act by both mechanisms. The low free energy barriers for BA and PEA reflect the preference that MAO B has for hydride transfer over the polar nucleophilic mechanism when catalyzing the oxidative deamination of neurotransmitters.

  8. Self-consistent phonons revisited. I. The role of thermal versus quantum fluctuations on structural transitions in large Lennard-Jones clusters

    NASA Astrophysics Data System (ADS)

    Georgescu, Ionuţ; Mandelshtam, Vladimir A.

    2012-10-01

    The theory of self-consistent phonons (SCP) was originally developed to address the anharmonic effects in condensed matter systems. The method seeks a harmonic, temperature-dependent Hamiltonian that provides the "best fit" for the physical Hamiltonian, the "best fit" being defined as the one that optimizes the Helmholtz free energy at a fixed temperature. The present developments provide a scalable O(N) unified framework that accounts for anharmonic effects in a many-body system, when it is probed by either thermal (ℏ → 0) or quantum fluctuations (T → 0). In these important limits, the solution of the nonlinear SCP equations can be reached in a manner that requires only the multiplication of 3N × 3N matrices, with no need of diagonalization. For short range potentials, such as Lennard-Jones, the Hessian, and other related matrices are highly sparse, so that the scaling of the matrix multiplications can be reduced from O(N3) to ˜ O(N). We investigate the role of quantum effects by continuously varying the de-Boer quantum delocalization parameter Λ and report the N-Λ (T = 0), and also the classical N-T (Λ = 0) phase diagrams for sizes up to N ˜ 104. Our results demonstrate that the harmonic approximation becomes inadequate already for such weakly quantum systems as neon clusters, or for classical systems much below the melting temperatures.

  9. Self-consistent phonons revisited. I. The role of thermal versus quantum fluctuations on structural transitions in large Lennard-Jones clusters.

    PubMed

    Georgescu, Ionuţ; Mandelshtam, Vladimir A

    2012-10-14

    The theory of self-consistent phonons (SCP) was originally developed to address the anharmonic effects in condensed matter systems. The method seeks a harmonic, temperature-dependent Hamiltonian that provides the "best fit" for the physical Hamiltonian, the "best fit" being defined as the one that optimizes the Helmholtz free energy at a fixed temperature. The present developments provide a scalable O(N) unified framework that accounts for anharmonic effects in a many-body system, when it is probed by either thermal (ℏ → 0) or quantum fluctuations (T → 0). In these important limits, the solution of the nonlinear SCP equations can be reached in a manner that requires only the multiplication of 3N × 3N matrices, with no need of diagonalization. For short range potentials, such as Lennard-Jones, the Hessian, and other related matrices are highly sparse, so that the scaling of the matrix multiplications can be reduced from O(N(3)) to ~O(N). We investigate the role of quantum effects by continuously varying the de-Boer quantum delocalization parameter Λ and report the N-Λ (T = 0), and also the classical N-T (Λ = 0) phase diagrams for sizes up to N ~ 10(4). Our results demonstrate that the harmonic approximation becomes inadequate already for such weakly quantum systems as neon clusters, or for classical systems much below the melting temperatures.

  10. Split kinetic energy method for quantum systems with competing potentials

    SciTech Connect

    Mineo, H.; Chao, Sheng D.

    2012-09-15

    For quantum systems with competing potentials, the conventional perturbation theory often yields an asymptotic series and the subsequent numerical outcome becomes uncertain. To tackle such a kind of problems, we develop a general solution scheme based on a new energy dissection idea. Instead of dividing the potential energy into 'unperturbed' and 'perturbed' terms, a partition of the kinetic energy is performed. By distributing the kinetic energy term in part into each individual potential, the Hamiltonian can be expressed as the sum of the subsystem Hamiltonians with respective competing potentials. The total wavefunction is expanded by using a linear combination of the basis sets of respective subsystem Hamiltonians. We first illustrate the solution procedure using a simple system consisting of a particle under the action of double {delta}-function potentials. Next, this method is applied to the prototype systems of a charged harmonic oscillator in strong magnetic field and the hydrogen molecule ion. Compared with the usual perturbation approach, this new scheme converges much faster to the exact solutions for both eigenvalues and eigenfunctions. When properly extended, this new solution scheme can be very useful for dealing with strongly coupling quantum systems. - Highlights: Black-Right-Pointing-Pointer A new basis set expansion method is proposed. Black-Right-Pointing-Pointer Split kinetic energy method is proposed to solve quantum eigenvalue problems. Black-Right-Pointing-Pointer Significant improvement has been obtained in converging to exact results. Black-Right-Pointing-Pointer Extension of such methods is promising and discussed.

  11. Solvothermal method to prepare graphene quantum dots by hydrogen peroxide

    NASA Astrophysics Data System (ADS)

    Tian, Renbing; Zhong, Suting; Wu, Juan; Jiang, Wei; Shen, Yewen; Jiang, Wei; Wang, Tianhe

    2016-10-01

    Graphene quantum dots (GQDs) have been synthesized by different chemical methods in recent years. For conventional chemical methods, it is inevitable to introduce a large amount of impurities in the preparation process. Long time of dialysis process increases the time cost extremely. Herein, we report a one-step solvothermal method for synthesizing GQDs with the application of hydrogen peroxide in N, N-Dimethylformamide (DMF) environment, which completely avoids the use of concentrated sulphuric acid and nitric acid to treat raw material and introduces no impurity in whole preparation process simultaneously for the first time. Pure GQDs can be obtained after evaporation/redissolution and filtration process with a strong blue emission at 15% quantum yield. This solvothermal method, not requiring dialysis process and complicated equipments, exhibits simple, eco-friendly and low time-cost properties. Besides high quantum yields, the as-prepared GQDs also show good photoluminescence stability in different pH conditions. The optical properties, morphology and structure of GQDs were studied by various equipments, implying potential application in biomedical fields and electronic device.

  12. ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy

    PubMed Central

    Andronov, Leonid; Orlov, Igor; Lutz, Yves; Vonesch, Jean-Luc; Klaholz, Bruno P.

    2016-01-01

    Super-resolution microscopy (PALM, STORM etc.) provides a plethora of fluorescent signals in dense cellular environments which can be difficult to interpret. Here we describe ClusterViSu, a method for image reconstruction, visualization and quantification of labelled protein clusters, based on Voronoi tessellation of the individual fluorescence events. The general applicability of this clustering approach for the segmentation of super-resolution microscopy data, including for co-localization, is illustrated on a series of important biological objects such as chromatin complexes, RNA polymerase, nuclear pore complexes and microtubules. PMID:27068792

  13. Least-squares finite element methods for quantum chromodynamics

    SciTech Connect

    Ketelsen, Christian; Brannick, J; Manteuffel, T; Mccormick, S

    2008-01-01

    A significant amount of the computational time in large Monte Carlo simulations of lattice quantum chromodynamics (QCD) is spent inverting the discrete Dirac operator. Unfortunately, traditional covariant finite difference discretizations of the Dirac operator present serious challenges for standard iterative methods. For interesting physical parameters, the discretized operator is large and ill-conditioned, and has random coefficients. More recently, adaptive algebraic multigrid (AMG) methods have been shown to be effective preconditioners for Wilson's discretization of the Dirac equation. This paper presents an alternate discretization of the Dirac operator based on least-squares finite elements. The discretization is systematically developed and physical properties of the resulting matrix system are discussed. Finally, numerical experiments are presented that demonstrate the effectiveness of adaptive smoothed aggregation ({alpha}SA ) multigrid as a preconditioner for the discrete field equations resulting from applying the proposed least-squares FE formulation to a simplified test problem, the 2d Schwinger model of quantum electrodynamics.

  14. K-means clustering method for auditory evoked potentials selection.

    PubMed

    Gourevitch, B; Le Bouquin-Jeannes, R

    2003-07-01

    Surface auditory evoked potentials are generally recorded using a headset of 32, 64 or 128 electrodes, but the quality of the responses is quite heterogeneous on the scalp surface. In some contexts, such as the analysis of auditory evoked potentials recorded in radio-frequency fields, the signal quality is essential, and it appears pertinent to consider only a limited number of electrodes. Therefore, before analysing signals influenced by radio-frequency fields, it is necessary to consider the preliminary step of selecting the channels where auditory activity is strong. This step is often realised by human visual selection and can take a considerable time. In this paper, a simple k-means clustering method is proposed, to select automatically the important channels, and the results are compared with traditional methods of selection. The method detected channels that showed a concordance rate of 86.5% with the visual selection (performed by five individuals) and gave the same final selection (only two extra electrodes in the automatic case). Moreover, the time needed for this automatic selection was 100 times less than that for the visual selection, and also human variability was avoided.

  15. Strategies for measurement-based quantum computation with cluster states transformed by stochastic local operations and classical communication

    SciTech Connect

    D'Souza, Adam G.; Feder, David L.

    2011-10-15

    We examine cluster states transformed by stochastic local operations and classical communication, as a resource for deterministic universal computation driven strictly by projective measurements. We identify circumstances under which such states in one dimension constitute resources for random-length single-qubit rotations, in one case quasideterministically (N-U-N states) and in another probabilistically (B-U-B states). In contrast to the cluster states, the N-U-N states exhibit spin correlation functions that decay exponentially with distance, while the B-U-B states can be arbitrarily locally pure. A two-dimensional square N-U-N lattice is a universal resource for quasideterministic measurement-based quantum computation. Measurements on cubic B-U-B states yield two-dimensional cluster states with bond defects, whose connectivity exceeds the percolation threshold for a critical value of the local purity.

  16. Quantum Error Correction

    NASA Astrophysics Data System (ADS)

    Lidar, Daniel A.; Brun, Todd A.

    2013-09-01

    Prologue; Preface; Part I. Background: 1. Introduction to decoherence and noise in open quantum systems Daniel Lidar and Todd Brun; 2. Introduction to quantum error correction Dave Bacon; 3. Introduction to decoherence-free subspaces and noiseless subsystems Daniel Lidar; 4. Introduction to quantum dynamical decoupling Lorenza Viola; 5. Introduction to quantum fault tolerance Panos Aliferis; Part II. Generalized Approaches to Quantum Error Correction: 6. Operator quantum error correction David Kribs and David Poulin; 7. Entanglement-assisted quantum error-correcting codes Todd Brun and Min-Hsiu Hsieh; 8. Continuous-time quantum error correction Ognyan Oreshkov; Part III. Advanced Quantum Codes: 9. Quantum convolutional codes Mark Wilde; 10. Non-additive quantum codes Markus Grassl and Martin Rötteler; 11. Iterative quantum coding systems David Poulin; 12. Algebraic quantum coding theory Andreas Klappenecker; 13. Optimization-based quantum error correction Andrew Fletcher; Part IV. Advanced Dynamical Decoupling: 14. High order dynamical decoupling Zhen-Yu Wang and Ren-Bao Liu; 15. Combinatorial approaches to dynamical decoupling Martin Rötteler and Pawel Wocjan; Part V. Alternative Quantum Computation Approaches: 16. Holonomic quantum computation Paolo Zanardi; 17. Fault tolerance for holonomic quantum computation Ognyan Oreshkov, Todd Brun and Daniel Lidar; 18. Fault tolerant measurement-based quantum computing Debbie Leung; Part VI. Topological Methods: 19. Topological codes Héctor Bombín; 20. Fault tolerant topological cluster state quantum computing Austin Fowler and Kovid Goyal; Part VII. Applications and Implementations: 21. Experimental quantum error correction Dave Bacon; 22. Experimental dynamical decoupling Lorenza Viola; 23. Architectures Jacob Taylor; 24. Error correction in quantum communication Mark Wilde; Part VIII. Critical Evaluation of Fault Tolerance: 25. Hamiltonian methods in QEC and fault tolerance Eduardo Novais, Eduardo Mucciolo and

  17. Stability and Clustering for Lattice Many-Body Quantum Hamiltonians with Multiparticle Potentials

    NASA Astrophysics Data System (ADS)

    Faria da Veiga, Paulo A.; O'Carroll, Michael

    2015-11-01

    We analyze a quantum system of N identical spinless particles of mass m, in the lattice Z^d, given by a Hamiltonian H_N=T_N+V_N, with kinetic energy T_N≥ 0 and potential V_N=V_{N,2}+V_{N,3} composed of attractive pair and repulsive 3-body contact-potentials. This Hamiltonian is motivated by the desire to understand the stability of quantum field theories, with massive single particles and bound states in the energy-momentum spectrum, in terms of an approximate Hamiltonian for their N-particle sector. We determine the role of the potentials V_{N,2} and V_{N,3} on the physical stability of the system, such as to avoid a collapse of the N particles. Mathematically speaking, stability is associated with an N-linear lower bound for the infimum of the H_N spectrum, \\underline{σ }(H_N)≥ -cN, for c>0 independent of N. For V_{N,3}=0, H_N is unstable, and the system collapses. If V_{N,3}not =0, H_N is stable and, for strong enough repulsion, we obtain \\underline{σ }(H_N)≥ -c' N, where c'N is the energy of ( N/2) isolated bound pairs. This result is physically expected. A much less trivial result is that, as N varies, we show [ \\underline{σ }(V_N)/N ] has qualitatively the same behavior as the well-known curve for minus the nuclear binding energy per nucleon. Moreover, it turns out that there exists a saturation value N_s of N at and above which the system presents a clustering: the N particles distributed in two fragments and, besides lattice translations of particle positions, there is an energy degeneracy of all two fragments with particle numbers N_r and N_s-N_r, with N_r=1,ldots ,N_s-1.

  18. Motion estimation using point cluster method and Kalman filter.

    PubMed

    Senesh, M; Wolf, A

    2009-05-01

    The most frequently used method in a three dimensional human gait analysis involves placing markers on the skin of the analyzed segment. This introduces a significant artifact, which strongly influences the bone position and orientation and joint kinematic estimates. In this study, we tested and evaluated the effect of adding a Kalman filter procedure to the previously reported point cluster technique (PCT) in the estimation of a rigid body motion. We demonstrated the procedures by motion analysis of a compound planar pendulum from indirect opto-electronic measurements of markers attached to an elastic appendage that is restrained to slide along the rigid body long axis. The elastic frequency is close to the pendulum frequency, as in the biomechanical problem, where the soft tissue frequency content is similar to the actual movement of the bones. Comparison of the real pendulum angle to that obtained by several estimation procedures--PCT, Kalman filter followed by PCT, and low pass filter followed by PCT--enables evaluation of the accuracy of the procedures. When comparing the maximal amplitude, no effect was noted by adding the Kalman filter; however, a closer look at the signal revealed that the estimated angle based only on the PCT method was very noisy with fluctuation, while the estimated angle based on the Kalman filter followed by the PCT was a smooth signal. It was also noted that the instantaneous frequencies obtained from the estimated angle based on the PCT method is more dispersed than those obtained from the estimated angle based on Kalman filter followed by the PCT method. Addition of a Kalman filter to the PCT method in the estimation procedure of rigid body motion results in a smoother signal that better represents the real motion, with less signal distortion than when using a digital low pass filter. Furthermore, it can be concluded that adding a Kalman filter to the PCT procedure substantially reduces the dispersion of the maximal and minimal

  19. Multidimensional quantum trajectories: Applications of the derivative propagation method

    SciTech Connect

    Trahan, Corey J.; Wyatt, Robert E.; Poirier, Bill

    2005-04-22

    In a previous publication [J. Chem. Phys. 118, 9911 (2003)], the derivative propagation method (DPM) was introduced as a novel numerical scheme for solving the quantum hydrodynamic equations of motion (QHEM) and computing the time evolution of quantum mechanical wave packets. These equations are a set of coupled, nonlinear partial differential equations governing the time evolution of the real-valued functions C and S in the complex action, S=C(r,t)+iS(r,t)/({Dirac_h}/2{pi}), where {psi}(r,t)=exp(S). Past numerical solutions to the QHEM were obtained via ensemble trajectory propagation, where the required first- and second-order spatial derivatives were evaluated using fitting techniques such as moving least squares. In the DPM, however, equations of motion are developed for the derivatives themselves, and a truncated set of these are integrated along quantum trajectories concurrently with the original QHEM equations for C and S. Using the DPM quantum effects can be included at various orders of approximation; no spatial fitting is involved; there is no basis set expansion; and single, uncoupled quantum trajectories can be propagated (in parallel) rather than in correlated ensembles. In this study, the DPM is extended from previous one-dimensional (1D) results to calculate transmission probabilities for 2D and 3D wave packet evolution on coupled Eckart barrier/harmonic oscillator surfaces. In the 2D problem, the DPM results are compared to standard numerical integration of the time-dependent Schroedinger equation. Also in this study, the practicality of implementing the DPM for systems with many more degrees of freedom is discussed.

  20. Multilevel Analysis Methods for Partially Nested Cluster Randomized Trials

    ERIC Educational Resources Information Center

    Sanders, Elizabeth A.

    2011-01-01

    This paper explores multilevel modeling approaches for 2-group randomized experiments in which a treatment condition involving clusters of individuals is compared to a control condition involving only ungrouped individuals, otherwise known as partially nested cluster randomized designs (PNCRTs). Strategies for comparing groups from a PNCRT in the…

  1. A Cluster-Based Method for Test Construction. Research Report 88-3.

    ERIC Educational Resources Information Center

    Boekkooi-Timminga, Ellen

    A new test construction method based on integer linear programming is described. This method selects optimal tests in small amounts of computer time. The new method, called the Cluster-Based Method, assumes that the items in the bank have been grouped according to their item information curves so that items within a group, or cluster, are…

  2. Theoretical study of small sodium-potassium alloy clusters through genetic algorithm and quantum chemical calculations.

    PubMed

    Silva, Mateus X; Galvão, Breno R L; Belchior, Jadson C

    2014-05-21

    Genetic algorithm is employed to survey an empirical potential energy surface for small Na(x)K(y) clusters with x + y ≤ 15, providing initial conditions for electronic structure methods. The minima of such empirical potential are assessed and corrected using high level ab initio methods such as CCSD(T), CR-CCSD(T)-L and MP2, and benchmark results are obtained for specific cases. The results are the first calculations for such small alloy clusters and may serve as a reference for further studies. The validity and choice of a proper functional and basis set for DFT calculations are then explored using the benchmark data, where it was found that the usual DFT approach may fail to provide the correct qualitative result for specific systems. The best general agreement to the benchmark calculations is achieved with def2-TZVPP basis set with SVWN5 functional, although the LANL2DZ basis set (with effective core potential) and SVWN5 functional provided the most cost-effective results. PMID:24691391

  3. Quantum state tomography of a single qubit: comparison of methods

    NASA Astrophysics Data System (ADS)

    Schmied, Roman

    2016-10-01

    The tomographic reconstruction of the state of a quantum-mechanical system is an essential component in the development of quantum technologies. We present an overview of different tomographic methods for determining the quantum-mechanical density matrix of a single qubit: (scaled) direct inversion, maximum likelihood estimation (MLE), minimum Fisher information distance and Bayesian mean estimation (BME). We discuss the different prior densities in the space of density matrices, on which both MLE and BME depend, as well as ways of including experimental errors and of estimating tomography errors. As a measure of the accuracy of these methods, we average the trace distance between a given density matrix and the tomographic density matrices it can give rise to through experimental measurements. We find that the BME provides the most accurate estimate of the density matrix, and suggest using either the pure-state prior, if the system is known to be in a rather pure state, or the Bures prior if any state is possible. The MLE is found to be slightly less accurate. We comment on the extrapolation of these results to larger systems.

  4. Matrix method analysis of quantum Hall effect device connections

    NASA Astrophysics Data System (ADS)

    Ortolano, M.; Callegaro, L.

    2012-02-01

    The modelling of electrical connections of single, or several, multiterminal quantum Hall effect (QHE) devices is relevant for electrical metrology: it is known, in fact, that certain particular connections allow (i) the realization of multiples or fractions of the quantized resistance, or (ii) the rejection of stray impedances, so that the configuration maintains the status of quantum standard. Ricketts-Kemeny and Delahaye equivalent circuits are known to be accurate models of the QHE: however, the numerical or analytical solution of electrical networks including these equivalent circuits can be difficult. In this paper, we introduce a method of analysis based on the representation of a QHE device by means of the indefinite admittance matrix: external connections are then represented with another matrix, easily written by inspection. Some examples, including the solution of double- and triple-series connections, are shown.

  5. Analytical Energy Gradients for Excited-State Coupled-Cluster Methods

    NASA Astrophysics Data System (ADS)

    Wladyslawski, Mark; Nooijen, Marcel

    The equation-of-motion coupled-cluster (EOM-CC) and similarity transformed equation-of-motion coupled-cluster (STEOM-CC) methods have been firmly established as accurate and routinely applicable extensions of single-reference coupled-cluster theory to describe electronically excited states. An overview of these methods is provided, with emphasis on the many-body similarity transform concept that is the key to a rationalization of their accuracy. The main topic of the paper is the derivation of analytical energy gradients for such non-variational electronic structure approaches, with an ultimate focus on obtaining their detailed algebraic working equations. A general theoretical framework using Lagrange's method of undetermined multipliers is presented, and the method is applied to formulate the EOM-CC and STEOM-CC gradients in abstract operator terms, following the previous work in [P.G. Szalay, Int. J. Quantum Chem. 55 (1995) 151] and [S.R. Gwaltney, R.J. Bartlett, M. Nooijen, J. Chem. Phys. 111 (1999) 58]. Moreover, the systematics of the Lagrange multiplier approach is suitable for automation by computer, enabling the derivation of the detailed derivative equations through a standardized and direct procedure. To this end, we have developed the SMART (Symbolic Manipulation and Regrouping of Tensors) package of automated symbolic algebra routines, written in the Mathematica programming language. The SMART toolkit provides the means to expand, differentiate, and simplify equations by manipulation of the detailed algebraic tensor expressions directly. The Lagrangian multiplier formulation establishes a uniform strategy to perform the automated derivation in a standardized manner: A Lagrange multiplier functional is constructed from the explicit algebraic equations that define the energy in the electronic method; the energy functional is then made fully variational with respect to all of its parameters, and the symbolic differentiations directly yield the explicit

  6. Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions.

    PubMed

    Dzierlenga, M W; Varga, M J; Schwartz, S D

    2016-01-01

    The mechanisms of enzymatic reactions are studied via a host of computational techniques. While previous methods have been used successfully, many fail to incorporate the full dynamical properties of enzymatic systems. This can lead to misleading results in cases where enzyme motion plays a significant role in the reaction coordinate, which is especially relevant in particle transfer reactions where nuclear tunneling may occur. In this chapter, we outline previous methods, as well as discuss newly developed dynamical methods to interrogate mechanisms of enzymatic particle transfer reactions. These new methods allow for the calculation of free energy barriers and kinetic isotope effects (KIEs) with the incorporation of quantum effects through centroid molecular dynamics (CMD) and the full complement of enzyme dynamics through transition path sampling (TPS). Recent work, summarized in this chapter, applied the method for calculation of free energy barriers to reaction in lactate dehydrogenase (LDH) and yeast alcohol dehydrogenase (YADH). We found that tunneling plays an insignificant role in YADH but plays a more significant role in LDH, though not dominant over classical transfer. Additionally, we summarize the application of a TPS algorithm for the calculation of reaction rates in tandem with CMD to calculate the primary H/D KIE of YADH from first principles. We found that the computationally obtained KIE is within the margin of error of experimentally determined KIEs and corresponds to the KIE of particle transfer in the enzyme. These methods provide new ways to investigate enzyme mechanism with the inclusion of protein and quantum dynamics.

  7. Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions.

    PubMed

    Dzierlenga, M W; Varga, M J; Schwartz, S D

    2016-01-01

    The mechanisms of enzymatic reactions are studied via a host of computational techniques. While previous methods have been used successfully, many fail to incorporate the full dynamical properties of enzymatic systems. This can lead to misleading results in cases where enzyme motion plays a significant role in the reaction coordinate, which is especially relevant in particle transfer reactions where nuclear tunneling may occur. In this chapter, we outline previous methods, as well as discuss newly developed dynamical methods to interrogate mechanisms of enzymatic particle transfer reactions. These new methods allow for the calculation of free energy barriers and kinetic isotope effects (KIEs) with the incorporation of quantum effects through centroid molecular dynamics (CMD) and the full complement of enzyme dynamics through transition path sampling (TPS). Recent work, summarized in this chapter, applied the method for calculation of free energy barriers to reaction in lactate dehydrogenase (LDH) and yeast alcohol dehydrogenase (YADH). We found that tunneling plays an insignificant role in YADH but plays a more significant role in LDH, though not dominant over classical transfer. Additionally, we summarize the application of a TPS algorithm for the calculation of reaction rates in tandem with CMD to calculate the primary H/D KIE of YADH from first principles. We found that the computationally obtained KIE is within the margin of error of experimentally determined KIEs and corresponds to the KIE of particle transfer in the enzyme. These methods provide new ways to investigate enzyme mechanism with the inclusion of protein and quantum dynamics. PMID:27497161

  8. FAST TRACK COMMUNICATION: A stable toolkit method in quantum control

    NASA Astrophysics Data System (ADS)

    Belhadj, M.; Salomon, J.; Turinici, G.

    2008-09-01

    Recently the 'toolkit' discretization introduced to accelerate the numerical resolution of the time-dependent Schrödinger equation arising in quantum optimal control problems demonstrated good results on a large range of models. However, when coupling this class of methods with the so-called monotonically convergent algorithms, numerical instabilities affect the convergence of the discretized scheme. We present an adaptation of the 'toolkit' method which preserves the monotonicity of the procedure. The theoretical properties of the new algorithm are illustrated by numerical simulations.

  9. The quantum inverse scattering method with anyonic grading

    NASA Astrophysics Data System (ADS)

    Batchelor, M. T.; Foerster, A.; Guan, X.-W.; Links, J.; Zhou, H.-Q.

    2008-11-01

    We formulate the quantum inverse scattering method for the case of anyonic grading. This provides a general framework for constructing integrable models describing interacting hard-core anyons. Through this method we reconstruct the known integrable model of hard core anyons associated with the XXX model, and as a new application we construct the anyonic t - J model. The energy spectrum for each model is derived by means of a generalization of the algebraic Bethe ansatz. The grading parameters implementing the anyonic signature give rise to sector-dependent phase factors in the Bethe ansatz equations.

  10. Characterizing a nonclassical carbene with coupled cluster methods: cyclobutylidene.

    PubMed

    Wang, Xiao; Agarwal, Jay; Schaefer Iii, Henry F

    2016-09-21

    Carbenes represent a special class of reactive compounds that possess a lone pair of electrons on a carbon atom. Among the myriad examples of carbenes in the literature, cyclobutylidene stands out as a unique nonclassical compound that includes transannular interaction between opposing C1 and C3 carbon atoms within a four-membered ring. On its lowest potential energy surface (X[combining tilde](1)A'), cyclobutylidene quickly rearranges, following three reaction paths: (i) 1,2-H migration; (ii) 1,2-C migration; and, (iii) 1,3-H migration. Herein, this reactivity is examined with high-level coupled-cluster methods [up to CCSDT(Q)]. At this level of theory, combined with extrapolation techniques to obtain energies at the complete basis set (CBS) limit, the long-standing disparity between theoretical and experimental results is resolved. Specifically, cyclobutylidene is predicted to prefer 1,2-C migration rather than 1,2-H migration. Rate constants for the three reaction paths are obtained from canonical variational transition state theory (CVT) and yield reasonable agreement with existing experimental results. Further characterization of cyclobutylidene is also reported: the singlet-triplet gap (ΔES-T) is found to be -9.3 kcal mol(-1) at the CCSDT(Q)/CBS level of theory, and anharmonic vibrational frequencies are determined with second-order vibrational perturbation theory (VPT2). PMID:27539444

  11. A short course on quantum mechanics and methods of quantization

    NASA Astrophysics Data System (ADS)

    Ercolessi, Elisa

    2015-07-01

    These notes collect the lectures given by the author to the "XXIII International Workshop on Geometry and Physics" held in Granada (Spain) in September 2014. The first part of this paper aims at introducing a mathematical oriented reader to the realm of Quantum Mechanics (QM) and then to present the geometric structures that underline the mathematical formalism of QM which, contrary to what is usually done in Classical Mechanics (CM), are usually not taught in introductory courses. The mathematics related to Hilbert spaces and Differential Geometry are assumed to be known by the reader. In the second part, we concentrate on some quantization procedures, that are founded on the geometric structures of QM — as we have described them in the first part — and represent the ones that are more operatively used in modern theoretical physics. We will discuss first the so-called Coherent State Approach which, mainly complemented by "Feynman Path Integral Technique", is the method which is most widely used in quantum field theory. Finally, we will describe the "Weyl Quantization Approach" which is at the origin of modern tomographic techniques, originally used in optics and now in quantum information theory.

  12. A comparison of confidence interval methods for the intraclass correlation coefficient in cluster randomized trials.

    PubMed

    Ukoumunne, Obioha C

    2002-12-30

    This study compared different methods for assigning confidence intervals to the analysis of variance estimator of the intraclass correlation coefficient (rho). The context of the comparison was the use of rho to estimate the variance inflation factor when planning cluster randomized trials. The methods were compared using Monte Carlo simulations of unbalanced clustered data and data from a cluster randomized trial of an intervention to improve the management of asthma in a general practice setting. The coverage and precision of the intervals were compared for data with different numbers of clusters, mean numbers of subjects per cluster and underlying values of rho. The performance of the methods was also compared for data with Normal and non-Normally distributed cluster specific effects. Results of the simulations showed that methods based upon the variance ratio statistic provided greater coverage levels than those based upon large sample approximations to the standard error of rho. Searle's method provided close to nominal coverage for data with Normally distributed random effects. Adjusted versions of Searle's method to allow for lack of balance in the data generally did not improve upon it either in terms of coverage or precision. Analyses of the trial data, however, showed that limits provided by Thomas and Hultquist's method may differ from those of the other variance ratio statistic methods when the arithmetic mean differs markedly from the harmonic mean cluster size. The simulation results demonstrated that marked non-Normality in the cluster level random effects compromised the performance of all methods. Confidence intervals for the methods were generally wide relative to the underlying size of rho suggesting that there may be great uncertainty associated with sample size calculations for cluster trials where large clusters are randomized. Data from cluster based studies with sample sizes much larger than those typical of cluster randomized trials are

  13. Cluster size statistic and cluster mass statistic: two novel methods for identifying changes in functional connectivity between groups or conditions.

    PubMed

    Ing, Alex; Schwarzbauer, Christian

    2014-01-01

    Functional connectivity has become an increasingly important area of research in recent years. At a typical spatial resolution, approximately 300 million connections link each voxel in the brain with every other. This pattern of connectivity is known as the functional connectome. Connectivity is often compared between experimental groups and conditions. Standard methods used to control the type 1 error rate are likely to be insensitive when comparisons are carried out across the whole connectome, due to the huge number of statistical tests involved. To address this problem, two new cluster based methods--the cluster size statistic (CSS) and cluster mass statistic (CMS)--are introduced to control the family wise error rate across all connectivity values. These methods operate within a statistical framework similar to the cluster based methods used in conventional task based fMRI. Both methods are data driven, permutation based and require minimal statistical assumptions. Here, the performance of each procedure is evaluated in a receiver operator characteristic (ROC) analysis, utilising a simulated dataset. The relative sensitivity of each method is also tested on real data: BOLD (blood oxygen level dependent) fMRI scans were carried out on twelve subjects under normal conditions and during the hypercapnic state (induced through the inhalation of 6% CO2 in 21% O2 and 73%N2). Both CSS and CMS detected significant changes in connectivity between normal and hypercapnic states. A family wise error correction carried out at the individual connection level exhibited no significant changes in connectivity.

  14. One-way quantum computing in the optical frequency comb.

    PubMed

    Menicucci, Nicolas C; Flammia, Steven T; Pfister, Olivier

    2008-09-26

    One-way quantum computing allows any quantum algorithm to be implemented easily using just measurements. The difficult part is creating the universal resource, a cluster state, on which the measurements are made. We propose a scalable method that uses a single, multimode optical parametric oscillator (OPO). The method is very efficient and generates a continuous-variable cluster state, universal for quantum computation, with quantum information encoded in the quadratures of the optical frequency comb of the OPO.

  15. Hyperspectral image clustering method based on artificial bee colony algorithm and Markov random fields

    NASA Astrophysics Data System (ADS)

    Sun, Xu; Yang, Lina; Gao, Lianru; Zhang, Bing; Li, Shanshan; Li, Jun

    2015-01-01

    Center-oriented hyperspectral image clustering methods have been widely applied to hyperspectral remote sensing image processing; however, the drawbacks are obvious, including the over-simplicity of computing models and underutilized spatial information. In recent years, some studies have been conducted trying to improve this situation. We introduce the artificial bee colony (ABC) and Markov random field (MRF) algorithms to propose an ABC-MRF-cluster model to solve the problems mentioned above. In this model, a typical ABC algorithm framework is adopted in which cluster centers and iteration conditional model algorithm's results are considered as feasible solutions and objective functions separately, and MRF is modified to be capable of dealing with the clustering problem. Finally, four datasets and two indices are used to show that the application of ABC-cluster and ABC-MRF-cluster methods could help to obtain better image accuracy than conventional methods. Specifically, the ABC-cluster method is superior when used for a higher power of spectral discrimination, whereas the ABC-MRF-cluster method can provide better results when used for an adjusted random index. In experiments on simulated images with different signal-to-noise ratios, ABC-cluster and ABC-MRF-cluster showed good stability.

  16. Higher-Order Equation-of-Motion Coupled-Cluster Methods for Ionization Processes

    SciTech Connect

    Kamiya, Muneaki; Hirata, So

    2006-08-21

    Compact algebraic equations defining the equation-of-motion coupled-cluster (EOM-CC) methods for ionization potentials (IP-EOM-CC) have been derived and computer implemented by virtue of a symbolic algebra system largely automating these processes. Models with connected cluster excitation operators truncated after double, triple, or quadruple level and with linear ionization operators truncated after two-hole-one-particle (2h1p), three-hole-two-particle (3h2p), or four-hole-three-particle (4h3p) level (abbreviated as IP-EOM-CCSD, CCSDT, and CCSDTQ, respectively) have been realized into parallel algorithms taking advantage of spin, spatial, and permutation symmetries with optimal size dependence of the computational costs. They are based on spin-orbital formalisms and can describe both {alpha} and {beta} and ionizations from open-shell (doublet, triplet, etc.) reference states into ionized states with various spin magnetic quantum numbers. The application of these methods to Koopmans and satellite ionizations of N{sub 2} and CO (with the ambiguity due to finite basis sets eliminated by extrapolation) has shown that IP-EOM-CCSD frequently accounts for orbital relaxation inadequately and displays errors exceeding a couple of eV. However, these errors can be systematically reduced to tenths or even hundredths of an eV by IP-EOM-CCSDT or CCSDTQ. Comparison of spectroscopic parameters of the FH{sup +} and NH{sup +} radicals between IP-EOM-CC and experiments has also underscored the importance of higher-order IP-EOM-CC treatments. For instance, the harmonic frequencies of the {tilde A} {sup 2}{Sigma}{sup -} state of NH{sup +}+ are predicted to be 1285, 1723, and 1705 cm{sup -1} by IP-EOM-CCSD, CCSDT, and CCSDTQ, respectively, as compared to the observed value of 1707 cm{sup -1}. The small adiabatic energy separation (observed 0.04 eV) between the {tilde X} {sup 2}II and {tilde a} {sup 4}{sigma}{sup -} states of NH{sup +} also requires IP-EOM-CCSDTQ for a quantitative

  17. Positioning nuclear spins in interacting clusters for quantum technologies and bioimaging

    NASA Astrophysics Data System (ADS)

    Wang, Zhen-Yu; Haase, Jan F.; Casanova, Jorge; Plenio, Martin B.

    2016-05-01

    We propose a method to measure the hyperfine vectors between a nitrogen-vacancy (NV) center and an environment of interacting nuclear spins. Our protocol enables the generation of tunable electron-nuclear coupling Hamiltonians while suppressing unwanted internuclear interactions. In this manner, each nucleus can be addressed and controlled individually, thereby permitting the reconstruction of the individual hyperfine vectors. With this ability the three-dimensional (3D) structure of spin ensembles and spins in biomolecules can be identified without the necessity of varying the direction of applied magnetic fields. We demonstrate examples including the complete reconstruction of an interacting spin cluster in diamond and 3D imaging of all the nuclear spins in a biomolecule.

  18. Bootstrap-based methods for estimating standard errors in Cox's regression analyses of clustered event times.

    PubMed

    Xiao, Yongling; Abrahamowicz, Michal

    2010-03-30

    We propose two bootstrap-based methods to correct the standard errors (SEs) from Cox's model for within-cluster correlation of right-censored event times. The cluster-bootstrap method resamples, with replacement, only the clusters, whereas the two-step bootstrap method resamples (i) the clusters, and (ii) individuals within each selected cluster, with replacement. In simulations, we evaluate both methods and compare them with the existing robust variance estimator and the shared gamma frailty model, which are available in statistical software packages. We simulate clustered event time data, with latent cluster-level random effects, which are ignored in the conventional Cox's model. For cluster-level covariates, both proposed bootstrap methods yield accurate SEs, and type I error rates, and acceptable coverage rates, regardless of the true random effects distribution, and avoid serious variance under-estimation by conventional Cox-based standard errors. However, the two-step bootstrap method over-estimates the variance for individual-level covariates. We also apply the proposed bootstrap methods to obtain confidence bands around flexible estimates of time-dependent effects in a real-life analysis of cluster event times.

  19. Hydrogen cluster/network in tobermorite as studied by multiple-quantum spin counting {sup 1}H NMR

    SciTech Connect

    Mogami, Yuuki; Yamazaki, Satoru; Matsuno, Shinya; Matsui, Kunio; Noda, Yasuto; Takegoshi, K.

    2014-12-15

    Proton multiple-quantum (MQ) spin-counting experiment has been employed to study arrangement of hydrogen atoms in 9 Å/11 Å natural/synthetic tobermorites. Even though all tobermorite samples give similar characterless, broad static-powder {sup 1}H NMR spectra, their MQ spin-counting spectra are markedly different; higher quanta in 11 Å tobermorite do not grow with the MQ excitation time, while those in 9 Å one do. A statistical analysis of the MQ results recently proposed [26] is applied to show that hydrogens align in 9 Å tobermorite one dimensionally, while in 11 Å tobermorite they exist as a cluster of 5–8 hydrogen atoms.

  20. Detection of moving clusters by a method of cinematic pairs

    NASA Astrophysics Data System (ADS)

    Khodjachikh, M. F.; Romanovsky, E. A.

    2000-01-01

    The algorithm of revealing of pairs stars with common movement is offered and is realized. The basic source is the catalogue HIPPARCOS. On concentration of kinematic pairs it is revealed three unknown earlier moving clusters in constellations: 1) Phe, 2) Cae, 3) Hor and, well known, in 4) UMa are revealed. On an original technique the members of clusters -- all 87 stars are allocated. Coordinates of the clusters convergent point α, delta; (in degrees), spatial speed (in km/s) and age (in 106 yr) from isochrone fitting have made: 1) 51, -29, 19.0, 500, 5/6; 2) 104, -32, 23.7, 300, 9/12; 3) 119, -27, 22.3, 100, 9/22; 4) 303, -31, 16.7, 500, 16/8 accordingly. Numerator of fraction -- number of stars identified as the members of clusters, denominator -- number of the probable members (with unknown radial speeds). The preliminary qualitative analysis of clusters spatial structure is carried in view of their dynamic evolution.

  1. Grinding Wheel Condition Monitoring with Hidden Markov Model-Based Clustering Methods

    SciTech Connect

    Liao, T. W.; Hua, G; Qu, Jun; Blau, Peter Julian

    2006-01-01

    Hidden Markov model (HMM) is well known for sequence modeling and has been used for condition monitoring. However, HMM-based clustering methods are developed only recently. This article proposes a HMM-based clustering method for monitoring the condition of grinding wheel used in grinding operations. The proposed method first extract features from signals based on discrete wavelet decomposition using a moving window approach. It then generates a distance (dissimilarity) matrix using HMM. Based on this distance matrix several hierarchical and partitioning-based clustering algorithms are applied to obtain clustering results. The proposed methodology was tested with feature sequences extracted from acoustic emission signals. The results show that clustering accuracy is dependent upon cutting condition. Higher material removal rate seems to produce more discriminatory signals/features than lower material removal rate. The effect of window size, wavelet decomposition level, wavelet basis, clustering algorithm, and data normalization were also studied.

  2. Classification of excessive domestic water consumption using Fuzzy Clustering Method

    NASA Astrophysics Data System (ADS)

    Zairi Zaidi, A.; Rasmani, Khairul A.

    2016-08-01

    Demand for clean and treated water is increasing all over the world. Therefore it is crucial to conserve water for better use and to avoid unnecessary, excessive consumption or wastage of this natural resource. Classification of excessive domestic water consumption is a difficult task due to the complexity in determining the amount of water usage per activity, especially as the data is known to vary between individuals. In this study, classification of excessive domestic water consumption is carried out using a well-known Fuzzy C-Means (FCM) clustering algorithm. Consumer data containing information on daily, weekly and monthly domestic water usage was employed for the purpose of classification. Using the same dataset, the result produced by the FCM clustering algorithm is compared with the result obtained from a statistical control chart. The finding of this study demonstrates the potential use of the FCM clustering algorithm for the classification of domestic consumer water consumption data.

  3. Large Scale Electronic Structure Calculations using Quantum Chemistry Methods

    NASA Astrophysics Data System (ADS)

    Scuseria, Gustavo E.

    1998-03-01

    This talk will address our recent efforts in developing fast, linear scaling electronic structure methods for large scale applications. Of special importance is our fast multipole method( M. C. Strain, G. E. Scuseria, and M. J. Frisch, Science 271), 51 (1996). (FMM) for achieving linear scaling for the quantum Coulomb problem (GvFMM), the traditional bottleneck in quantum chemistry calculations based on Gaussian orbitals. Fast quadratures(R. E. Stratmann, G. E. Scuseria, and M. J. Frisch, Chem. Phys. Lett. 257), 213 (1996). combined with methods that avoid the Hamiltonian diagonalization( J. M. Millam and G. E. Scuseria, J. Chem. Phys. 106), 5569 (1997) have resulted in density functional theory (DFT) programs that can be applied to systems containing many hundreds of atoms and ---depending on computational resources or level of theory-- to many thousands of atoms.( A. D. Daniels, J. M. Millam and G. E. Scuseria, J. Chem. Phys. 107), 425 (1997). Three solutions for the diagonalization bottleneck will be analyzed and compared: a conjugate gradient density matrix search (CGDMS), a Hamiltonian polynomial expansion of the density matrix, and a pseudo-diagonalization method. Besides DFT, our near-field exchange method( J. C. Burant, G. E. Scuseria, and M. J. Frisch, J. Chem. Phys. 105), 8969 (1996). for linear scaling Hartree-Fock calculations will be discussed. Based on these improved capabilities, we have also developed programs to obtain vibrational frequencies (via analytic energy second derivatives) and excitation energies (through time-dependent DFT) of large molecules like porphyn or C_70. Our GvFMM has been extended to periodic systems( K. N. Kudin and G. E. Scuseria, Chem. Phys. Lett., in press.) and progress towards a Gaussian-based DFT and HF program for polymers and solids will be reported. Last, we will discuss our progress on a Laplace-transformed \\cal O(N^2) second-order pertubation theory (MP2) method.

  4. Method for quantum-jump continuous-time quantum error correction

    NASA Astrophysics Data System (ADS)

    Hsu, Kung-Chuan; Brun, Todd A.

    2016-02-01

    Continuous-time quantum error correction (CTQEC) is a technique for protecting quantum information against decoherence, where both the decoherence and error correction processes are considered continuous in time. Given any [[n ,k ,d

  5. Platinum-ruthenium bimetallic clusters on graphite: a comparison of vapor deposition and electroless deposition methods.

    PubMed

    Galhenage, Randima P; Xie, Kangmin; Diao, Weijian; Tengco, John Meynard M; Seuser, Grant S; Monnier, John R; Chen, Donna A

    2015-11-14

    Bimetallic Pt-Ru clusters have been grown on highly ordered pyrolytic graphite (HOPG) surfaces by vapor deposition and by electroless deposition. These studies help to bridge the material gap between well-characterized vapor deposited clusters and electrolessly deposited clusters, which are better suited for industrial catalyst preparation. In the vapor deposition experiments, bimetallic clusters were formed by the sequential deposition of Pt on Ru or Ru on Pt. Seed clusters of the first metal were grown on HOPG surfaces that were sputtered with Ar(+) to introduce defects, which act as nucleation sites for Pt or Ru. On the unmodified HOPG surface, both Pt and Ru clusters preferentially nucleated at the step edges, whereas on the sputtered surface, clusters with relatively uniform sizes and spatial distributions were formed. Low energy ion scattering experiments showed that the surface compositions of the bimetallic clusters are Pt-rich, regardless of the order of deposition, indicating that the interdiffusion of metals within the clusters is facile at room temperature. Bimetallic clusters on sputtered HOPG were prepared by the electroless deposition of Pt on Ru seed clusters from a Pt(+2) solution using dimethylamine borane as the reducing agent at pH 11 and 40 °C. After exposure to the electroless deposition bath, Pt was selectively deposited on Ru, as demonstrated by the detection of Pt on the surface by XPS, and the increase in the average cluster height without an increase in the number of clusters, indicating that Pt atoms are incorporated into the Ru seed clusters. Electroless deposition of Ru on Pt seed clusters was also achieved, but it should be noted that this deposition method is extremely sensitive to the presence of other metal ions in solution that have a higher reduction potential than the metal ion targeted for deposition.

  6. Platinum-ruthenium bimetallic clusters on graphite: a comparison of vapor deposition and electroless deposition methods.

    PubMed

    Galhenage, Randima P; Xie, Kangmin; Diao, Weijian; Tengco, John Meynard M; Seuser, Grant S; Monnier, John R; Chen, Donna A

    2015-11-14

    Bimetallic Pt-Ru clusters have been grown on highly ordered pyrolytic graphite (HOPG) surfaces by vapor deposition and by electroless deposition. These studies help to bridge the material gap between well-characterized vapor deposited clusters and electrolessly deposited clusters, which are better suited for industrial catalyst preparation. In the vapor deposition experiments, bimetallic clusters were formed by the sequential deposition of Pt on Ru or Ru on Pt. Seed clusters of the first metal were grown on HOPG surfaces that were sputtered with Ar(+) to introduce defects, which act as nucleation sites for Pt or Ru. On the unmodified HOPG surface, both Pt and Ru clusters preferentially nucleated at the step edges, whereas on the sputtered surface, clusters with relatively uniform sizes and spatial distributions were formed. Low energy ion scattering experiments showed that the surface compositions of the bimetallic clusters are Pt-rich, regardless of the order of deposition, indicating that the interdiffusion of metals within the clusters is facile at room temperature. Bimetallic clusters on sputtered HOPG were prepared by the electroless deposition of Pt on Ru seed clusters from a Pt(+2) solution using dimethylamine borane as the reducing agent at pH 11 and 40 °C. After exposure to the electroless deposition bath, Pt was selectively deposited on Ru, as demonstrated by the detection of Pt on the surface by XPS, and the increase in the average cluster height without an increase in the number of clusters, indicating that Pt atoms are incorporated into the Ru seed clusters. Electroless deposition of Ru on Pt seed clusters was also achieved, but it should be noted that this deposition method is extremely sensitive to the presence of other metal ions in solution that have a higher reduction potential than the metal ion targeted for deposition. PMID:26018140

  7. An Empirical Comparison of Variable Standardization Methods in Cluster Analysis.

    ERIC Educational Resources Information Center

    Schaffer, Catherine M.; Green, Paul E.

    1996-01-01

    The common marketing research practice of standardizing the columns of a persons-by-variables data matrix prior to clustering the entities corresponding to the rows was evaluated with 10 large-scale data sets. Results indicate that the column standardization practice may be problematic for some kinds of data that marketing researchers used for…

  8. Robustness of serial clustering of extra-tropical cyclones to the choice of tracking method

    NASA Astrophysics Data System (ADS)

    Pinto, Joaquim G.; Ulbrich, Sven; Karremann, Melanie K.; Stephenson, David B.; Economou, Theodoros; Shaffrey, Len C.

    2016-04-01

    Cyclone families are a frequent synoptic weather feature in the Euro-Atlantic area in winter. Given appropriate large-scale conditions, the occurrence of such series (clusters) of storms may lead to large socio-economic impacts and cumulative losses. Recent studies analyzing Reanalysis data using single cyclone tracking methods have shown that serial clustering of cyclones occurs on both flanks and downstream regions of the North Atlantic storm track. This study explores the sensitivity of serial clustering to the choice of tracking method. With this aim, the IMILAST cyclone track database based on ERA-interim data is analysed. Clustering is estimated by the dispersion (ratio of variance to mean) of winter (DJF) cyclones passages near each grid point over the Euro-Atlantic area. Results indicate that while the general pattern of clustering is identified for all methods, there are considerable differences in detail. This can primarily be attributed to the differences in the variance of cyclone counts between the methods, which range up to one order of magnitude. Nevertheless, clustering over the Eastern North Atlantic and Western Europe can be identified for all methods and can thus be generally considered as a robust feature. The statistical links between large-scale patterns like the NAO and clustering are obtained for all methods, though with different magnitudes. We conclude that the occurrence of cyclone clustering over the Eastern North Atlantic and Western Europe is largely independent from the choice of tracking method and hence from the definition of a cyclone.

  9. Random Sampling of Quantum States: a Survey of Methods. And Some Issues Regarding the Overparametrized Method

    NASA Astrophysics Data System (ADS)

    Maziero, Jonas

    2015-12-01

    The numerical generation of random quantum states (RQS) is an important procedure for investigations in quantum information science. Here, we review some methods that may be used for performing that task. We start by presenting a simple procedure for generating random state vectors, for which the main tool is the random sampling of unbiased discrete probability distributions (DPD). Afterwards, the creation of random density matrices is addressed. In this context, we first present the standard method, which consists in using the spectral decomposition of a quantum state for getting RQS from random DPDs and random unitary matrices. In the sequence, the Bloch vector parametrization method is described. This approach, despite being useful in several instances, is not in general convenient for RQS generation. In the last part of the article, we regard the overparametrized method (OPM) and the related Ginibre and Bures techniques. The OPM can be used to create random positive semidefinite matrices with unit trace from randomly produced general complex matrices in a simple way that is friendly for numerical implementations. We consider a physically relevant issue related to the possible domains that may be used for the real and imaginary parts of the elements of such general complex matrices. Subsequently, a too fast concentration of measure in the quantum state space that appears in this parametrization is noticed.

  10. Hydrogen-bond cooperative effects in small cyclic water clusters as revealed by the interacting quantum atoms approach.

    PubMed

    Guevara-Vela, José Manuel; Chávez-Calvillo, Rodrigo; García-Revilla, Marco; Hernández-Trujillo, Jesús; Christiansen, Ove; Francisco, Evelio; Martín Pendás, Angel; Rocha-Rinza, Tomás

    2013-10-11

    The cooperative effects of hydrogen bonding in small water clusters (H2 O)n (n=3-6) have been studied by using the partition of the electronic energy in accordance with the interacting quantum atoms (IQA) approach. The IQA energy splitting is complemented by a topological analysis of the electron density (ρ(r)) compliant with the quantum theory of atoms-in-molecules (QTAIM) and the calculation of electrostatic interactions by using one- and two-electron integrals, thereby avoiding convergence issues inherent to a multipolar expansion. The results show that the cooperative effects of hydrogen bonding in small water clusters arise from a compromise between: 1) the deformation energy (i.e., the energy necessary to modify the electron density and the configuration of the nuclei of the isolated water molecules to those within the water clusters), and 2) the interaction energy (Eint ) of these contorted molecules in (H2 O)n . Whereas the magnitude of both deformation and interaction energies is enhanced as water molecules are added to the system, the augmentation of the latter becomes dominant when the size of the cluster is increased. In addition, the electrostatic, classic, and exchange components of Eint for a pair of water molecules in the cluster (H2 O)n-1 become more attractive when a new H2 O unit is incorporated to generate the system (H2 O)n with the last-mentioned contribution being consistently the most important part of Eint throughout the hydrogen bonds under consideration. This is opposed to the traditional view, which regards hydrogen bonding in water as an electrostatically driven interaction. Overall, the trends of the delocalization indices, δ(Ω,Ω'), the QTAIM atomic charges, the topology of ρ(r), and the IQA results altogether show how polarization, charge transfer, electrostatics, and covalency contribute to the cooperative effects of hydrogen bonding in small water clusters. It is our hope that the analysis presented in this paper could

  11. An Algebraic Method for Exploring Quantum Monodromy and Quantum Phase Transitions in Non-Rigid Molecules

    NASA Astrophysics Data System (ADS)

    Larese, D.; Iachello, F.

    2011-06-01

    A simple algebraic Hamiltonian has been used to explore the vibrational and rotational spectra of the skeletal bending modes of HCNO, BrCNO, NCNCS, and other ``floppy`` (quasi-linear or quasi-bent) molecules. These molecules have large-amplitude, low-energy bending modes and champagne-bottle potential surfaces, making them good candidates for observing quantum phase transitions (QPT). We describe the geometric phase transitions from bent to linear in these and other non-rigid molecules, quantitatively analysing the spectroscopy signatures of ground state QPT, excited state QPT, and quantum monodromy.The algebraic framework is ideal for this work because of its small calculational effort yet robust results. Although these methods have historically found success with tri- and four-atomic molecules, we now address five-atomic and simple branched molecules such as CH_3NCO and GeH_3NCO. Extraction of potential functions is completed for several molecules, resulting in predictions of barriers to linearity and equilibrium bond angles.

  12. Quantum Simulations of Solvated Biomolecules Using Hybrid Methods

    NASA Astrophysics Data System (ADS)

    Hodak, Miroslav

    2009-03-01

    One of the most important challenges in quantum simulations on biomolecules is efficient and accurate inclusion of the solvent, because the solvent atoms usually outnumber those in the biomolecule of interest. We have developed a hybrid method that allows for explicit quantum-mechanical treatment of the solvent at low computational cost. In this method, Kohn-Sham (KS) density functional theory (DFT) is combined with an orbital-free (OF) DFT. Kohn-Sham (KS) DFT is used to describe the biomolecule and its first solvation shells, while the orbital-free (OF) DFT is employed for the rest of the solvent. The OF part is fully O(N) and capable of handling 10^5 solvent molecules on current parallel supercomputers, while taking only ˜ 10 % of the total time. The compatibility between the KS and OF DFT methods enables seamless integration between the two. In particular, the flow of solvent molecules across the KS/OF interface is allowed and the total energy is conserved. As the first large-scale applications, the hybrid method has been used to investigate the binding of copper ions to proteins involved in prion (PrP) and Parkinson's diseases. Our results for the PrP, which causes mad cow disease when misfolded, resolve a contradiction found in experiments, in which a stronger binding mode is replaced by a weaker one when concentration of copper ions is increased, and show how it can act as a copper buffer. Furthermore, incorporation of copper stabilizes the structure of the full-length PrP, suggesting its protective role in prion diseases. For alpha-synuclein, a Parkinson's disease (PD) protein, we show that Cu binding modifies the protein structurally, making it more susceptible to misfolding -- an initial step in the onset of PD. In collaboration with W. Lu, F. Rose and J. Bernholc.

  13. A heuristic method for finding the optimal number of clusters with application in medical data.

    PubMed

    Bayati, Hamidreza; Davoudi, Heydar; Fatemizadeh, Emad

    2008-01-01

    In this paper, a heuristic method for determining the optimal number of clusters is proposed. Four clustering algorithms, namely K-means, Growing Neural Gas, Simulated Annealing based technique, and Fuzzy C-means in conjunction with three well known cluster validity indices, namely Davies-Bouldin index, Calinski-Harabasz index, Maulik-Bandyopadhyay index, in addition to the proposed index are used. Our simulations evaluate capability of mentioned indices in some artificial and medical datasets. PMID:19163761

  14. A cluster merging method for time series microarray with production values.

    PubMed

    Chira, Camelia; Sedano, Javier; Camara, Monica; Prieto, Carlos; Villar, Jose R; Corchado, Emilio

    2014-09-01

    A challenging task in time-course microarray data analysis is to cluster genes meaningfully combining the information provided by multiple replicates covering the same key time points. This paper proposes a novel cluster merging method to accomplish this goal obtaining groups with highly correlated genes. The main idea behind the proposed method is to generate a clustering starting from groups created based on individual temporal series (representing different biological replicates measured in the same time points) and merging them by taking into account the frequency by which two genes are assembled together in each clustering. The gene groups at the level of individual time series are generated using several shape-based clustering methods. This study is focused on a real-world time series microarray task with the aim to find co-expressed genes related to the production and growth of a certain bacteria. The shape-based clustering methods used at the level of individual time series rely on identifying similar gene expression patterns over time which, in some models, are further matched to the pattern of production/growth. The proposed cluster merging method is able to produce meaningful gene groups which can be naturally ranked by the level of agreement on the clustering among individual time series. The list of clusters and genes is further sorted based on the information correlation coefficient and new problem-specific relevant measures. Computational experiments and results of the cluster merging method are analyzed from a biological perspective and further compared with the clustering generated based on the mean value of time series and the same shape-based algorithm.

  15. An introduction to quantum chemical methods applied to drug design.

    PubMed

    Stenta, Marco; Dal Peraro, Matteo

    2011-06-01

    The advent of molecular medicine allowed identifying the malfunctioning of subcellular processes as the source of many diseases. Since then, drugs are not only discovered, but actually designed to fulfill a precise task. Modern computational techniques, based on molecular modeling, play a relevant role both in target identification and drug lead development. By flanking and integrating standard experimental techniques, modeling has proven itself as a powerful tool across the drug design process. The success of computational methods depends on a balance between cost (computation time) and accuracy. Thus, the integration of innovative theories and more powerful hardware architectures allows molecular modeling to be used as a reliable tool for rationalizing the results of experiments and accelerating the development of new drug design strategies. We present an overview of the most common quantum chemistry computational approaches, providing for each one a general theoretical introduction to highlight limitations and strong points. We then discuss recent developments in software and hardware resources, which have allowed state-of-the-art of computational quantum chemistry to be applied to drug development.

  16. An extended affinity propagation clustering method based on different data density types.

    PubMed

    Zhao, XiuLi; Xu, WeiXiang

    2015-01-01

    Affinity propagation (AP) algorithm, as a novel clustering method, does not require the users to specify the initial cluster centers in advance, which regards all data points as potential exemplars (cluster centers) equally and groups the clusters totally by the similar degree among the data points. But in many cases there exist some different intensive areas within the same data set, which means that the data set does not distribute homogeneously. In such situation the AP algorithm cannot group the data points into ideal clusters. In this paper, we proposed an extended AP clustering algorithm to deal with such a problem. There are two steps in our method: firstly the data set is partitioned into several data density types according to the nearest distances of each data point; and then the AP clustering method is, respectively, used to group the data points into clusters in each data density type. Two experiments are carried out to evaluate the performance of our algorithm: one utilizes an artificial data set and the other uses a real seismic data set. The experiment results show that groups are obtained more accurately by our algorithm than OPTICS and AP clustering algorithm itself.

  17. An Extended Affinity Propagation Clustering Method Based on Different Data Density Types

    PubMed Central

    Zhao, XiuLi; Xu, WeiXiang

    2015-01-01

    Affinity propagation (AP) algorithm, as a novel clustering method, does not require the users to specify the initial cluster centers in advance, which regards all data points as potential exemplars (cluster centers) equally and groups the clusters totally by the similar degree among the data points. But in many cases there exist some different intensive areas within the same data set, which means that the data set does not distribute homogeneously. In such situation the AP algorithm cannot group the data points into ideal clusters. In this paper, we proposed an extended AP clustering algorithm to deal with such a problem. There are two steps in our method: firstly the data set is partitioned into several data density types according to the nearest distances of each data point; and then the AP clustering method is, respectively, used to group the data points into clusters in each data density type. Two experiments are carried out to evaluate the performance of our algorithm: one utilizes an artificial data set and the other uses a real seismic data set. The experiment results show that groups are obtained more accurately by our algorithm than OPTICS and AP clustering algorithm itself. PMID:25685144

  18. Non-unitary probabilistic quantum computing circuit and method

    NASA Technical Reports Server (NTRS)

    Williams, Colin P. (Inventor); Gingrich, Robert M. (Inventor)

    2009-01-01

    A quantum circuit performing quantum computation in a quantum computer. A chosen transformation of an initial n-qubit state is probabilistically obtained. The circuit comprises a unitary quantum operator obtained from a non-unitary quantum operator, operating on an n-qubit state and an ancilla state. When operation on the ancilla state provides a success condition, computation is stopped. When operation on the ancilla state provides a failure condition, computation is performed again on the ancilla state and the n-qubit state obtained in the previous computation, until a success condition is obtained.

  19. Using full configuration interaction quantum Monte Carlo in a seniority zero space to investigate the correlation energy equivalence of pair coupled cluster doubles and doubly occupied configuration interaction

    NASA Astrophysics Data System (ADS)

    Shepherd, James J.; Henderson, Thomas M.; Scuseria, Gustavo E.

    2016-03-01

    Over the past few years, pair coupled cluster doubles (pCCD) has shown promise for the description of strong correlation. This promise is related to its apparent ability to match results from doubly occupied configuration interaction (DOCI), even though the latter method has exponential computational cost. Here, by modifying the full configuration interaction quantum Monte Carlo algorithm to sample only the seniority zero sector of Hilbert space, we show that the DOCI and pCCD energies are in agreement for a variety of 2D Hubbard models, including for systems well out of reach for conventional configuration interaction algorithms. Our calculations are aided by the sign problem being much reduced in the seniority zero space compared with the full space. We present evidence for this and then discuss the sign problem in terms of the wave function of the system which appears to have a simplified sign structure.

  20. Nonzero-temperature entanglement negativity of quantum spin models: Area law, linked cluster expansions, and sudden death.

    PubMed

    Sherman, Nicholas E; Devakul, Trithep; Hastings, Matthew B; Singh, Rajiv R P

    2016-02-01

    We show that the bipartite logarithmic entanglement negativity (EN) of quantum spin models obeys an area law at all nonzero temperatures. We develop numerical linked cluster (NLC) expansions for the "area-law" logarithmic entanglement negativity as a function of temperature and other parameters. For one-dimensional models the results of NLC are compared with exact diagonalization on finite systems and are found to agree very well. The NLC results are also obtained for two dimensional XXZ and transverse field Ising models. In all cases, we find a sudden onset (or sudden death) of negativity at a finite temperature above which the negativity is zero. We use perturbation theory to develop a physical picture for this sudden onset (or sudden death). The onset of EN or its magnitude are insensitive to classical finite-temperature phase transitions, supporting the argument for absence of any role of quantum mechanics at such transitions. On approach to a quantum critical point at T=0, negativity shows critical scaling in size and temperature. PMID:26986309

  1. Nonzero-temperature entanglement negativity of quantum spin models: Area law, linked cluster expansions, and sudden death.

    PubMed

    Sherman, Nicholas E; Devakul, Trithep; Hastings, Matthew B; Singh, Rajiv R P

    2016-02-01

    We show that the bipartite logarithmic entanglement negativity (EN) of quantum spin models obeys an area law at all nonzero temperatures. We develop numerical linked cluster (NLC) expansions for the "area-law" logarithmic entanglement negativity as a function of temperature and other parameters. For one-dimensional models the results of NLC are compared with exact diagonalization on finite systems and are found to agree very well. The NLC results are also obtained for two dimensional XXZ and transverse field Ising models. In all cases, we find a sudden onset (or sudden death) of negativity at a finite temperature above which the negativity is zero. We use perturbation theory to develop a physical picture for this sudden onset (or sudden death). The onset of EN or its magnitude are insensitive to classical finite-temperature phase transitions, supporting the argument for absence of any role of quantum mechanics at such transitions. On approach to a quantum critical point at T=0, negativity shows critical scaling in size and temperature.

  2. Nonzero-temperature entanglement negativity of quantum spin models: Area law, linked cluster expansions, and sudden death

    NASA Astrophysics Data System (ADS)

    Sherman, Nicholas E.; Devakul, Trithep; Hastings, Matthew B.; Singh, Rajiv R. P.

    2016-02-01

    We show that the bipartite logarithmic entanglement negativity (EN) of quantum spin models obeys an area law at all nonzero temperatures. We develop numerical linked cluster (NLC) expansions for the "area-law" logarithmic entanglement negativity as a function of temperature and other parameters. For one-dimensional models the results of NLC are compared with exact diagonalization on finite systems and are found to agree very well. The NLC results are also obtained for two dimensional X X Z and transverse field Ising models. In all cases, we find a sudden onset (or sudden death) of negativity at a finite temperature above which the negativity is zero. We use perturbation theory to develop a physical picture for this sudden onset (or sudden death). The onset of EN or its magnitude are insensitive to classical finite-temperature phase transitions, supporting the argument for absence of any role of quantum mechanics at such transitions. On approach to a quantum critical point at T =0 , negativity shows critical scaling in size and temperature.

  3. New variable stars in open clusters. I. Methods and results for 20 open clusters

    NASA Astrophysics Data System (ADS)

    Paunzen, E.; Zwintz, K.; Maitzen, H. M.; Pintado, O. I.; Rode-Paunzen, M.

    2004-04-01

    We present high precision CCD photometry of 1791 objects in 20 open clusters with an age of 10 Myr to 1 Gyr. These observations were performed within the Δ a photometric system which is primarily used to detect chemically peculiar stars of the upper main sequence. Time bases range from 30 min up to 60 days with data from several nights. We describe the time series analysis reaching a detection limit of down to 0.006 mag for apparent variability. In total, we have detected 35 variable objects of which four are not members of their corresponding clusters. The variables cover the entire Hertzsprung-Russell diagram, hence they are interesting targets for follow-up observations. Based on observations obtained at Complejo Astronómico el Leoncito (CASLEO), operated under the agreement between the Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina and the National Universities of La Plata, Córdoba y San Juan; ESO-La Silla and UTSO-Las Campanas.

  4. Spectral methods and cluster structure in correlation-based networks

    NASA Astrophysics Data System (ADS)

    Heimo, Tapio; Tibély, Gergely; Saramäki, Jari; Kaski, Kimmo; Kertész, János

    2008-10-01

    We investigate how in complex systems the eigenpairs of the matrices derived from the correlations of multichannel observations reflect the cluster structure of the underlying networks. For this we use daily return data from the NYSE and focus specifically on the spectral properties of weight W=|-δ and diffusion matrices D=W/sj-δ, where C is the correlation matrix and si=∑jW the strength of node j. The eigenvalues (and corresponding eigenvectors) of the weight matrix are ranked in descending order. As in the earlier observations, the first eigenvector stands for a measure of the market correlations. Its components are, to first approximation, equal to the strengths of the nodes and there is a second order, roughly linear, correction. The high ranking eigenvectors, excluding the highest ranking one, are usually assigned to market sectors and industrial branches. Our study shows that both for weight and diffusion matrices the eigenpair analysis is not capable of easily deducing the cluster structure of the network without a priori knowledge. In addition we have studied the clustering of stocks using the asset graph approach with and without spectrum based noise filtering. It turns out that asset graphs are quite insensitive to noise and there is no sharp percolation transition as a function of the ratio of bonds included, thus no natural threshold value for that ratio seems to exist. We suggest that these observations can be of use for other correlation based networks as well.

  5. A NEW METHOD TO QUANTIFY X-RAY SUBSTRUCTURES IN CLUSTERS OF GALAXIES

    SciTech Connect

    Andrade-Santos, Felipe; Lima Neto, Gastao B.; Lagana, Tatiana F.

    2012-02-20

    We present a new method to quantify substructures in clusters of galaxies, based on the analysis of the intensity of structures. This analysis is done in a residual image that is the result of the subtraction of a surface brightness model, obtained by fitting a two-dimensional analytical model ({beta}-model or Sersic profile) with elliptical symmetry, from the X-ray image. Our method is applied to 34 clusters observed by the Chandra Space Telescope that are in the redshift range z in [0.02, 0.2] and have a signal-to-noise ratio (S/N) greater than 100. We present the calibration of the method and the relations between the substructure level with physical quantities, such as the mass, X-ray luminosity, temperature, and cluster redshift. We use our method to separate the clusters in two sub-samples of high- and low-substructure levels. We conclude, using Monte Carlo simulations, that the method recuperates very well the true amount of substructure for small angular core radii clusters (with respect to the whole image size) and good S/N observations. We find no evidence of correlation between the substructure level and physical properties of the clusters such as gas temperature, X-ray luminosity, and redshift; however, analysis suggest a trend between the substructure level and cluster mass. The scaling relations for the two sub-samples (high- and low-substructure level clusters) are different (they present an offset, i.e., given a fixed mass or temperature, low-substructure clusters tend to be more X-ray luminous), which is an important result for cosmological tests using the mass-luminosity relation to obtain the cluster mass function, since they rely on the assumption that clusters do not present different scaling relations according to their dynamical state.

  6. Percolation of the site random-cluster model by Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Wang, Songsong; Zhang, Wanzhou; Ding, Chengxiang

    2015-08-01

    We propose a site random-cluster model by introducing an additional cluster weight in the partition function of the traditional site percolation. To simulate the model on a square lattice, we combine the color-assignation and the Swendsen-Wang methods to design a highly efficient cluster algorithm with a small critical slowing-down phenomenon. To verify whether or not it is consistent with the bond random-cluster model, we measure several quantities, such as the wrapping probability Re, the percolating cluster density P∞, and the magnetic susceptibility per site χp, as well as two exponents, such as the thermal exponent yt and the fractal dimension yh of the percolating cluster. We find that for different exponents of cluster weight q =1.5 , 2, 2.5 , 3, 3.5 , and 4, the numerical estimation of the exponents yt and yh are consistent with the theoretical values. The universalities of the site random-cluster model and the bond random-cluster model are completely identical. For larger values of q , we find obvious signatures of the first-order percolation transition by the histograms and the hysteresis loops of percolating cluster density and the energy per site. Our results are helpful for the understanding of the percolation of traditional statistical models.

  7. Performance Optimization of Tensor Contraction Expressions for Many Body Methods in Quantum Chemistry

    SciTech Connect

    Krishnamoorthy, Sriram; Bernholdt, David E; Pitzer, R. M.; Sadayappan, Ponnuswamy

    2009-01-01

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations, such as minimization of cache misses and utilization of multimedia vector instructions, are discussed. A library for efficient index permutation of multidimensional tensors is described, and experimental performance data is provided that demonstrates its effectiveness.

  8. Performance Optimization of Tensor Contraction Expressions for Many Body Methods in Quantum Chemistry

    SciTech Connect

    Hartono, Albert; Lu, Qingda; henretty, thomas; Krishnamoorthy, Sriram; zhang, huaijian; Baumgartner, Gerald; Bernholdt, David E.; Nooijen, Marcel; Pitzer, Russell M.; Ramanujam, J.; Sadayappan, Ponnuswamy

    2009-11-12

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations such as minimization of cache misses and utilization of multimedia vector instructions are discussed. A library for efficient index permutation of multi-dimensional tensors is described and experimental performance data is provided that demonstrates its effectiveness.

  9. Performance optimization of tensor contraction expressions for many-body methods in quantum chemistry.

    PubMed

    Hartono, Albert; Lu, Qingda; Henretty, Thomas; Krishnamoorthy, Sriram; Zhang, Huaijian; Baumgartner, Gerald; Bernholdt, David E; Nooijen, Marcel; Pitzer, Russell; Ramanujam, J; Sadayappan, P

    2009-11-12

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations, such as minimization of cache misses and utilization of multimedia vector instructions, are discussed. A library for efficient index permutation of multidimensional tensors is described, and experimental performance data is provided that demonstrates its effectiveness. PMID:19888780

  10. Method of precisely modifying predetermined surface layers of a workpiece by cluster ion impact therewith

    DOEpatents

    Friedman, Lewis; Buehler, Robert J.; Matthew, Michael W.; Ledbetter, Myron

    1985-01-01

    A method of precisely modifying a selected area of a workpiece by producing a beam of charged cluster ions that is narrowly mass selected to a predetermined mean size of cluster ions within a range of 25 to 10.sup.6 atoms per cluster ion, and accelerated in a beam to a critical velocity. The accelerated beam is used to impact a selected area of an outer surface of the workpiece at a preselected rate of impacts of cluster ions/cm.sup.2 /sec. in order to effect a precise modification in that selected area of the workpiece.

  11. Method of precisely modifying predetermined surface layers of a workpiece by cluster ion impact therewith

    DOEpatents

    Friedman, L.; Beuhler, R.J.; Matthew, M.W.; Ledbetter, M.

    1984-06-25

    A method of precisely modifying a selected area of a workpiece by producing a beam of charged cluster ions that is narrowly mass selected to a predetermined mean size of cluster ions within a range of 25 to 10/sup 6/ atoms per cluster ion, and accelerated in a beam to a critical velocity. The accelerated beam is used to impact a selected area of an outer surface of the workpiece at a preselected rate of impacts of cluster ions/cm/sup 2//sec in order to effect a precise modification in that selected area of the workpiece.

  12. High quantum yield ZnO quantum dots synthesizing via an ultrasonication microreactor method.

    PubMed

    Yang, Weimin; Yang, Huafang; Ding, Wenhao; Zhang, Bing; Zhang, Le; Wang, Lixi; Yu, Mingxun; Zhang, Qitu

    2016-11-01

    Green emission ZnO quantum dots were synthesized by an ultrasonic microreactor. Ultrasonic radiation brought bubbles through ultrasonic cavitation. These bubbles built microreactor inside the microreactor. The photoluminescence properties of ZnO quantum dots synthesized with different flow rate, ultrasonic power and temperature were discussed. Flow rate, ultrasonic power and temperature would influence the type and quantity of defects in ZnO quantum dots. The sizes of ZnO quantum dots would be controlled by those conditions as well. Flow rate affected the reaction time. With the increasing of flow rate, the sizes of ZnO quantum dots decreased and the quantum yields first increased then decreased. Ultrasonic power changed the ultrasonic cavitation intensity, which affected the reaction energy and the separation of the solution. With the increasing of ultrasonic power, sizes of ZnO quantum dots first decreased then increased, while the quantum yields kept increasing. The effect of ultrasonic temperature on the photoluminescence properties of ZnO quantum dots was influenced by the flow rate. Different flow rate related to opposite changing trend. Moreover, the quantum yields of ZnO QDs synthesized by ultrasonic microreactor could reach 64.7%, which is higher than those synthesized only under ultrasonic radiation or only by microreactor. PMID:27245962

  13. High quantum yield ZnO quantum dots synthesizing via an ultrasonication microreactor method.

    PubMed

    Yang, Weimin; Yang, Huafang; Ding, Wenhao; Zhang, Bing; Zhang, Le; Wang, Lixi; Yu, Mingxun; Zhang, Qitu

    2016-11-01

    Green emission ZnO quantum dots were synthesized by an ultrasonic microreactor. Ultrasonic radiation brought bubbles through ultrasonic cavitation. These bubbles built microreactor inside the microreactor. The photoluminescence properties of ZnO quantum dots synthesized with different flow rate, ultrasonic power and temperature were discussed. Flow rate, ultrasonic power and temperature would influence the type and quantity of defects in ZnO quantum dots. The sizes of ZnO quantum dots would be controlled by those conditions as well. Flow rate affected the reaction time. With the increasing of flow rate, the sizes of ZnO quantum dots decreased and the quantum yields first increased then decreased. Ultrasonic power changed the ultrasonic cavitation intensity, which affected the reaction energy and the separation of the solution. With the increasing of ultrasonic power, sizes of ZnO quantum dots first decreased then increased, while the quantum yields kept increasing. The effect of ultrasonic temperature on the photoluminescence properties of ZnO quantum dots was influenced by the flow rate. Different flow rate related to opposite changing trend. Moreover, the quantum yields of ZnO QDs synthesized by ultrasonic microreactor could reach 64.7%, which is higher than those synthesized only under ultrasonic radiation or only by microreactor.

  14. A Comparison of Single Sample and Bootstrap Methods to Assess Mediation in Cluster Randomized Trials

    ERIC Educational Resources Information Center

    Pituch, Keenan A.; Stapleton, Laura M.; Kang, Joo Youn

    2006-01-01

    A Monte Carlo study examined the statistical performance of single sample and bootstrap methods that can be used to test and form confidence interval estimates of indirect effects in two cluster randomized experimental designs. The designs were similar in that they featured random assignment of clusters to one of two treatment conditions and…

  15. Selective spin transport through a quantum heterostructure: Transfer matrix method

    NASA Astrophysics Data System (ADS)

    Dey, Moumita; Maiti, Santanu K.

    2016-09-01

    In the present work, we propose that a one-dimensional quantum heterostructure composed of magnetic and non-magnetic (NM) atomic sites can be utilized as a spin filter for a wide range of applied bias voltage. A simple tight-binding framework is given to describe the conducting junction where the heterostructure is coupled to two semi-infinite one-dimensional NM electrodes. Based on transfer matrix method, all the calculations are performed numerically which describe two-terminal spin-dependent transmission probability along with junction current through the wire. Our detailed analysis may provide fundamental aspects of selective spin transport phenomena in one-dimensional heterostructures at nanoscale level.

  16. Atomistic Modeling of Nanostructures via the BFS Quantum Approximate Method

    NASA Technical Reports Server (NTRS)

    Bozzolo, Guillermo; Garces, Jorge E.; Noebe, Ronald D.; Farias, D.

    2003-01-01

    Ideally, computational modeling techniques for nanoscopic physics would be able to perform free of limitations on the type and number of elements, while providing comparable accuracy when dealing with bulk or surface problems. Computational efficiency is also desirable, if not mandatory, for properly dealing with the complexity of typical nano-strucured systems. A quantum approximate technique, the BFS method for alloys, which attempts to meet these demands, is introduced for the calculation of the energetics of nanostructures. The versatility of the technique is demonstrated through analysis of diverse systems, including multi-phase precipitation in a five element Ni-Al-Ti-Cr-Cu alloy and the formation of mixed composition Co-Cu islands on a metallic Cu(III) substrate.

  17. An incremental DPMM-based method for trajectory clustering, modeling, and retrieval.

    PubMed

    Hu, Weiming; Li, Xi; Tian, Guodong; Maybank, Stephen; Zhang, Zhongfei

    2013-05-01

    Trajectory analysis is the basis for many applications, such as indexing of motion events in videos, activity recognition, and surveillance. In this paper, the Dirichlet process mixture model (DPMM) is applied to trajectory clustering, modeling, and retrieval. We propose an incremental version of a DPMM-based clustering algorithm and apply it to cluster trajectories. An appropriate number of trajectory clusters is determined automatically. When trajectories belonging to new clusters arrive, the new clusters can be identified online and added to the model without any retraining using the previous data. A time-sensitive Dirichlet process mixture model (tDPMM) is applied to each trajectory cluster for learning the trajectory pattern which represents the time-series characteristics of the trajectories in the cluster. Then, a parameterized index is constructed for each cluster. A novel likelihood estimation algorithm for the tDPMM is proposed, and a trajectory-based video retrieval model is developed. The tDPMM-based probabilistic matching method and the DPMM-based model growing method are combined to make the retrieval model scalable and adaptable. Experimental comparisons with state-of-the-art algorithms demonstrate the effectiveness of our algorithm. PMID:23520251

  18. Cryptanalysis of Controlled Quantum Secure Direct Communication and Authentication Protocol Based on Five-Particle Cluster State and Quantum One-Time Pad

    NASA Astrophysics Data System (ADS)

    Liu, Zhihao; Chen, Hanwu; Liu, Wenjie

    2016-10-01

    A new attack strategy, the so-called intercept-selectively-measure-resend attack is put forward. It shows that there are some security issues in the controlled quantum secure direct communication (CQSDC) and authentication protocol based on five-particle cluster states and quantum one-time pad. Firstly, an eavesdropper (Eve) can use this attack to eavesdrop on 0.656 bit of every bit of the identity string of the receiver and 1.406 bits of every couple of the corresponding bits of the secret message without being detected. Also, she can eavesdrop on 0.311 bit of every bit of the identity string of the controller. Secondly, the receiver can also take this attack to obtain 1.311 bits of every couple of the corresponding bits of the secret message without the permission of the controller, which is not allowed in the CQSDC protocols. In fact, there is another security issue in this protocol, that is, one half of the information about the secret is leaked out unconsciously. In addition, an alternative attack strategy which is called as the selective-CNOT-operation attack strategy to attack this protocol is discussed.

  19. Cryptanalysis of Controlled Quantum Secure Direct Communication and Authentication Protocol Based on Five-Particle Cluster State and Quantum One-Time Pad

    NASA Astrophysics Data System (ADS)

    Liu, Zhihao; Chen, Hanwu; Liu, Wenjie

    2016-06-01

    A new attack strategy, the so-called intercept-selectively-measure-resend attack is put forward. It shows that there are some security issues in the controlled quantum secure direct communication (CQSDC) and authentication protocol based on five-particle cluster states and quantum one-time pad. Firstly, an eavesdropper (Eve) can use this attack to eavesdrop on 0.656 bit of every bit of the identity string of the receiver and 1.406 bits of every couple of the corresponding bits of the secret message without being detected. Also, she can eavesdrop on 0.311 bit of every bit of the identity string of the controller. Secondly, the receiver can also take this attack to obtain 1.311 bits of every couple of the corresponding bits of the secret message without the permission of the controller, which is not allowed in the CQSDC protocols. In fact, there is another security issue in this protocol, that is, one half of the information about the secret is leaked out unconsciously. In addition, an alternative attack strategy which is called as the selective-CNOT-operation attack strategy to attack this protocol is discussed.

  20. Vibrational spectroscopy of cluster ions: Two novel methods

    SciTech Connect

    Yeh, L.I.; Okumura, M.; Myers, J.D.; Lee, Y.T.

    1987-07-01

    Two sensitive techniques are discussed for obtaining vibrational spectra of cluster ions. The first approach is to attach a H/sub 2/ molecule to the hydrated hydronium ions. Because the original goal was to study the hydrated hydronium ions, the attached H/sub 2/ is hoped to have only a small effect on the spectrum. After an O-H stretch of the cluster ion has been excited, it vibrationally predissociates, losing the H/sub 2/. By monitoring the dissociation product as a function of laser frequency, the absorption spectra of these H/sub 3/O/sup +/ . (H/sub 2/O)/sub n/ . H/sub 2/ (n = 1,2,3) ions have been found. The second approach is to detect the vibrationally excited H/sub 3/O/sup +/ . (H/sub 2/O)/sub n/ (n = 1,2,3) ions using an infrared multiphoton dissociation process. The procedure is to first excite from v = 0 to v = 1 in the O-H stretch using a tunable ir laser. We then make use of the fact that the density of states near v = 0 and v = 1 are very different, and the vibrationally excited ionic clusters, which contain many low frequency vibrations, are likely to be in the quasicontinuum region for the sequential excitation by a fixed frequency laser. This means that one can distinguish between ground state and vibrationally excited H/sub 3/O/sup +/ . (H/sub 2/O)/sub n/ by using a multiphoton dissociation (MPD) process to selectively dissociate the latter using a CO/sub 2/ laser. Once again, we monitor the dissociation product ion signal as a function of the excitation frequency of the first laser to get the absorption spectra of the H/sub 3/O/sup +/ . (H/sub 2/O)/sub n/ ions. 5 refs.

  1. Communication: Improved pair approximations in local coupled-cluster methods

    SciTech Connect

    Schwilk, Max; Werner, Hans-Joachim; Usvyat, Denis

    2015-03-28

    In local coupled cluster treatments the electron pairs can be classified according to the magnitude of their energy contributions or distances into strong, close, weak, and distant pairs. Different approximations are introduced for the latter three classes. In this communication, an improved simplified treatment of close and weak pairs is proposed, which is based on long-range cancellations of individually slowly decaying contributions in the amplitude equations. Benchmark calculations for correlation, reaction, and activation energies demonstrate that these approximations work extremely well, while pair approximations based on local second-order Møller-Plesset theory can lead to errors that are 1-2 orders of magnitude larger.

  2. Frequency-domain multiscale quantum mechanics/electromagnetics simulation method

    SciTech Connect

    Meng, Lingyi; Yin, Zhenyu; Yam, ChiYung E-mail: ghc@everest.hku.hk; Koo, SiuKong; Chen, GuanHua E-mail: ghc@everest.hku.hk; Chen, Quan; Wong, Ngai

    2013-12-28

    A frequency-domain quantum mechanics and electromagnetics (QM/EM) method is developed. Compared with the time-domain QM/EM method [Meng et al., J. Chem. Theory Comput. 8, 1190–1199 (2012)], the newly developed frequency-domain QM/EM method could effectively capture the dynamic properties of electronic devices over a broader range of operating frequencies. The system is divided into QM and EM regions and solved in a self-consistent manner via updating the boundary conditions at the QM and EM interface. The calculated potential distributions and current densities at the interface are taken as the boundary conditions for the QM and EM calculations, respectively, which facilitate the information exchange between the QM and EM calculations and ensure that the potential, charge, and current distributions are continuous across the QM/EM interface. Via Fourier transformation, the dynamic admittance calculated from the time-domain and frequency-domain QM/EM methods is compared for a carbon nanotube based molecular device.

  3. A two-stage method for microcalcification cluster segmentation in mammography by deformable models

    SciTech Connect

    Arikidis, N.; Kazantzi, A.; Skiadopoulos, S.; Karahaliou, A.; Costaridou, L.; Vassiou, K.

    2015-10-15

    Purpose: Segmentation of microcalcification (MC) clusters in x-ray mammography is a difficult task for radiologists. Accurate segmentation is prerequisite for quantitative image analysis of MC clusters and subsequent feature extraction and classification in computer-aided diagnosis schemes. Methods: In this study, a two-stage semiautomated segmentation method of MC clusters is investigated. The first stage is targeted to accurate and time efficient segmentation of the majority of the particles of a MC cluster, by means of a level set method. The second stage is targeted to shape refinement of selected individual MCs, by means of an active contour model. Both methods are applied in the framework of a rich scale-space representation, provided by the wavelet transform at integer scales. Segmentation reliability of the proposed method in terms of inter and intraobserver agreements was evaluated in a case sample of 80 MC clusters originating from the digital database for screening mammography, corresponding to 4 morphology types (punctate: 22, fine linear branching: 16, pleomorphic: 18, and amorphous: 24) of MC clusters, assessing radiologists’ segmentations quantitatively by two distance metrics (Hausdorff distance—HDIST{sub cluster}, average of minimum distance—AMINDIST{sub cluster}) and the area overlap measure (AOM{sub cluster}). The effect of the proposed segmentation method on MC cluster characterization accuracy was evaluated in a case sample of 162 pleomorphic MC clusters (72 malignant and 90 benign). Ten MC cluster features, targeted to capture morphologic properties of individual MCs in a cluster (area, major length, perimeter, compactness, and spread), were extracted and a correlation-based feature selection method yielded a feature subset to feed in a support vector machine classifier. Classification performance of the MC cluster features was estimated by means of the area under receiver operating characteristic curve (Az ± Standard Error) utilizing

  4. Fast optimization of binary clusters using a novel dynamic lattice searching method.

    PubMed

    Wu, Xia; Cheng, Wen

    2014-09-28

    Global optimization of binary clusters has been a difficult task despite of much effort and many efficient methods. Directing toward two types of elements (i.e., homotop problem) in binary clusters, two classes of virtual dynamic lattices are constructed and a modified dynamic lattice searching (DLS) method, i.e., binary DLS (BDLS) method, is developed. However, it was found that the BDLS can only be utilized for the optimization of binary clusters with small sizes because homotop problem is hard to be solved without atomic exchange operation. Therefore, the iterated local search (ILS) method is adopted to solve homotop problem and an efficient method based on the BDLS method and ILS, named as BDLS-ILS, is presented for global optimization of binary clusters. In order to assess the efficiency of the proposed method, binary Lennard-Jones clusters with up to 100 atoms are investigated. Results show that the method is proved to be efficient. Furthermore, the BDLS-ILS method is also adopted to study the geometrical structures of (AuPd)79 clusters with DFT-fit parameters of Gupta potential.

  5. Fast optimization of binary clusters using a novel dynamic lattice searching method

    SciTech Connect

    Wu, Xia Cheng, Wen

    2014-09-28

    Global optimization of binary clusters has been a difficult task despite of much effort and many efficient methods. Directing toward two types of elements (i.e., homotop problem) in binary clusters, two classes of virtual dynamic lattices are constructed and a modified dynamic lattice searching (DLS) method, i.e., binary DLS (BDLS) method, is developed. However, it was found that the BDLS can only be utilized for the optimization of binary clusters with small sizes because homotop problem is hard to be solved without atomic exchange operation. Therefore, the iterated local search (ILS) method is adopted to solve homotop problem and an efficient method based on the BDLS method and ILS, named as BDLS-ILS, is presented for global optimization of binary clusters. In order to assess the efficiency of the proposed method, binary Lennard-Jones clusters with up to 100 atoms are investigated. Results show that the method is proved to be efficient. Furthermore, the BDLS-ILS method is also adopted to study the geometrical structures of (AuPd){sub 79} clusters with DFT-fit parameters of Gupta potential.

  6. Quantum Calculations on Hydrogen Bonds in Certain Water Clusters Show Cooperative Effects

    SciTech Connect

    Znamenskiy, Vasiliy S.; Green, Michael E.

    2007-01-09

    Water molecules in clefts and small clusters are in a significantly different environment than those in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point-charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen-bonded pair of water molecules. The cluster as a whole is in a vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen-bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen-bonding pair; the potential of interaction of two water molecules varies with the number of donor and acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length and changes in energy and length as a function of the number of neighboring donor and acceptor molecules. The energy varies by approximately 6 kBT near room temperature from the highest to the lowest energy when bond length alone is varied, enough to seriously affect simulations.

  7. Quantum Calculations on Hydrogen Bonds in Certain Water Clusters Show Cooperative Effects.

    SciTech Connect

    Znamenskiy, Vasiliy S.; Green, Michael E.

    2006-12-08

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Water molecules in clefts and small clusters are in a significantly different environment than those in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point-charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen-bonded pair of water molecules. The cluster as a whole is in a vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen-bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen-bonding pair; the potential of interaction of two water molecules varies with the number of donor and acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length and changes in energy and length as a function of the number of neighboring donor and acceptor molecules. The energy varies by approximately 6 kBT near room temperature from the highest to the lowest energy when bond length alone is

  8. The swift UVOT stars survey. I. Methods and test clusters

    SciTech Connect

    Siegel, Michael H.; Porterfield, Blair L.; Linevsky, Jacquelyn S.; Bond, Howard E.; Hoversten, Erik A.; Berrier, Joshua L.; Gronwall, Caryl A.; Holland, Stephen T.; Breeveld, Alice A.; Brown, Peter J. E-mail: blp14@psu.edu E-mail: caryl@astro.psu.edu E-mail: aab@mssl.ucl.ac.uk

    2014-12-01

    We describe the motivations and background of a large survey of nearby stellar populations using the Ultraviolet Optical Telescope (UVOT) on board the Swift Gamma-Ray Burst Mission. UVOT, with its wide field, near-UV sensitivity, and 2.″3 spatial resolution, is uniquely suited to studying nearby stellar populations and providing insight into the near-UV properties of hot stars and the contribution of those stars to the integrated light of more distant stellar populations. We review the state of UV stellar photometry, outline the survey, and address problems specific to wide- and crowded-field UVOT photometry. We present color–magnitude diagrams of the nearby open clusters M67, NGC 188, and NGC 2539, and the globular cluster M79. We demonstrate that UVOT can easily discern the young- and intermediate-age main sequences, blue stragglers, and hot white dwarfs, producing results consistent with previous studies. We also find that it characterizes the blue horizontal branch of M79 and easily identifies a known post-asymptotic giant branch star.

  9. Tunneling dynamics with a mixed quantum-classical method: Quantum corrected propagator combined with frozen Gaussian wave packets

    SciTech Connect

    Gelman, David; Schwartz, Steven D.

    2008-07-14

    The recently developed mixed quantum-classical propagation method is extended to treat tunneling effects in multidimensional systems. Formulated for systems consisting of a quantum primary part and a classical bath of heavier particles, the method employs a frozen Gaussian description for the bath degrees of freedom, while the dynamics of the quantum subsystem is governed by a corrected propagator. The corrections are defined in terms of matrix elements of zeroth-order propagators. The method is applied to a model system of a double-well potential bilinearly coupled to a harmonic oscillator. The extension of the method, which includes nondiagonal elements of the correction propagator, enables an accurate treatment of tunneling in an antisymmetric double-well potential.

  10. Quantum chemical study of small BnCm cluster structures and their physical properties

    NASA Astrophysics Data System (ADS)

    Sharipov, Alexander S.; Loukhovitski, Boris I.; Starik, Alexander M.

    2015-09-01

    Different isomeric forms of BnCm clusters with n = 0, ..., 5, m = 0, ..., 5 with the isomerization energy up to 5 eV have been identified by using the multi-step heuristic algorithm based on semiempirical, ab initio and density functional theory calculations. Physical properties, such as rotational constants and characteristic vibrational temperatures, collision diameter, enthalpy of formation, cohesive energy, dipole moment, static isotropic polarizability and magnetic moment of different isomeric forms have been obtained with the usage of density functional theory. It has been revealed that the electric properties of clusters depend on their structure. It was found that the isomers with linear structure contribute mostly to the average polarizability of the ensemble of the isomeric forms of given class of clusters. Temperature-dependent thermodynamic properties of clusters including specific heat capacity and entropy were calculated taking into account the contribution of excited electronic states and possible isomeric forms in the anharmonic oscillator approximation for vibrational degrees of freedom. It was shown that the effect of structural isomers on the thermodynamic properties of the Boltzmann ensemble of clusters can be significant. Supplementary material in the form of one zip file available from the Journal web page at http://dx.doi.org/10.1140/epjd/e2015-60308-0

  11. Clustering Scientific Publications Based on Citation Relations: A Systematic Comparison of Different Methods.

    PubMed

    Šubelj, Lovro; van Eck, Nees Jan; Waltman, Ludo

    2016-01-01

    Clustering methods are applied regularly in the bibliometric literature to identify research areas or scientific fields. These methods are for instance used to group publications into clusters based on their relations in a citation network. In the network science literature, many clustering methods, often referred to as graph partitioning or community detection techniques, have been developed. Focusing on the problem of clustering the publications in a citation network, we present a systematic comparison of the performance of a large number of these clustering methods. Using a number of different citation networks, some of them relatively small and others very large, we extensively study the statistical properties of the results provided by different methods. In addition, we also carry out an expert-based assessment of the results produced by different methods. The expert-based assessment focuses on publications in the field of scientometrics. Our findings seem to indicate that there is a trade-off between different properties that may be considered desirable for a good clustering of publications. Overall, map equation methods appear to perform best in our analysis, suggesting that these methods deserve more attention from the bibliometric community.

  12. Clustering Scientific Publications Based on Citation Relations: A Systematic Comparison of Different Methods

    PubMed Central

    Šubelj, Lovro; van Eck, Nees Jan; Waltman, Ludo

    2016-01-01

    Clustering methods are applied regularly in the bibliometric literature to identify research areas or scientific fields. These methods are for instance used to group publications into clusters based on their relations in a citation network. In the network science literature, many clustering methods, often referred to as graph partitioning or community detection techniques, have been developed. Focusing on the problem of clustering the publications in a citation network, we present a systematic comparison of the performance of a large number of these clustering methods. Using a number of different citation networks, some of them relatively small and others very large, we extensively study the statistical properties of the results provided by different methods. In addition, we also carry out an expert-based assessment of the results produced by different methods. The expert-based assessment focuses on publications in the field of scientometrics. Our findings seem to indicate that there is a trade-off between different properties that may be considered desirable for a good clustering of publications. Overall, map equation methods appear to perform best in our analysis, suggesting that these methods deserve more attention from the bibliometric community. PMID:27124610

  13. Quantum electrical dipole in triangular systems: A model for spontaneous polarity in metal clusters

    SciTech Connect

    Allen, Philip B.; Abanov, Alexander G.; Requist, Ryan

    2005-04-01

    Triangular symmetric molecules with mirror symmetry perpendicular to the threefold axis are forbidden to have a fixed electrical dipole moment. However, if the ground state is orbitally degenerate and lacks inversion symmetry, then a 'quantum' dipole moment does exist. The system of three electrons in D{sub 3h} symmetry is our example. This system is realized in triatomic molecules like Na{sub 3}. Unlike the fixed dipole of a molecule like water, the quantum moment does not point in a fixed direction, but lies in the plane of the molecule and takes quantized values {+-}{mu}{sub 0} along any direction of measurement in the plane. An electric field F-vector in the plane leads to a linear Stark splitting {+-}{mu}{sub 0} vertical bar F-vector vertical bar. We introduce a toy model to study the effect of Jahn-Teller distortions on the quantum dipole moment. We find that the quantum dipole property survives when the dynamic Jahn-Teller effect is included if the distortion of the molecule is small. Linear Stark splittings are suppressed in low fields by molecular rotation, just as the linear Stark shift of water is suppressed, but will be revealed in moderately large applied fields and low temperatures. Coulomb correlations also give a partial suppression.

  14. Cluster membership probabilities from proper motions and multi-wavelength photometric catalogues. I. Method and application to the Pleiades cluster

    NASA Astrophysics Data System (ADS)

    Sarro, L. M.; Bouy, H.; Berihuete, A.; Bertin, E.; Moraux, E.; Bouvier, J.; Cuillandre, J.-C.; Barrado, D.; Solano, E.

    2014-03-01

    Context. With the advent of deep wide surveys, large photometric and astrometric catalogues of literally all nearby clusters and associations have been produced. The unprecedented accuracy and sensitivity of these data sets and their broad spatial, temporal and wavelength coverage make obsolete the classical membership selection methods that were based on a handful of colours and luminosities. We present a new technique designed to take full advantage of the high dimensionality (photometric, astrometric, temporal) of such a survey to derive self-consistent and robust membership probabilities of the Pleiades cluster. Aims: We aim at developing a methodology to infer membership probabilities to the Pleiades cluster from the DANCe multidimensional astro-photometric data set in a consistent way throughout the entire derivation. The determination of the membership probabilities has to be applicable to censored data and must incorporate the measurement uncertainties into the inference procedure. Methods: We use Bayes' theorem and a curvilinear forward model for the likelihood of the measurements of cluster members in the colour-magnitude space, to infer posterior membership probabilities. The distribution of the cluster members proper motions and the distribution of contaminants in the full multidimensional astro-photometric space is modelled with a mixture-of-Gaussians likelihood. Results: We analyse several representation spaces composed of the proper motions plus a subset of the available magnitudes and colour indices. We select two prominent representation spaces composed of variables selected using feature relevance determination techniques based in Random Forests, and analyse the resulting samples of high probability candidates. We consistently find lists of high probability (p > 0.9975) candidates with ≈1000 sources, 4 to 5 times more than obtained in the most recent astro-photometric studies of the cluster. Conclusions: Multidimensional data sets require

  15. One-way quantum computing with arbitrarily large time-frequency continuous-variable cluster states from a single optical parametric oscillator

    NASA Astrophysics Data System (ADS)

    Alexander, Rafael N.; Wang, Pei; Sridhar, Niranjan; Chen, Moran; Pfister, Olivier; Menicucci, Nicolas C.

    2016-09-01

    One-way quantum computing is experimentally appealing because it requires only local measurements on an entangled resource called a cluster state. Record-size, but nonuniversal, continuous-variable cluster states were recently demonstrated separately in the time and frequency domains. We propose to combine these approaches into a scalable architecture in which a single optical parametric oscillator and simple interferometer entangle up to (3 ×103 frequencies) × (unlimited number of temporal modes) into a computationally universal continuous-variable cluster state. We introduce a generalized measurement protocol to enable improved computational performance on this entanglement resource.

  16. Relation between financial market structure and the real economy: comparison between clustering methods.

    PubMed

    Musmeci, Nicoló; Aste, Tomaso; Di Matteo, T

    2015-01-01

    We quantify the amount of information filtered by different hierarchical clustering methods on correlations between stock returns comparing the clustering structure with the underlying industrial activity classification. We apply, for the first time to financial data, a novel hierarchical clustering approach, the Directed Bubble Hierarchical Tree and we compare it with other methods including the Linkage and k-medoids. By taking the industrial sector classification of stocks as a benchmark partition, we evaluate how the different methods retrieve this classification. The results show that the Directed Bubble Hierarchical Tree can outperform other methods, being able to retrieve more information with fewer clusters. Moreover,we show that the economic information is hidden at different levels of the hierarchical structures depending on the clustering method. The dynamical analysis on a rolling window also reveals that the different methods show different degrees of sensitivity to events affecting financial markets, like crises. These results can be of interest for all the applications of clustering methods to portfolio optimization and risk hedging [corrected].

  17. Relation between Financial Market Structure and the Real Economy: Comparison between Clustering Methods

    PubMed Central

    Musmeci, Nicoló; Aste, Tomaso; Di Matteo, T.

    2015-01-01

    We quantify the amount of information filtered by different hierarchical clustering methods on correlations between stock returns comparing the clustering structure with the underlying industrial activity classification. We apply, for the first time to financial data, a novel hierarchical clustering approach, the Directed Bubble Hierarchical Tree and we compare it with other methods including the Linkage and k-medoids. By taking the industrial sector classification of stocks as a benchmark partition, we evaluate how the different methods retrieve this classification. The results show that the Directed Bubble Hierarchical Tree can outperform other methods, being able to retrieve more information with fewer clusters. Moreover, we show that the economic information is hidden at different levels of the hierarchical structures depending on the clustering method. The dynamical analysis on a rolling window also reveals that the different methods show different degrees of sensitivity to events affecting financial markets, like crises. These results can be of interest for all the applications of clustering methods to portfolio optimization and risk hedging. PMID:25786703

  18. Learning and Retention of Quantum Concepts with Different Teaching Methods

    ERIC Educational Resources Information Center

    Deslauriers, Louis; Wieman, Carl

    2011-01-01

    We measured mastery and retention of conceptual understanding of quantum mechanics in a modern physics course. This was studied for two equivalent cohorts of students taught with different pedagogical approaches using the Quantum Mechanics Conceptual Survey. We measured the impact of pedagogical approach both on the original conceptual learning…

  19. A Synthetic Approach to the Transfer Matrix Method in Classical and Quantum Physics

    ERIC Educational Resources Information Center

    Pujol, O.; Perez, J. P.

    2007-01-01

    The aim of this paper is to propose a synthetic approach to the transfer matrix method in classical and quantum physics. This method is an efficient tool to deal with complicated physical systems of practical importance in geometrical light or charged particle optics, classical electronics, mechanics, electromagnetics and quantum physics. Teaching…

  20. A Spatial Division Clustering Method and Low Dimensional Feature Extraction Technique Based Indoor Positioning System

    PubMed Central

    Mo, Yun; Zhang, Zhongzhao; Meng, Weixiao; Ma, Lin; Wang, Yao

    2014-01-01

    Indoor positioning systems based on the fingerprint method are widely used due to the large number of existing devices with a wide range of coverage. However, extensive positioning regions with a massive fingerprint database may cause high computational complexity and error margins, therefore clustering methods are widely applied as a solution. However, traditional clustering methods in positioning systems can only measure the similarity of the Received Signal Strength without being concerned with the continuity of physical coordinates. Besides, outage of access points could result in asymmetric matching problems which severely affect the fine positioning procedure. To solve these issues, in this paper we propose a positioning system based on the Spatial Division Clustering (SDC) method for clustering the fingerprint dataset subject to physical distance constraints. With the Genetic Algorithm and Support Vector Machine techniques, SDC can achieve higher coarse positioning accuracy than traditional clustering algorithms. In terms of fine localization, based on the Kernel Principal Component Analysis method, the proposed positioning system outperforms its counterparts based on other feature extraction methods in low dimensionality. Apart from balancing online matching computational burden, the new positioning system exhibits advantageous performance on radio map clustering, and also shows better robustness and adaptability in the asymmetric matching problem aspect. PMID:24451470

  1. WEIGHING GALAXY CLUSTERS WITH GAS. I. ON THE METHODS OF COMPUTING HYDROSTATIC MASS BIAS

    SciTech Connect

    Lau, Erwin T.; Nagai, Daisuke; Nelson, Kaylea

    2013-11-10

    Mass estimates of galaxy clusters from X-ray and Sunyeav-Zel'dovich observations assume the intracluster gas is in hydrostatic equilibrium with their gravitational potential. However, since galaxy clusters are dynamically active objects whose dynamical states can deviate significantly from the equilibrium configuration, the departure from the hydrostatic equilibrium assumption is one of the largest sources of systematic uncertainties in cluster cosmology. In the literature there have been two methods for computing the hydrostatic mass bias based on the Euler and the modified Jeans equations, respectively, and there has been some confusion about the validity of these two methods. The word 'Jeans' was a misnomer, which incorrectly implies that the gas is collisionless. To avoid further confusion, we instead refer these methods as 'summation' and 'averaging' methods respectively. In this work, we show that these two methods for computing the hydrostatic mass bias are equivalent by demonstrating that the equation used in the second method can be derived from taking spatial averages of the Euler equation. Specifically, we identify the correspondences of individual terms in these two methods mathematically and show that these correspondences are valid to within a few percent level using hydrodynamical simulations of galaxy cluster formation. In addition, we compute the mass bias associated with the acceleration of gas and show that its contribution is small in the virialized regions in the interior of galaxy clusters, but becomes non-negligible in the outskirts of massive galaxy clusters. We discuss future prospects of understanding and characterizing biases in the mass estimate of galaxy clusters using both hydrodynamical simulations and observations and their implications for cluster cosmology.

  2. Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

    SciTech Connect

    Steenbergen, K. G.; Gaston, N.

    2014-02-14

    Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

  3. Spin-polarized Rb2 interacting with bosonic He atoms: potential energy surface and quantum structures of small clusters.

    PubMed

    Rodríguez-Cantano, R; López-Durán, David; González-Lezana, T; Delgado-Barrio, G; Villarreal, P; Yurtsever, E; Gianturco, F A

    2012-03-15

    A new full-dimension potential energy surface of the three-body He-Rb₂(³Σ(u)(+)) complex and a quantum study of small (⁴He)(N)-Rb₂(³Σ(u)(+)) clusters, 1 ≤ N ≤ 4, are presented. We have accurately fitted the ab initio points of the interaction to an analytical form and addressed the dopant's vibration, which is found to be negligible. A Variational approach and a Diffusion Monte Carlo technique have been applied to yield energy and geometric properties of the selected species. Our quantum structure calculations show a transition in the arrangements of the helium atoms from N = 2, where they tend to be separated across the diatomic bond, to N = 4, in which a closer packing of the rare gas particles is reached, guided by the dominance of the He-He potential over the weaker interaction of the latter adatoms with the doping dimer. The deepest well of the He-Rb₂ interaction is placed at the T-shape configuration, a feature which causes the dopant to be located as parallel to the helium "minidroplet". Our results are shown to agree with previous findings on this and on similar systems.

  4. Comparison of 2D fingerprint types and hierarchy level selection methods for structural grouping using Ward's clustering

    PubMed

    Wild; Blankley

    2000-01-01

    Four different two-dimensional fingerprint types (MACCS, Unity, BCI, and Daylight) and nine methods of selecting optimal cluster levels from the output of a hierarchical clustering algorithm were evaluated for their ability to select clusters that represent chemical series present in some typical examples of chemical compound data sets. The methods were evaluated using a Ward's clustering algorithm on subsets of the publicly available National Cancer Institute HIV data set, as well as with compounds from our corporate data set. We make a number of observations and recommendations about the choice of fingerprint type and cluster level selection methods for use in this type of clustering

  5. Quantum electrical dipole in triangular systems: A model for spontaneous polarity in metal clusters

    NASA Astrophysics Data System (ADS)

    Allen, Philip B.; Abanov, Alexander G.; Requist, Ryan

    2005-04-01

    Triangular symmetric molecules with mirror symmetry perpendicular to the threefold axis are forbidden to have a fixed electrical dipole moment. However, if the ground state is orbitally degenerate and lacks inversion symmetry, then a “quantum” dipole moment does exist. The system of three electrons in D3h symmetry is our example. This system is realized in triatomic molecules like Na3 . Unlike the fixed dipole of a molecule like water, the quantum moment does not point in a fixed direction, but lies in the plane of the molecule and takes quantized values ±μ0 along any direction of measurement in the plane. An electric field F⃗ in the plane leads to a linear Stark splitting ±μ0∣F⃗∣ . We introduce a toy model to study the effect of Jahn-Teller distortions on the quantum dipole moment. We find that the quantum dipole property survives when the dynamic Jahn-Teller effect is included if the distortion of the molecule is small. Linear Stark splittings are suppressed in low fields by molecular rotation, just as the linear Stark shift of water is suppressed, but will be revealed in moderately large applied fields and low temperatures. Coulomb correlations also give a partial suppression.

  6. Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics

    USGS Publications Warehouse

    Safner, T.; Miller, M.P.; McRae, B.H.; Fortin, M.-J.; Manel, S.

    2011-01-01

    Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods' effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance. ?? 2011 by the authors; licensee MDPI, Basel, Switzerland.

  7. Continuous-variable quantum computing in optical time-frequency modes using quantum memories.

    PubMed

    Humphreys, Peter C; Kolthammer, W Steven; Nunn, Joshua; Barbieri, Marco; Datta, Animesh; Walmsley, Ian A

    2014-09-26

    We develop a scheme for time-frequency encoded continuous-variable cluster-state quantum computing using quantum memories. In particular, we propose a method to produce, manipulate, and measure two-dimensional cluster states in a single spatial mode by exploiting the intrinsic time-frequency selectivity of Raman quantum memories. Time-frequency encoding enables the scheme to be extremely compact, requiring a number of memories that are a linear function of only the number of different frequencies in which the computational state is encoded, independent of its temporal duration. We therefore show that quantum memories can be a powerful component for scalable photonic quantum information processing architectures.

  8. Indium clustering in a-plane InGaN quantum wells as evidenced by atom probe tomography

    SciTech Connect

    Tang, Fengzai; Zhu, Tongtong; Oehler, Fabrice; Fu, Wai Yuen; Griffiths, James T.; Massabuau, Fabien C.-P.; Kappers, Menno J.; Oliver, Rachel A.; Martin, Tomas L.; Bagot, Paul A. J.; Moody, Michael P.

    2015-02-16

    Atom probe tomography (APT) has been used to characterize the distribution of In atoms within non-polar a-plane InGaN quantum wells (QWs) grown on a GaN pseudo-substrate produced using epitaxial lateral overgrowth. Application of the focused ion beam microscope enabled APT needles to be prepared from the low defect density regions of the grown sample. A complementary analysis was also undertaken on QWs having comparable In contents grown on polar c-plane sample pseudo-substrates. Both frequency distribution and modified nearest neighbor analyses indicate a statistically non-randomized In distribution in the a-plane QWs, but a random distribution in the c-plane QWs. This work not only provides insights into the structure of non-polar a-plane QWs but also shows that APT is capable of detecting as-grown nanoscale clustering in InGaN and thus validates the reliability of earlier APT analyses of the In distribution in c-plane InGaN QWs which show no such clustering.

  9. Quantum chemical analysis of thermodynamics of 2D cluster formation of alkanes at the water/vapor interface in the presence of aliphatic alcohols.

    PubMed

    Vysotsky, Yu B; Kartashynska, E S; Belyaeva, E A; Fainerman, V B; Vollhardt, D; Miller, R

    2015-11-21

    Using the quantum chemical semi-empirical PM3 method it is shown that aliphatic alcohols favor the spontaneous clusterization of vaporous alkanes at the water surface due to the change of adsorption from the barrier to non-barrier mechanism. A theoretical model of the non-barrier mechanism for monolayer formation is developed. In the framework of this model alcohols (or any other surfactants) act as 'floats', which interact with alkane molecules of the vapor phase using their hydrophobic part, whereas the hydrophilic part is immersed into the water phase. This results in a significant increase of contact effectiveness of alkanes with the interface during the adsorption and film formation. The obtained results are in good agreement with the existing experimental data. To test the model the thermodynamic and structural parameters of formation and clusterization are calculated for vaporous alkanes C(n)H(2n+2) (n(CH3) = 6-16) at the water surface in the presence of aliphatic alcohols C(n)H(2n+1)OH (n(OH) = 8-16) at 298 K. It is shown that the values of clusterization enthalpy, entropy and Gibbs' energy per one monomer of the cluster depend on the chain lengths of corresponding alcohols and alkanes, the alcohol molar fraction in the monolayers formed, and the shift of the alkane molecules with respect to the alcohol molecules Δn. Two possible competitive structures of mixed 2D film alkane-alcohol are considered: 2D films 1 with single alcohol molecules enclosed by alkane molecules (the alcohols do not form domains) and 2D films 2 that contain alcohol domains enclosed by alkane molecules. The formation of the alkane films of the first type is nearly independent of the surfactant type present at the interface, but depends on their molar fraction in the monolayer formed and the chain length of the compounds participating in the clusterization, whereas for the formation of the films of the second type the interaction between the hydrophilic parts of the surfactant is

  10. Bayesian Analysis of Two Stellar Populations in Galactic Globular Clusters. I. Statistical and Computational Methods

    NASA Astrophysics Data System (ADS)

    Stenning, D. C.; Wagner-Kaiser, R.; Robinson, E.; van Dyk, D. A.; von Hippel, T.; Sarajedini, A.; Stein, N.

    2016-07-01

    We develop a Bayesian model for globular clusters composed of multiple stellar populations, extending earlier statistical models for open clusters composed of simple (single) stellar populations. Specifically, we model globular clusters with two populations that differ in helium abundance. Our model assumes a hierarchical structuring of the parameters in which physical properties—age, metallicity, helium abundance, distance, absorption, and initial mass—are common to (i) the cluster as a whole or to (ii) individual populations within a cluster, or are unique to (iii) individual stars. An adaptive Markov chain Monte Carlo (MCMC) algorithm is devised for model fitting that greatly improves convergence relative to its precursor non-adaptive MCMC algorithm. Our model and computational tools are incorporated into an open-source software suite known as BASE-9. We use numerical studies to demonstrate that our method can recover parameters of two-population clusters, and also show how model misspecification can potentially be identified. As a proof of concept, we analyze the two stellar populations of globular cluster NGC 5272 using our model and methods. (BASE-9 is available from GitHub: https://github.com/argiopetech/base/releases).

  11. Quantum dynamics of X{sub 2}BC van der Waals clusters

    SciTech Connect

    Gray, S.K.

    1992-12-31

    Wave packet calculations modeling vibrational predissociation in X{sub 2}BC(v{sup {prime}}) van der Waals clusters are discussed. A model involving three active degrees of freedom is used. Cluster lifetimes and BC vibrational product distributions are obtained, and compared with available experimental results for He{sub 2}Cl{sub 2}, and Ne{sub 2}Cl{sub 2}. Some preliminary results for He{sub 2}I{sub 2} and Ne{sub 2}I{sub 2} are also discussed. Mechanistic issues, including the role of direct versus sequential mechanisms in leading to the production of 2X {plus} BC are addressed, as well as the role of intramolecular vibrational relaxation (IVR). Higher dimension extensions of the model are suggested. 3 figs., 3 tabs., 22 refs.

  12. Dynamic quantum clustering: a tool for visual exploration of structures in data

    SciTech Connect

    Weinstein, Marvin; Horn, David; /Tel Aviv U.

    2009-10-17

    A given set of data-points in some feature space may be associated with a Schroedinger equation whose potential is determined by the data. This is known to lead to good clustering solutions. Here we extend this approach into a full-fledged dynamical scheme using a time-dependent Schroedinger equation. Moreover, we approximate this Hamiltonian formalism by a truncated calculation within a set of Gaussian wave functions (coherent states) centered around the original points. This allows for analytic evaluation of the time evolution of all such states, opening up the possibility of exploration of relationships among data-points through observation of varying dynamical-distances among points and convergence of points into clusters. This formalism may be further supplemented by preprocessing, such as dimensional reduction through singular value decomposition or feature filtering.

  13. Dynamic Quantum Clustering: A Tool for Unsupervised Exploration of Structures in Data

    SciTech Connect

    Weinstein, Marvin; Horn, David; /Tel Aviv U.

    2008-10-30

    A given set of data-points in some feature space may be associated with a Schroedinger equation whose potential is determined by the data. This is known to lead to good clustering solutions. Here we extend this approach into a full-fledged dynamical scheme using a time-dependent Schroedinger equation with a small diffusion component. Moreover, we approximate this Hamiltonian formalism by a truncated calculation within a set of Gaussian wave functions (coherent states) centered around the original points. This allows for analytic evaluation of the time evolution of all such states, opening up the possibility of exploration of relationships among data-points through observation of varying dynamical-distances among points and convergence of points into clusters. This formalism may be further supplemented by preprocessing, such as dimensional reduction through singular value decomposition or feature filtering.

  14. A new method to search for high-redshift clusters using photometric redshifts

    SciTech Connect

    Castignani, G.; Celotti, A.; Chiaberge, M.; Norman, C.

    2014-09-10

    We describe a new method (Poisson probability method, PPM) to search for high-redshift galaxy clusters and groups by using photometric redshift information and galaxy number counts. The method relies on Poisson statistics and is primarily introduced to search for megaparsec-scale environments around a specific beacon. The PPM is tailored to both the properties of the FR I radio galaxies in the Chiaberge et al. sample, which are selected within the COSMOS survey, and to the specific data set used. We test the efficiency of our method of searching for cluster candidates against simulations. Two different approaches are adopted. (1) We use two z ∼ 1 X-ray detected cluster candidates found in the COSMOS survey and we shift them to higher redshift up to z = 2. We find that the PPM detects the cluster candidates up to z = 1.5, and it correctly estimates both the redshift and size of the two clusters. (2) We simulate spherically symmetric clusters of different size and richness, and we locate them at different redshifts (i.e., z = 1.0, 1.5, and 2.0) in the COSMOS field. We find that the PPM detects the simulated clusters within the considered redshift range with a statistical 1σ redshift accuracy of ∼0.05. The PPM is an efficient alternative method for high-redshift cluster searches that may also be applied to both present and future wide field surveys such as SDSS Stripe 82, LSST, and Euclid. Accurate photometric redshifts and a survey depth similar or better than that of COSMOS (e.g., I < 25) are required.

  15. Simple method for sub-diffraction resolution imaging of cellular structures on standard confocal microscopes by three-photon absorption of quantum dots.

    PubMed

    Sporbert, Anje; Cseresnyes, Zoltan; Heidbreder, Meike; Domaing, Petra; Hauser, Stefan; Kaltschmidt, Barbara; Kaltschmidt, Christian; Heilemann, Mike; Widera, Darius

    2013-01-01

    This study describes a simple technique that improves a recently developed 3D sub-diffraction imaging method based on three-photon absorption of commercially available quantum dots. The method combines imaging of biological samples via tri-exciton generation in quantum dots with deconvolution and spectral multiplexing, resulting in a novel approach for multi-color imaging of even thick biological samples at a 1.4 to 1.9-fold better spatial resolution. This approach is realized on a conventional confocal microscope equipped with standard continuous-wave lasers. We demonstrate the potential of multi-color tri-exciton imaging of quantum dots combined with deconvolution on viral vesicles in lentivirally transduced cells as well as intermediate filaments in three-dimensional clusters of mouse-derived neural stem cells (neurospheres) and dense microtubuli arrays in myotubes formed by stacks of differentiated C2C12 myoblasts.

  16. An efficient method of key-frame extraction based on a cluster algorithm.

    PubMed

    Zhang, Qiang; Yu, Shao-Pei; Zhou, Dong-Sheng; Wei, Xiao-Peng

    2013-12-18

    This paper proposes a novel method of key-frame extraction for use with motion capture data. This method is based on an unsupervised cluster algorithm. First, the motion sequence is clustered into two classes by the similarity distance of the adjacent frames so that the thresholds needed in the next step can be determined adaptively. Second, a dynamic cluster algorithm called ISODATA is used to cluster all the frames and the frames nearest to the center of each class are automatically extracted as key-frames of the sequence. Unlike many other clustering techniques, the present improved cluster algorithm can automatically address different motion types without any need for specified parameters from users. The proposed method is capable of summarizing motion capture data reliably and efficiently. The present work also provides a meaningful comparison between the results of the proposed key-frame extraction technique and other previous methods. These results are evaluated in terms of metrics that measure reconstructed motion and the mean absolute error value, which are derived from the reconstructed data and the original data.

  17. Comparison of Bayesian Clustering and Edge Detection Methods for Inferring Boundaries in Landscape Genetics

    PubMed Central

    Safner, Toni; Miller, Mark P.; McRae, Brad H.; Fortin, Marie-Josée; Manel, Stéphanie

    2011-01-01

    Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods’ effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance. PMID:21541031

  18. Cluster detection of diseases in heterogeneous populations: an alternative to scan methods.

    PubMed

    Ramis, Rebeca; Gómez-Barroso, Diana; López-Abente, Gonzalo

    2014-05-01

    Cluster detection has become an important part of the agenda of epidemiologists and public health authorities, the identification of high- and low-risk areas is fundamental in the definition of public health strategies and in the suggestion of potential risks factors. Currently, there are different cluster detection techniques available, the most popular being those using windows to scan the areas within the studied region. However, when these areas are heterogeneous in populations' sizes, scan window methods can lead to inaccurate conclusions. In order to perform cluster detection over heterogeneously populated areas, we developed a method not based on scanning windows but instead on standard mortality ratios (SMR) using irregular spatial aggregation (ISA). Its extension, i.e. irregular spatial aggregation with covariates (ISAC), includes covariates with residuals from Poisson regression. We compared the performance of the method with the flexible shaped spatial scan statistic (FlexScan) using mortality data for stomach and bladder cancer for 8,098 Spanish towns. The results show a collection of clusters for stomach and bladder cancer similar to that detected by ISA and FlexScan. However, in general, clusters detected by FlexScan were bigger and include towns with SMR, which were not statistically significant. For bladder cancer, clusters detected by ISAC differed from those detected by ISA and FlexScan in shape and location. The ISA and ISAC methods could be an alternative to the traditional scan window methods for cluster detection over aggregated data when the areas under study are heterogeneous in terms of population. The simplicity and flexibility of the methods make them more attractive than methods based on more complicated algorithms. PMID:24893029

  19. Cool Cluster Correctly Correlated

    SciTech Connect

    Varganov, Sergey Aleksandrovich

    2005-01-01

    Atomic clusters are unique objects, which occupy an intermediate position between atoms and condensed matter systems. For a long time it was thought that physical and chemical properties of atomic dusters monotonically change with increasing size of the cluster from a single atom to a condensed matter system. However, recently it has become clear that many properties of atomic clusters can change drastically with the size of the clusters. Because physical and chemical properties of clusters can be adjusted simply by changing the cluster's size, different applications of atomic clusters were proposed. One example is the catalytic activity of clusters of specific sizes in different chemical reactions. Another example is a potential application of atomic clusters in microelectronics, where their band gaps can be adjusted by simply changing cluster sizes. In recent years significant advances in experimental techniques allow one to synthesize and study atomic clusters of specified sizes. However, the interpretation of the results is often difficult. The theoretical methods are frequently used to help in interpretation of complex experimental data. Most of the theoretical approaches have been based on empirical or semiempirical methods. These methods allow one to study large and small dusters using the same approximations. However, since empirical and semiempirical methods rely on simple models with many parameters, it is often difficult to estimate the quantitative and even qualitative accuracy of the results. On the other hand, because of significant advances in quantum chemical methods and computer capabilities, it is now possible to do high quality ab-initio calculations not only on systems of few atoms but on clusters of practical interest as well. In addition to accurate results for specific clusters, such methods can be used for benchmarking of different empirical and semiempirical approaches. The atomic clusters studied in this work contain from a few atoms to

  20. Quantum image pseudocolor coding based on the density-stratified method

    NASA Astrophysics Data System (ADS)

    Jiang, Nan; Wu, Wenya; Wang, Luo; Zhao, Na

    2015-05-01

    Pseudocolor processing is a branch of image enhancement. It dyes grayscale images to color images to make the images more beautiful or to highlight some parts on the images. This paper proposes a quantum image pseudocolor coding scheme based on the density-stratified method which defines a colormap and changes the density value from gray to color parallel according to the colormap. Firstly, two data structures: quantum image GQIR and quantum colormap QCR are reviewed or proposed. Then, the quantum density-stratified algorithm is presented. Based on them, the quantum realization in the form of circuits is given. The main advantages of the quantum version for pseudocolor processing over the classical approach are that it needs less memory and can speed up the computation. Two kinds of examples help us to describe the scheme further. Finally, the future work are analyzed.

  1. A semantics-based method for clustering of Chinese web search results

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Wang, Deqing; Wang, Li; Bi, Zhuming; Chen, Yong

    2014-01-01

    Information explosion is a critical challenge to the development of modern information systems. In particular, when the application of an information system is over the Internet, the amount of information over the web has been increasing exponentially and rapidly. Search engines, such as Google and Baidu, are essential tools for people to find the information from the Internet. Valuable information, however, is still likely submerged in the ocean of search results from those tools. By clustering the results into different groups based on subjects automatically, a search engine with the clustering feature allows users to select most relevant results quickly. In this paper, we propose an online semantics-based method to cluster Chinese web search results. First, we employ the generalised suffix tree to extract the longest common substrings (LCSs) from search snippets. Second, we use the HowNet to calculate the similarities of the words derived from the LCSs, and extract the most representative features by constructing the vocabulary chain. Third, we construct a vector of text features and calculate snippets' semantic similarities. Finally, we improve the Chameleon algorithm to cluster snippets. Extensive experimental results have shown that the proposed algorithm has outperformed over the suffix tree clustering method and other traditional clustering methods.

  2. Quantum Monte Carlo Methods for First Principles Simulation of Liquid Water

    ERIC Educational Resources Information Center

    Gergely, John Robert

    2009-01-01

    Obtaining an accurate microscopic description of water structure and dynamics is of great interest to molecular biology researchers and in the physics and quantum chemistry simulation communities. This dissertation describes efforts to apply quantum Monte Carlo methods to this problem with the goal of making progress toward a fully "ab initio"…

  3. An effective trust-based recommendation method using a novel graph clustering algorithm

    NASA Astrophysics Data System (ADS)

    Moradi, Parham; Ahmadian, Sajad; Akhlaghian, Fardin

    2015-10-01

    Recommender systems are programs that aim to provide personalized recommendations to users for specific items (e.g. music, books) in online sharing communities or on e-commerce sites. Collaborative filtering methods are important and widely accepted types of recommender systems that generate recommendations based on the ratings of like-minded users. On the other hand, these systems confront several inherent issues such as data sparsity and cold start problems, caused by fewer ratings against the unknowns that need to be predicted. Incorporating trust information into the collaborative filtering systems is an attractive approach to resolve these problems. In this paper, we present a model-based collaborative filtering method by applying a novel graph clustering algorithm and also considering trust statements. In the proposed method first of all, the problem space is represented as a graph and then a sparsest subgraph finding algorithm is applied on the graph to find the initial cluster centers. Then, the proposed graph clustering algorithm is performed to obtain the appropriate users/items clusters. Finally, the identified clusters are used as a set of neighbors to recommend unseen items to the current active user. Experimental results based on three real-world datasets demonstrate that the proposed method outperforms several state-of-the-art recommender system methods.

  4. Note: Excited State Studies of Ozone using State-Specific Multireference Coupled Cluster Methods

    SciTech Connect

    Bhaskaran-Nair, Kiran; Kowalski, Karol

    2012-12-07

    Vertical excitation energies obtained with state-specific multi-reference coupled cluster (MRCC) methods are reported for the ozone molecule. Using state-specific MRCC non-iterative methods with singles, doubles, and non-iterative triples (MRCCSD(T)) we obtain 4.40 eV for the challenging doubly excited 21A1 state when using a reliable model space. This estimate is in good agreement with experiment (4.5 eV). We also compare our MRCC results with the excitation energies obtained with high-order equation-of-motion coupled cluster methods

  5. A fusion method of Gabor wavelet transform and unsupervised clustering algorithms for tissue edge detection.

    PubMed

    Ergen, Burhan

    2014-01-01

    This paper proposes two edge detection methods for medical images by integrating the advantages of Gabor wavelet transform (GWT) and unsupervised clustering algorithms. The GWT is used to enhance the edge information in an image while suppressing noise. Following this, the k-means and Fuzzy c-means (FCM) clustering algorithms are used to convert a gray level image into a binary image. The proposed methods are tested using medical images obtained through Computed Tomography (CT) and Magnetic Resonance Imaging (MRI) devices, and a phantom image. The results prove that the proposed methods are successful for edge detection, even in noisy cases.

  6. Cluster Method Analysis of K. S. C. Image

    NASA Technical Reports Server (NTRS)

    Rodriguez, Joe, Jr.; Desai, M.

    1997-01-01

    Information obtained from satellite-based systems has moved to the forefront as a method in the identification of many land cover types. Identification of different land features through remote sensing is an effective tool for regional and global assessment of geometric characteristics. Classification data acquired from remote sensing images have a wide variety of applications. In particular, analysis of remote sensing images have special applications in the classification of various types of vegetation. Results obtained from classification studies of a particular area or region serve towards a greater understanding of what parameters (ecological, temporal, etc.) affect the region being analyzed. In this paper, we make a distinction between both types of classification approaches although, focus is given to the unsupervised classification method using 1987 Thematic Mapped (TM) images of Kennedy Space Center.

  7. Analytical method for determining quantum well exciton properties in a magnetic field

    NASA Astrophysics Data System (ADS)

    Stépnicki, Piotr; Piétka, Barbara; Morier-Genoud, François; Deveaud, Benoît; Matuszewski, Michał

    2015-05-01

    We develop an analytical approximate method for determining the Bohr radii of Wannier-Mott excitons in thin quantum wells under the influence of magnetic field perpendicular to the quantum well plane. Our hybrid variational-perturbative method allows us to obtain simple closed formulas for exciton binding energies and optical transition rates. We confirm the reliability of our method through exciton-polariton experiments realized in a GaAs/AlAs microcavity with an 8 nm InxGa1 -xAs quantum well and magnetic field strengths as high as 14 T.

  8. Water-soluble luminescent quantum dots and biomolecular conjugates thereof and related compositions and methods of use

    DOEpatents

    Nie, Shuming; Chan, Warren C. W.; Emory, Stephen

    2007-03-20

    The present invention provides a water-soluble luminescent quantum dot, a biomolecular conjugate thereof and a composition comprising such a quantum dot or conjugate. Additionally, the present invention provides a method of obtaining a luminescent quantum dot, a method of making a biomolecular conjugate thereof, and methods of using a biomolecular conjugate for ultrasensitive nonisotopic detection in vitro and in vivo.

  9. Water-soluble luminescent quantum dots and biomolecular conjugates thereof and related compositions and method of use

    DOEpatents

    Nie, Shuming; Chan, Warren C. W.; Emory, Steven R.

    2002-01-01

    The present invention provides a water-soluble luminescent quantum dot, a biomolecular conjugate thereof and a composition comprising such a quantum dot or conjugate. Additionally, the present invention provides a method of obtaining a luminescent quantum dot, a method of making a biomolecular conjugate thereof, and methods of using a biomolecular conjugate for ultrasensitive nonisotopic detection in vitro and in vivo.

  10. Coresets vs clustering: comparison of methods for redundancy reduction in very large white matter fiber sets

    NASA Astrophysics Data System (ADS)

    Alexandroni, Guy; Zimmerman Moreno, Gali; Sochen, Nir; Greenspan, Hayit

    2016-03-01

    Recent advances in Diffusion Weighted Magnetic Resonance Imaging (DW-MRI) of white matter in conjunction with improved tractography produce impressive reconstructions of White Matter (WM) pathways. These pathways (fiber sets) often contain hundreds of thousands of fibers, or more. In order to make fiber based analysis more practical, the fiber set needs to be preprocessed to eliminate redundancies and to keep only essential representative fibers. In this paper we demonstrate and compare two distinctive frameworks for selecting this reduced set of fibers. The first framework entails pre-clustering the fibers using k-means, followed by Hierarchical Clustering and replacing each cluster with one representative. For the second clustering stage seven distance metrics were evaluated. The second framework is based on an efficient geometric approximation paradigm named coresets. Coresets present a new approach to optimization and have huge success especially in tasks requiring large computation time and/or memory. We propose a modified version of the coresets algorithm, Density Coreset. It is used for extracting the main fibers from dense datasets, leaving a small set that represents the main structures and connectivity of the brain. A novel approach, based on a 3D indicator structure, is used for comparing the frameworks. This comparison was applied to High Angular Resolution Diffusion Imaging (HARDI) scans of 4 healthy individuals. We show that among the clustering based methods, that cosine distance gives the best performance. In comparing the clustering schemes with coresets, Density Coreset method achieves the best performance.

  11. Study of Optical Properties on Fractal Aggregation Using the GMM Method by Different Cluster Parameters

    NASA Astrophysics Data System (ADS)

    Chang, Kuo-En; Lin, Tang-Huang; Lien, Wei-Hung

    2015-04-01

    Anthropogenic pollutants or smoke from biomass burning contribute significantly to global particle aggregation emissions, yet their aggregate formation and resulting ensemble optical properties are poorly understood and parameterized in climate models. Particle aggregation refers to formation of clusters in a colloidal suspension. In clustering algorithms, many parameters, such as fractal dimension, number of monomers, radius of monomer, and refractive index real part and image part, will alter the geometries and characteristics of the fractal aggregation and change ensemble optical properties further. The cluster-cluster aggregation algorithm (CCA) is used to specify the geometries of soot and haze particles. In addition, the Generalized Multi-particle Mie (GMM) method is utilized to compute the Mie solution from a single particle to the multi particle case. This computer code for the calculation of the scattering by an aggregate of spheres in a fixed orientation and the experimental data have been made publicly available. This study for the model inputs of optical determination of the monomer radius, the number of monomers per cluster, and the fractal dimension is presented. The main aim in this study is to analyze and contrast several parameters of cluster aggregation aforementioned which demonstrate significant differences of optical properties using the GMM method finally. Keywords: optical properties, fractal aggregation, GMM, CCA

  12. A Cluster-based Method to Map Urban Area from DMSP/OLS Nightlights

    SciTech Connect

    Zhou, Yuyu; Smith, Steven J.; Elvidge, Christopher; Zhao, Kaiguang; Thomson, Allison M.; Imhoff, Marc L.

    2014-05-05

    Accurate information of urban areas at regional and global scales is important for both the science and policy-making communities. The Defense Meteorological Satellite Program/Operational Linescan System (DMSP/OLS) nighttime stable light data (NTL) provide a potential way to map urban area and its dynamics economically and timely. In this study, we developed a cluster-based method to estimate the optimal thresholds and map urban extents from the DMSP/OLS NTL data in five major steps, including data preprocessing, urban cluster segmentation, logistic model development, threshold estimation, and urban extent delineation. Different from previous fixed threshold method with over- and under-estimation issues, in our method the optimal thresholds are estimated based on cluster size and overall nightlight magnitude in the cluster, and they vary with clusters. Two large countries of United States and China with different urbanization patterns were selected to map urban extents using the proposed method. The result indicates that the urbanized area occupies about 2% of total land area in the US ranging from lower than 0.5% to higher than 10% at the state level, and less than 1% in China, ranging from lower than 0.1% to about 5% at the province level with some municipalities as high as 10%. The derived thresholds and urban extents were evaluated using high-resolution land cover data at the cluster and regional levels. It was found that our method can map urban area in both countries efficiently and accurately. Compared to previous threshold techniques, our method reduces the over- and under-estimation issues, when mapping urban extent over a large area. More important, our method shows its potential to map global urban extents and temporal dynamics using the DMSP/OLS NTL data in a timely, cost-effective way.

  13. Evaluation of hierarchical agglomerative cluster analysis methods for discrimination of primary biological aerosol

    NASA Astrophysics Data System (ADS)

    Crawford, I.; Ruske, S.; Topping, D. O.; Gallagher, M. W.

    2015-11-01

    In this paper we present improved methods for discriminating and quantifying primary biological aerosol particles (PBAPs) by applying hierarchical agglomerative cluster analysis to multi-parameter ultraviolet-light-induced fluorescence (UV-LIF) spectrometer data. The methods employed in this study can be applied to data sets in excess of 1 × 106 points on a desktop computer, allowing for each fluorescent particle in a data set to be explicitly clustered. This reduces the potential for misattribution found in subsampling and comparative attribution methods used in previous approaches, improving our capacity to discriminate and quantify PBAP meta-classes. We evaluate the performance of several hierarchical agglomerative cluster analysis linkages and data normalisation methods using laboratory samples of known particle types and an ambient data set. Fluorescent and non-fluorescent polystyrene latex spheres were sampled with a Wideband Integrated Bioaerosol Spectrometer (WIBS-4) where the optical size, asymmetry factor and fluorescent measurements were used as inputs to the analysis package. It was found that the Ward linkage with z-score or range normalisation performed best, correctly attributing 98 and 98.1 % of the data points respectively. The best-performing methods were applied to the BEACHON-RoMBAS (Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen-Rocky Mountain Biogenic Aerosol Study) ambient data set, where it was found that the z-score and range normalisation methods yield similar results, with each method producing clusters representative of fungal spores and bacterial aerosol, consistent with previous results. The z-score result was compared to clusters generated with previous approaches (WIBS AnalysiS Program, WASP) where we observe that the subsampling and comparative attribution method employed by WASP results in the overestimation of the fungal spore concentration by a factor of 1.5 and the underestimation of

  14. Evaluation of hierarchical agglomerative cluster analysis methods for discrimination of primary biological aerosol

    NASA Astrophysics Data System (ADS)

    Crawford, I.; Ruske, S.; Topping, D. O.; Gallagher, M. W.

    2015-07-01

    In this paper we present improved methods for discriminating and quantifying Primary Biological Aerosol Particles (PBAP) by applying hierarchical agglomerative cluster analysis to multi-parameter ultra violet-light induced fluorescence (UV-LIF) spectrometer data. The methods employed in this study can be applied to data sets in excess of 1×106 points on a desktop computer, allowing for each fluorescent particle in a dataset to be explicitly clustered. This reduces the potential for misattribution found in subsampling and comparative attribution methods used in previous approaches, improving our capacity to discriminate and quantify PBAP meta-classes. We evaluate the performance of several hierarchical agglomerative cluster analysis linkages and data normalisation methods using laboratory samples of known particle types and an ambient dataset. Fluorescent and non-fluorescent polystyrene latex spheres were sampled with a Wideband Integrated Bioaerosol Spectrometer (WIBS-4) where the optical size, asymmetry factor and fluorescent measurements were used as inputs to the analysis package. It was found that the Ward linkage with z-score or range normalisation performed best, correctly attributing 98 and 98.1 % of the data points respectively. The best performing methods were applied to the BEACHON-RoMBAS ambient dataset where it was found that the z-score and range normalisation methods yield similar results with each method producing clusters representative of fungal spores and bacterial aerosol, consistent with previous results. The z-score result was compared to clusters generated with previous approaches (WIBS AnalysiS Program, WASP) where we observe that the subsampling and comparative attribution method employed by WASP results in the overestimation of the fungal spore concentration by a factor of 1.5 and the underestimation of bacterial aerosol concentration by a factor of 5. We suggest that this likely due to errors arising from misatrribution due to poor

  15. Numerical simulation of quantum systems using the Particle-In-Cell method

    NASA Astrophysics Data System (ADS)

    Dirkmann, Sven; Youssef, Ziad; Hemke, Torben; Mussenbrock, Thomas

    2014-10-01

    The Particle-In-Cell (PIC) method is a very powerful method for studying the dynamics of plasmas. It has been primarily developed for tracking the charged particle trajectories subject to selfconsistent and external electromagnetic fields. Exploiting the power of modern computers, one is able to track the classical paths of tens of millions of particles at the same time. In the late 1980th, it was Dawson (and later Dauger) who had the idea to apply the PIC method to the classical part in the semiclassical approach to quantum systems via path integral methods. One could estimate that if a thousands of classical paths are sufficient to describe the dynamics of one quantum particle, then millions classical paths could describe the dynamics of a quantum particle system. A PIC code in the frame of a semiclassical approach would therefore enable the investigation of a number of quantum phenomena, e.g., optical properties, electrical properties, and, ultimately, chemical reactions. In this contribution we explain the use of the PIC code yapic (developed by the authors) in the frame of the path integral method and discuss the numerical results for simple quantum phenomena, i.e., the quantum harmonic oscillator and quantum tunneling. This work is supported by the German Research Foundation in the frame of FOR 2093.

  16. System and Method for Outlier Detection via Estimating Clusters

    NASA Technical Reports Server (NTRS)

    Iverson, David J. (Inventor)

    2016-01-01

    An efficient method and system for real-time or offline analysis of multivariate sensor data for use in anomaly detection, fault detection, and system health monitoring is provided. Models automatically derived from training data, typically nominal system data acquired from sensors in normally operating conditions or from detailed simulations, are used to identify unusual, out of family data samples (outliers) that indicate possible system failure or degradation. Outliers are determined through analyzing a degree of deviation of current system behavior from the models formed from the nominal system data. The deviation of current system behavior is presented as an easy to interpret numerical score along with a measure of the relative contribution of each system parameter to any off-nominal deviation. The techniques described herein may also be used to "clean" the training data.

  17. An Efficient Initialization Method for K-Means Clustering of Hyperspectral Data

    NASA Astrophysics Data System (ADS)

    Alizade Naeini, A.; Jamshidzadeh, A.; Saadatseresht, M.; Homayouni, S.

    2014-10-01

    K-means is definitely the most frequently used partitional clustering algorithm in the remote sensing community. Unfortunately due to its gradient decent nature, this algorithm is highly sensitive to the initial placement of cluster centers. This problem deteriorates for the high-dimensional data such as hyperspectral remotely sensed imagery. To tackle this problem, in this paper, the spectral signatures of the endmembers in the image scene are extracted and used as the initial positions of the cluster centers. For this purpose, in the first step, A Neyman-Pearson detection theory based eigen-thresholding method (i.e., the HFC method) has been employed to estimate the number of endmembers in the image. Afterwards, the spectral signatures of the endmembers are obtained using the Minimum Volume Enclosing Simplex (MVES) algorithm. Eventually, these spectral signatures are used to initialize the k-means clustering algorithm. The proposed method is implemented on a hyperspectral dataset acquired by ROSIS sensor with 103 spectral bands over the Pavia University campus, Italy. For comparative evaluation, two other commonly used initialization methods (i.e., Bradley & Fayyad (BF) and Random methods) are implemented and compared. The confusion matrix, overall accuracy and Kappa coefficient are employed to assess the methods' performance. The evaluations demonstrate that the proposed solution outperforms the other initialization methods and can be applied for unsupervised classification of hyperspectral imagery for landcover mapping.

  18. Economical five-party quantum state sharing of an arbitrary m-atom with five-atom cluster state in cavity QED

    NASA Astrophysics Data System (ADS)

    Yang, Yu-Guang; Xia, Juan; Jia, Xin; Shi, Lei; Zhang, Hua

    2013-03-01

    We present an economical scheme of five-party quantum state sharing (FQSTS) of an arbitrary m-atom with five-atom cluster state in cavity QED. It is found that the five-partite cluster state can be used for FQSTS of an arbitrary m-atom state. The implementation of this scheme does not involve Bell-basis or GHZ-basis measurements, which makes it more convenient in a practical application than some previous schemes. The scheme is also insensitive to the cavity decay and the thermal field.

  19. Combined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL): A Robust Method for Selection of Cluster Number, K.

    PubMed

    Sweeney, Timothy E; Chen, Albert C; Gevaert, Olivier

    2015-11-19

    In order to discover new subsets (clusters) of a data set, researchers often use algorithms that perform unsupervised clustering, namely, the algorithmic separation of a dataset into some number of distinct clusters. Deciding whether a particular separation (or number of clusters, K) is correct is a sort of 'dark art', with multiple techniques available for assessing the validity of unsupervised clustering algorithms. Here, we present a new technique for unsupervised clustering that uses multiple clustering algorithms, multiple validity metrics, and progressively bigger subsets of the data to produce an intuitive 3D map of cluster stability that can help determine the optimal number of clusters in a data set, a technique we call COmbined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL). COMMUNAL locally optimizes algorithms and validity measures for the data being used. We show its application to simulated data with a known K, and then apply this technique to several well-known cancer gene expression datasets, showing that COMMUNAL provides new insights into clustering behavior and stability in all tested cases. COMMUNAL is shown to be a useful tool for determining K in complex biological datasets, and is freely available as a package for R.

  20. Weighing the Giants - I. Weak-lensing masses for 51 massive galaxy clusters: project overview, data analysis methods and cluster images

    NASA Astrophysics Data System (ADS)

    von der Linden, Anja; Allen, Mark T.; Applegate, Douglas E.; Kelly, Patrick L.; Allen, Steven W.; Ebeling, Harald; Burchat, Patricia R.; Burke, David L.; Donovan, David; Morris, R. Glenn; Blandford, Roger; Erben, Thomas; Mantz, Adam

    2014-03-01

    uncertainty for our weak-lensing mass measurements. In accompanying papers, we discuss the key aspects of our photometric calibration and photometric redshift measurements (Kelly et al.), and measure cluster masses using two methods, including a novel Bayesian weak-lensing approach that makes full use of the photometric redshift probability distributions for individual background galaxies (Applegate et al.). In subsequent papers, we will incorporate these weak-lensing mass measurements into a self-consistent framework to simultaneously determine cluster scaling relations and cosmological parameters.

  1. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.

    PubMed

    Friesner, Richard A; Guallar, Victor

    2005-01-01

    We describe large scale ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic reactions. First, technical aspects of the methodology are reviewed, including the hybrid density functional theory (DFT) methods that are typically employed for the QM aspect of the calculations, and various approaches to defining the interface between the QM and MM regions in QM/MM approaches. The modeling of the enzymatic catalytic cycle for three examples--methane monooxygenase, cytochrome P450, and triose phosphate isomerase--are discussed in some depth, followed by a brief summary of other systems that have been investigated by ab initio methods over the past several years. Finally, a discussion of the qualitative and quantitative conclusions concerning enzymatic catalysis that are available from modern ab initio approaches is presented, followed by a conclusion briefly summarizing future prospects.

  2. Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics?

    SciTech Connect

    Jang, Seogjoo; Sinitskiy, Anton V.; Voth, Gregory A.

    2014-04-21

    The ring polymer molecular dynamics (RPMD) method has gained popularity in recent years as a simple approximation for calculating real time quantum correlation functions in condensed media. However, the extent to which RPMD captures real dynamical quantum effects and why it fails under certain situations have not been clearly understood. Addressing this issue has been difficult in the absence of a genuine justification for the RPMD algorithm starting from the quantum Liouville equation. To this end, a new and exact path integral formalism for the calculation of real time quantum correlation functions is presented in this work, which can serve as a rigorous foundation for the analysis of the RPMD method as well as providing an alternative derivation of the well established centroid molecular dynamics method. The new formalism utilizes the cyclic symmetry of the imaginary time path integral in the most general sense and enables the expression of Kubo-transformed quantum time correlation functions as that of physical observables pre-averaged over the imaginary time path. Upon filtering with a centroid constraint function, the formulation results in the centroid dynamics formalism. Upon filtering with the position representation of the imaginary time path integral, we obtain an exact quantum dynamics formalism involving the same variables as the RPMD method. The analysis of the RPMD approximation based on this approach clarifies that an explicit quantum dynamical justification does not exist for the use of the ring polymer harmonic potential term (imaginary time kinetic energy) as implemented in the RPMD method. It is analyzed why this can cause substantial errors in nonlinear correlation functions of harmonic oscillators. Such errors can be significant for general correlation functions of anharmonic systems. We also demonstrate that the short time accuracy of the exact path integral limit of RPMD is of lower order than those for finite discretization of path. The

  3. Hidden algebra method (quasi-exact-solvability in quantum mechanics)

    SciTech Connect

    Turbiner, Alexander

    1996-02-20

    A general introduction to quasi-exactly-solvable problems of quantum mechanics is presented. Main attention is given to multidimensional quasi-exactly-solvable and exactly-solvable Schroedinger operators. Exact-solvability of the Calogero and Sutherland N-body problems ass ociated with an existence of the hidden algebra slN is discussed extensively.

  4. Clustering of attitudes towards obesity: a mixed methods study of Australian parents and children

    PubMed Central

    2013-01-01

    Background Current population-based anti-obesity campaigns often target individuals based on either weight or socio-demographic characteristics, and give a ‘mass’ message about personal responsibility. There is a recognition that attempts to influence attitudes and opinions may be more effective if they resonate with the beliefs that different groups have about the causes of, and solutions for, obesity. Limited research has explored how attitudinal factors may inform the development of both upstream and downstream social marketing initiatives. Methods Computer-assisted face-to-face interviews were conducted with 159 parents and 184 of their children (aged 9–18 years old) in two Australian states. A mixed methods approach was used to assess attitudes towards obesity, and elucidate why different groups held various attitudes towards obesity. Participants were quantitatively assessed on eight dimensions relating to the severity and extent, causes and responsibility, possible remedies, and messaging strategies. Cluster analysis was used to determine attitudinal clusters. Participants were also able to qualify each answer. Qualitative responses were analysed both within and across attitudinal clusters using a constant comparative method. Results Three clusters were identified. Concerned Internalisers (27% of the sample) judged that obesity was a serious health problem, that Australia had among the highest levels of obesity in the world and that prevalence was rapidly increasing. They situated the causes and remedies for the obesity crisis in individual choices. Concerned Externalisers (38% of the sample) held similar views about the severity and extent of the obesity crisis. However, they saw responsibility and remedies as a societal rather than an individual issue. The final cluster, the Moderates, which contained significantly more children and males, believed that obesity was not such an important public health issue, and judged the extent of obesity to be

  5. Validation tests of an improved kernel density estimation method for identifying disease clusters

    NASA Astrophysics Data System (ADS)

    Cai, Qiang; Rushton, Gerard; Bhaduri, Budhendra

    2012-07-01

    The spatial filter method, which belongs to the class of kernel density estimation methods, has been used to make morbidity and mortality maps in several recent studies. We propose improvements in the method to include spatially adaptive filters to achieve constant standard error of the relative risk estimates; a staircase weight method for weighting observations to reduce estimation bias; and a parameter selection tool to enhance disease cluster detection performance, measured by sensitivity, specificity, and false discovery rate. We test the performance of the method using Monte Carlo simulations of hypothetical disease clusters over a test area of four counties in Iowa. The simulations include different types of spatial disease patterns and high-resolution population distribution data. Results confirm that the new features of the spatial filter method do substantially improve its performance in realistic situations comparable to those where the method is likely to be used.

  6. Mayer sampling: calculation of cluster integrals using free-energy perturbation methods.

    PubMed

    Singh, Jayant K; Kofke, David A

    2004-06-01

    Free-energy simulation methods are applied toward the calculation of cluster integrals that appear in diagrammatic methods of statistical mechanics. In this approach, Monte Carlo sampling is performed on a number of molecules equal to the order of the integral, and configurations are weighted according to the absolute value of the integrand. An umbrella-sampling average yields the value of the cluster integral in reference to a known integral. Virial coefficients, up to the sixth for the Lennard-Jones model and the fifth for the SPCE model of water, are calculated as a demonstration.

  7. Clustering method and representative feeder selection for the California solar initiative

    SciTech Connect

    Broderick, Robert Joseph; Williams, Joseph R.; Munoz-Ramos, Karina

    2014-02-01

    The screening process for DG interconnection procedures needs to be improved in order to increase the PV deployment level on the distribution grid. A significant improvement in the current screening process could be achieved by finding a method to classify the feeders in a utility service territory and determine the sensitivity of particular groups of distribution feeders to the impacts of high PV deployment levels. This report describes the utility distribution feeder characteristics in California for a large dataset of 8,163 feeders and summarizes the California feeder population including the range of characteristics identified and most important to hosting capacity. The report describes the set of feeders that are identified for modeling and analysis as well as feeders identified for the control group. The report presents a method for separating a utilitys distribution feeders into unique clusters using the k-means clustering algorithm. An approach for determining the feeder variables of interest for use in a clustering algorithm is also described. The report presents an approach for choosing the feeder variables to be utilized in the clustering process and a method is identified for determining the optimal number of representative clusters.

  8. The Modeling Library of Eavesdropping Methods in Quantum Cryptography Protocols by Model Checking

    NASA Astrophysics Data System (ADS)

    Yang, Fan; Yang, Guowu; Hao, Yujie

    2016-07-01

    The most crucial issue of quantum cryptography protocols is its security. There exists many ways to attack the quantum communication process. In this paper, we present a model checking method for modeling the eavesdropping in quantum information protocols. So when the security properties of a certain protocol are needed to be verified, we can directly use the models which are already built. Here we adopt the probabilistic model checking tool—PRISM to model these attack methods. The verification results show that the detection rate of eavesdropping is approximately close to 1 when enough photons are transmitted.

  9. A multi-similarity spectral clustering method for community detection in dynamic networks.

    PubMed

    Qin, Xuanmei; Dai, Weidi; Jiao, Pengfei; Wang, Wenjun; Yuan, Ning

    2016-01-01

    Community structure is one of the fundamental characteristics of complex networks. Many methods have been proposed for community detection. However, most of these methods are designed for static networks and are not suitable for dynamic networks that evolve over time. Recently, the evolutionary clustering framework was proposed for clustering dynamic data, and it can also be used for community detection in dynamic networks. In this paper, a multi-similarity spectral (MSSC) method is proposed as an improvement to the former evolutionary clustering method. To detect the community structure in dynamic networks, our method considers the different similarity metrics of networks. First, multiple similarity matrices are constructed for each snapshot of dynamic networks. Then, a dynamic co-training algorithm is proposed by bootstrapping the clustering of different similarity measures. Compared with a number of baseline models, the experimental results show that the proposed MSSC method has better performance on some widely used synthetic and real-world datasets with ground-truth community structure that change over time. PMID:27528179

  10. A multi-similarity spectral clustering method for community detection in dynamic networks

    NASA Astrophysics Data System (ADS)

    Qin, Xuanmei; Dai, Weidi; Jiao, Pengfei; Wang, Wenjun; Yuan, Ning

    2016-08-01

    Community structure is one of the fundamental characteristics of complex networks. Many methods have been proposed for community detection. However, most of these methods are designed for static networks and are not suitable for dynamic networks that evolve over time. Recently, the evolutionary clustering framework was proposed for clustering dynamic data, and it can also be used for community detection in dynamic networks. In this paper, a multi-similarity spectral (MSSC) method is proposed as an improvement to the former evolutionary clustering method. To detect the community structure in dynamic networks, our method considers the different similarity metrics of networks. First, multiple similarity matrices are constructed for each snapshot of dynamic networks. Then, a dynamic co-training algorithm is proposed by bootstrapping the clustering of different similarity measures. Compared with a number of baseline models, the experimental results show that the proposed MSSC method has better performance on some widely used synthetic and real-world datasets with ground-truth community structure that change over time.

  11. A multi-similarity spectral clustering method for community detection in dynamic networks

    PubMed Central

    Qin, Xuanmei; Dai, Weidi; Jiao, Pengfei; Wang, Wenjun; Yuan, Ning

    2016-01-01

    Community structure is one of the fundamental characteristics of complex networks. Many methods have been proposed for community detection. However, most of these methods are designed for static networks and are not suitable for dynamic networks that evolve over time. Recently, the evolutionary clustering framework was proposed for clustering dynamic data, and it can also be used for community detection in dynamic networks. In this paper, a multi-similarity spectral (MSSC) method is proposed as an improvement to the former evolutionary clustering method. To detect the community structure in dynamic networks, our method considers the different similarity metrics of networks. First, multiple similarity matrices are constructed for each snapshot of dynamic networks. Then, a dynamic co-training algorithm is proposed by bootstrapping the clustering of different similarity measures. Compared with a number of baseline models, the experimental results show that the proposed MSSC method has better performance on some widely used synthetic and real-world datasets with ground-truth community structure that change over time. PMID:27528179

  12. Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method

    NASA Astrophysics Data System (ADS)

    Monteferrante, Michele; Bonella, Sara; Ciccotti, Giovanni

    2013-02-01

    We apply the phase integration method for quasiclassical quantum time correlation functions [M. Monteferrante, S. Bonella, and G. Ciccotti, Mol. Phys. 109, 3015 (2011), 10.1080/00268976.2011.619506] to compute the dynamic structure factor of liquid neon. So far the method had been tested only on model systems. By comparing our results for neon with experiments and previous calculations, we demonstrate that the scheme is accurate and efficient also for a realistic model of a condensed phase system showing quantum behavior.

  13. A test of the possibility of calculating absorption spectra by mixed quantum-classical methods

    NASA Astrophysics Data System (ADS)

    Haug, Kenneth; Metiu, Horia

    1992-10-01

    Some of the most efficient methods for studying systems having a large number of degrees of freedom treat a few degrees of freedom quantum mechanically and the remainder classically. Here we examine how these methods fare when used to calculate the cross section for photon absorption by a quantum system imbedded in a medium. To test the method, we study a model which has two degrees of freedom and mimicks the properties of a one-dimensional alkali atom-He dimer. We treat the electron motion quantum mechanically and the distance between the He atom and the alkali ion classically. Light absorption occurs because the electron is coupled to radiation. The calculation of the absorption cross section by quantum-classical methods fails rather dramatically-at certain frequencies, the absorption coefficient is negative. By comparing with exact quantum calculations, we show that this failure takes place because the time evolution of the classical variables influences the dynamics of the quantum degree of freedom through the Hamiltonian only; important information, which a fully quantum treatment would put in the wave function, is missing. To repair this flaw, we experiment with a method which uses a swarm of classical trajectories to generate a ``classical wave function.'' The results are encouraging, but require substantial computer time when the number of classical variables is large. We argue that in the limit of many classical degrees of freedom, accurate calculations can be performed by using the time-dependent Hartree method and treating some degrees of freedom by exact numerical methods (e.g., a fast Fourier transform procedure) and the others by Gaussian wave packets or any other propagation method that is accurate for a very short time. This procedure leads to a simple time domain picture of dephasing and line broadening in the case of a localized quantum system imbedded in a medium with heavy atoms.

  14. A semiclassical method in the theory of light scattering by semiconductor quantum dots

    SciTech Connect

    Lang, I. G.; Korovin, L. I. Pavlov, S. T.

    2008-06-15

    A semiclassical method is proposed for the theoretical description of elastic light scattering by arbitrary semiconductor quantum dots under conditions of size quantization. This method involves retarded potentials and allows one to dispense with boundary conditions for electric and magnetic fields. Exact results for the Umov-Poynting vector at large distances from quantum dots in the case of monochromatic and pulsed irradiation and formulas for differential scattering cross sections are obtained.

  15. Ramsey's method of separated oscillating fields and its application to gravitationally induced quantum phase shifts

    SciTech Connect

    Abele, H.; Jenke, T.; Leeb, H.; Schmiedmayer, J.

    2010-03-15

    We propose to apply Ramsey's method of separated oscillating fields to the spectroscopy of the quantum states in the gravity potential above a horizontal mirror. This method allows a precise measurement of quantum mechanical phaseshifts of a Schroedinger wave packet bouncing off a hard surface in the gravitational field of the Earth. Measurements with ultracold neutrons will offer a sensitivity to Newton's law or hypothetical short-ranged interactions, which is about 21 orders of magnitude below the energy scale of electromagnetism.

  16. Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method.

    PubMed

    Monteferrante, Michele; Bonella, Sara; Ciccotti, Giovanni

    2013-02-01

    We apply the phase integration method for quasiclassical quantum time correlation functions [M. Monteferrante, S. Bonella, and G. Ciccotti, Mol. Phys. 109, 3015 (2011)] to compute the dynamic structure factor of liquid neon. So far the method had been tested only on model systems. By comparing our results for neon with experiments and previous calculations, we demonstrate that the scheme is accurate and efficient also for a realistic model of a condensed phase system showing quantum behavior.

  17. Cluster-continuum quantum mechanical models to guide the choice of anions for Li{sup +}-conducting ionomers

    SciTech Connect

    Shiau, Huai-Suen; Janik, Michael J.; Liu, Wenjuan; Colby, Ralph H.

    2013-11-28

    A quantum-mechanical investigation on Li poly(ethylene oxide)-based ionomers was performed in the cluster-continuum solvation model (CCM) that includes specific solvation in the first shell surrounding the cation, all surrounded by a polarizable continuum. A four-state model, including a free Li cation, Li{sup +}-anion pair, triple ion, and quadrupole was used to represent the states of Li{sup +} within the ionomer in the CCM. The relative energy of each state was calculated for Li{sup +} with various anions, with dimethyl ether representing the ether oxygen solvation. The population distribution of Li{sup +} ions among states was estimated by applying Boltzmann statistics to the CCM energies. Entropy difference estimates are needed for populations to better match the true ionomer system. The total entropy change is considered to consist of four contributions: translational, rotational, electrostatic, and solvent immobilization entropies. The population of ion states is reported as a function of Bjerrum length divided by ion-pair separation with/without entropy considered to investigate the transition between states. Predicted concentrations of Li{sup +}-conducting states (free Li{sup +} and positive triple ions) are compared among a series of anions to indicate favorable features for design of an optimal Li{sup +}-conducting ionomer; the perfluorotetraphenylborate anion maximizes the conducting positive triple ion population among the series of anions considered.

  18. Transition-state searches in metal clusters by first-principle methods.

    PubMed

    Cruz-Olvera, Domingo; Vasquez, Alejandra de la Trinidad; Geudtner, Gerald; Vásquez-Pérez, José Manuel; Calaminici, Patrizia; Köster, Andreas M

    2015-03-01

    Elucidation of the chemical reactivity of metal clusters is often cumbersome due to the nonintuitive structures of the corresponding transition states. In this work, a hierarchical transition-state algorithm as implemented in the deMon2k code has been applied to locate transition states of small sodium clusters with 6-10 atoms. This algorithm combines the so-called double-ended interpolation method with the uphill trust region method. The minimum structures needed as input were obtained from Born-Oppenheimer molecular dynamics simulations. To connect the found transition states with the corresponding minimum structures, the intrinsic reaction coordinates were calculated. This work demonstrates how nonintuitive rearrangement mechanisms can be studied in metal clusters. PMID:25072358

  19. Form gene clustering method about pan-ethnic-group products based on emotional semantic

    NASA Astrophysics Data System (ADS)

    Chen, Dengkai; Ding, Jingjing; Gao, Minzhuo; Ma, Danping; Liu, Donghui

    2016-09-01

    The use of pan-ethnic-group products form knowledge primarily depends on a designer's subjective experience without user participation. The majority of studies primarily focus on the detection of the perceptual demands of consumers from the target product category. A pan-ethnic-group products form gene clustering method based on emotional semantic is constructed. Consumers' perceptual images of the pan-ethnic-group products are obtained by means of product form gene extraction and coding and computer aided product form clustering technology. A case of form gene clustering about the typical pan-ethnic-group products is investigated which indicates that the method is feasible. This paper opens up a new direction for the future development of product form design which improves the agility of product design process in the era of Industry 4.0.

  20. Coupled quantum-classical method for long range charge transfer: relevance of the nuclear motion to the quantum electron dynamics

    NASA Astrophysics Data System (ADS)

    da Silva, Robson; Hoff, Diego A.; Rego, Luis G. C.

    2015-04-01

    Charge and excitonic-energy transfer phenomena are fundamental for energy conversion in solar cells as well as artificial photosynthesis. Currently, much interest is being paid to light-harvesting and energy transduction processes in supramolecular structures, where nuclear dynamics has a major influence on electronic quantum dynamics. For this reason, the simulation of long range electron transfer in supramolecular structures, under environmental conditions described within an atomistic framework, has been a difficult problem to study. This work describes a coupled quantum mechanics/molecular mechanics method that aims at describing long range charge transfer processes in supramolecular systems, taking into account the atomistic details of large molecular structures, the underlying nuclear motion, and environmental effects. The method is applied to investigate the relevance of electron-nuclei interaction on the mechanisms for photo-induced electron-hole pair separation in dye-sensitized interfaces as well as electronic dynamics in molecular structures.

  1. Computational method for the long time propagation of quantum channeled particles in crystals and carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Ćosić, M.; Petrović, S.; Nešković, N.

    2014-07-01

    This work reports on the computational method for the long time propagation of the quantum channeled particles in infinite and finite harmonic interaction wells and in a realistic carbon nanotube interaction potential well. This method is based on the Chebyshev global propagation method for solving of the corresponding time dependent Schrödinger equation. For comparison, the computational method based on the Crank-Nicolson propagation method is also presented. In the case of quantum particle motion in infinite harmonic potential well, when the analytical solution of the corresponding time-dependent Schrödinger equation exists, we show that the obtained propagation method is efficient, very accurate and numerically stable. It is superior with respect to the method based on the Crank-Nicolson propagation method. A detailed study of the long time quantum particle motion in the finite harmonic interaction potential well shows that the obtained computational method based on the Chebyshev global propagation method can be successfully applied for following of the channeled quantum particle in crystals and carbon nanotubes. This is demonstrated in the case of quantum particle motion in a realistic carbon nanotube interaction potential well.

  2. Geometric and Topological Methods for Quantum Field Theory

    NASA Astrophysics Data System (ADS)

    Cardona, Alexander; Contreras, Iván.; Reyes-Lega, Andrés. F.

    2013-05-01

    Introduction; 1. A brief introduction to Dirac manifolds Henrique Bursztyn; 2. Differential geometry of holomorphic vector bundles on a curve Florent Schaffhauser; 3. Paths towards an extension of Chern-Weil calculus to a class of infinite dimensional vector bundles Sylvie Paycha; 4. Introduction to Feynman integrals Stefan Weinzierl; 5. Iterated integrals in quantum field theory Francis Brown; 6. Geometric issues in quantum field theory and string theory Luis J. Boya; 7. Geometric aspects of the standard model and the mysteries of matter Florian Scheck; 8. Absence of singular continuous spectrum for some geometric Laplacians Leonardo A. Cano García; 9. Models for formal groupoids Iván Contreras; 10. Elliptic PDEs and smoothness of weakly Einstein metrics of Hölder regularity Andrés Vargas; 11. Regularized traces and the index formula for manifolds with boundary Alexander Cardona and César Del Corral; Index.

  3. Enchanced methods of hydrophilized CdSe quantum dots synthesis

    NASA Astrophysics Data System (ADS)

    Potapkin, D. V.; Zharkova, I. S.; Goryacheva, I. Y.

    2015-03-01

    Quantum dots are bright and stable fluorescence signal sources, but for most of applications they need an additional hydrophilization step. Unfortunately, most of existing approaches lead to QD's fluorescence quenching, so there is a need for additional enhancing of hydrophilized QD's brightness like UV irradiation, which can be used both on water insoluble QD's with oleic acid ligands (in toluene) and on hydrophilized QD's covered with UV-stable polymer (in aqueous solution). For synthesis of bright water-soluble fluorescent labels CdSe/CdS/ZnS colloidal quantum dots were covered with PAMAM dendrimer and irradiated with UV lamp in quartz cuvettes for 3 hours at the room temperature and then compared with control sample.

  4. Hidden algebra method (quasi-exact-solvability in quantum mechanics)

    SciTech Connect

    Turbiner, A. |

    1996-02-01

    A general introduction to quasi-exactly-solvable problems of quantum mechanics is presented. Main attention is given to multidimensional quasi-exactly-solvable and exactly-solvable Schroedinger operators. Exact-solvability of the Calogero and Sutherland {ital N}-body problems ass ociated with an existence of the hidden algebra {ital sl}{sub {ital N}} is discussed extensively. {copyright} {ital 1996 American Institute of Physics.}

  5. Method of making an improved superconducting quantum interference device

    DOEpatents

    Wu, Cheng-Teh; Falco, Charles M.; Kampwirth, Robert T.

    1977-01-01

    An improved superconducting quantum interference device is made by sputtering a thin film of an alloy of three parts niobium to one part tin in a pattern comprising a closed loop with a narrow region, depositing a thin film of a radiation shield such as copper over the niobium-tin, scribing a narrow line in the copper over the narrow region, exposing the structure at the scribed line to radiation and removing the deposited copper.

  6. Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Auletta, Gennaro; Fortunato, Mauro; Parisi, Giorgio

    2014-01-01

    Introduction; Part I. Basic Features of Quantum Mechanics: 1. From classical mechanics to quantum mechanics; 2. Quantum observable and states; 3. Quantum dynamics; 4. Examples of quantum dynamics; 5. Density matrix; Part II. More Advanced Topics: 6. Angular momentum and spin; 7. Identical particles; 8. Symmetries and conservation laws; 9. The measurement problem; Part III. Matter and Light: 10. Perturbations and approximation methods; 11. Hydrogen and helium atoms; 12. Hydrogen molecular ion; 13. Quantum optics; Part IV. Quantum Information: State and Correlations: 14. Quantum theory of open systems; 15. State measurement in quantum mechanics; 16. Entanglement: non-separability; 17. Entanglement: quantum information; References; Index.

  7. Geometric and Topological Methods for Quantum Field Theory

    NASA Astrophysics Data System (ADS)

    Ocampo, Hernan; Pariguan, Eddy; Paycha, Sylvie

    2010-04-01

    Introduction; 1. The impact of QFT on low-dimensional topology Paul Kirk; 2. Differential equations aspects of quantum cohomology Martin A. Guest; 3. Index theory and groupoids Claire Debord and Jean-Marie Lescure; 4. Renormalization Hopf algebras and combinatorial groups Alessandra Frabetti; 5. BRS invariance for massive boson fields José M. Gracia-Bondía; 6. Large N field theories and geometry David Berenstein; 7. Functional renormalization group equations, asymptotic safety, and quantum Einstein gravity Martin Reuter and Frank Saueressig; 8. When is a differentiable manifold the boundary of an orbifold? Andrés Angel; 9. Canonical group quantization, rotation generators and quantum indistinguishability Carlos Benavides and Andrés Reyes-Lega; 10. Conserved currents in Kähler manifolds Jaime R. Camacaro and Juan Carlos Moreno; 11. A symmetrized canonical determinant on odd-class pseudodifferential operators Marie-Françoise Ouedraogo; 12. Some remarks about cosymplectic metrics on maximal flag manifolds Marlio Paredes and Sofia Pinzón; 13. Heisenberg modules over real multiplication noncommutative tori and related algebraic structures Jorge Plazas; Index.

  8. A method to determine the number of nanoparticles in a cluster using conventional optical microscopes

    SciTech Connect

    Kang, Hyeonggon; Attota, Ravikiran Tondare, Vipin; Vladár, András E.; Kavuri, Premsagar

    2015-09-07

    We present a method that uses conventional optical microscopes to determine the number of nanoparticles in a cluster, which is typically not possible using traditional image-based optical methods due to the diffraction limit. The method, called through-focus scanning optical microscopy (TSOM), uses a series of optical images taken at varying focus levels to achieve this. The optical images cannot directly resolve the individual nanoparticles, but contain information related to the number of particles. The TSOM method makes use of this information to determine the number of nanoparticles in a cluster. Initial good agreement between the simulations and the measurements is also presented. The TSOM method can be applied to fluorescent and non-fluorescent as well as metallic and non-metallic nano-scale materials, including soft materials, making it attractive for tag-less, high-speed, optical analysis of nanoparticles down to 45 nm diameter.

  9. Quantum simulation of quantum field theory using continuous variables

    DOE PAGES

    Marshall, Kevin; Pooser, Raphael C.; Siopsis, George; Weedbrook, Christian

    2015-12-14

    Much progress has been made in the field of quantum computing using continuous variables over the last couple of years. This includes the generation of extremely large entangled cluster states (10,000 modes, in fact) as well as a fault tolerant architecture. This has lead to the point that continuous-variable quantum computing can indeed be thought of as a viable alternative for universal quantum computing. With that in mind, we present a new algorithm for continuous-variable quantum computers which gives an exponential speedup over the best known classical methods. Specifically, this relates to efficiently calculating the scattering amplitudes in scalar bosonicmore » quantum field theory, a problem that is known to be hard using a classical computer. Thus, we give an experimental implementation based on cluster states that is feasible with today's technology.« less

  10. Quantum simulation of quantum field theory using continuous variables

    SciTech Connect

    Marshall, Kevin; Pooser, Raphael C.; Siopsis, George; Weedbrook, Christian

    2015-12-14

    Much progress has been made in the field of quantum computing using continuous variables over the last couple of years. This includes the generation of extremely large entangled cluster states (10,000 modes, in fact) as well as a fault tolerant architecture. This has lead to the point that continuous-variable quantum computing can indeed be thought of as a viable alternative for universal quantum computing. With that in mind, we present a new algorithm for continuous-variable quantum computers which gives an exponential speedup over the best known classical methods. Specifically, this relates to efficiently calculating the scattering amplitudes in scalar bosonic quantum field theory, a problem that is known to be hard using a classical computer. Thus, we give an experimental implementation based on cluster states that is feasible with today's technology.

  11. A Combinational Clustering Based Method for cDNA Microarray Image Segmentation.

    PubMed

    Shao, Guifang; Li, Tiejun; Zuo, Wangda; Wu, Shunxiang; Liu, Tundong

    2015-01-01

    Microarray technology plays an important role in drawing useful biological conclusions by analyzing thousands of gene expressions simultaneously. Especially, image analysis is a key step in microarray analysis and its accuracy strongly depends on segmentation. The pioneering works of clustering based segmentation have shown that k-means clustering algorithm and moving k-means clustering algorithm are two commonly used methods in microarray image processing. However, they usually face unsatisfactory results because the real microarray image contains noise, artifacts and spots that vary in size, shape and contrast. To improve the segmentation accuracy, in this article we present a combination clustering based segmentation approach that may be more reliable and able to segment spots automatically. First, this new method starts with a very simple but effective contrast enhancement operation to improve the image quality. Then, an automatic gridding based on the maximum between-class variance is applied to separate the spots into independent areas. Next, among each spot region, the moving k-means clustering is first conducted to separate the spot from background and then the k-means clustering algorithms are combined for those spots failing to obtain the entire boundary. Finally, a refinement step is used to replace the false segmentation and the inseparable ones of missing spots. In addition, quantitative comparisons between the improved method and the other four segmentation algorithms--edge detection, thresholding, k-means clustering and moving k-means clustering--are carried out on cDNA microarray images from six different data sets. Experiments on six different data sets, 1) Stanford Microarray Database (SMD), 2) Gene Expression Omnibus (GEO), 3) Baylor College of Medicine (BCM), 4) Swiss Institute of Bioinformatics (SIB), 5) Joe DeRisi's individual tiff files (DeRisi), and 6) University of California, San Francisco (UCSF), indicate that the improved approach is

  12. A Combinational Clustering Based Method for cDNA Microarray Image Segmentation

    PubMed Central

    Shao, Guifang; Li, Tiejun; Zuo, Wangda; Wu, Shunxiang; Liu, Tundong

    2015-01-01

    Microarray technology plays an important role in drawing useful biological conclusions by analyzing thousands of gene expressions simultaneously. Especially, image analysis is a key step in microarray analysis and its accuracy strongly depends on segmentation. The pioneering works of clustering based segmentation have shown that k-means clustering algorithm and moving k-means clustering algorithm are two commonly used methods in microarray image processing. However, they usually face unsatisfactory results because the real microarray image contains noise, artifacts and spots that vary in size, shape and contrast. To improve the segmentation accuracy, in this article we present a combination clustering based segmentation approach that may be more reliable and able to segment spots automatically. First, this new method starts with a very simple but effective contrast enhancement operation to improve the image quality. Then, an automatic gridding based on the maximum between-class variance is applied to separate the spots into independent areas. Next, among each spot region, the moving k-means clustering is first conducted to separate the spot from background and then the k-means clustering algorithms are combined for those spots failing to obtain the entire boundary. Finally, a refinement step is used to replace the false segmentation and the inseparable ones of missing spots. In addition, quantitative comparisons between the improved method and the other four segmentation algorithms--edge detection, thresholding, k-means clustering and moving k-means clustering--are carried out on cDNA microarray images from six different data sets. Experiments on six different data sets, 1) Stanford Microarray Database (SMD), 2) Gene Expression Omnibus (GEO), 3) Baylor College of Medicine (BCM), 4) Swiss Institute of Bioinformatics (SIB), 5) Joe DeRisi’s individual tiff files (DeRisi), and 6) University of California, San Francisco (UCSF), indicate that the improved approach is

  13. A Combinational Clustering Based Method for cDNA Microarray Image Segmentation.

    PubMed

    Shao, Guifang; Li, Tiejun; Zuo, Wangda; Wu, Shunxiang; Liu, Tundong

    2015-01-01

    Microarray technology plays an important role in drawing useful biological conclusions by analyzing thousands of gene expressions simultaneously. Especially, image analysis is a key step in microarray analysis and its accuracy strongly depends on segmentation. The pioneering works of clustering based segmentation have shown that k-means clustering algorithm and moving k-means clustering algorithm are two commonly used methods in microarray image processing. However, they usually face unsatisfactory results because the real microarray image contains noise, artifacts and spots that vary in size, shape and contrast. To improve the segmentation accuracy, in this article we present a combination clustering based segmentation approach that may be more reliable and able to segment spots automatically. First, this new method starts with a very simple but effective contrast enhancement operation to improve the image quality. Then, an automatic gridding based on the maximum between-class variance is applied to separate the spots into independent areas. Next, among each spot region, the moving k-means clustering is first conducted to separate the spot from background and then the k-means clustering algorithms are combined for those spots failing to obtain the entire boundary. Finally, a refinement step is used to replace the false segmentation and the inseparable ones of missing spots. In addition, quantitative comparisons between the improved method and the other four segmentation algorithms--edge detection, thresholding, k-means clustering and moving k-means clustering--are carried out on cDNA microarray images from six different data sets. Experiments on six different data sets, 1) Stanford Microarray Database (SMD), 2) Gene Expression Omnibus (GEO), 3) Baylor College of Medicine (BCM), 4) Swiss Institute of Bioinformatics (SIB), 5) Joe DeRisi's individual tiff files (DeRisi), and 6) University of California, San Francisco (UCSF), indicate that the improved approach is

  14. Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field

    PubMed Central

    2015-01-01

    A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework. PMID:25691830

  15. Multipolar Ewald methods, 2: applications using a quantum mechanical force field.

    PubMed

    Giese, Timothy J; Panteva, Maria T; Chen, Haoyuan; York, Darrin M

    2015-02-10

    A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework.

  16. Ab initio centroid molecular dynamics: a fully quantum method for condensed-phase dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pavese, Marc; Berard, Daniel R.; Voth, Gregory A.

    1999-01-01

    A fully quantum molecular dynamics method is presented which combines ab initio Car-Parrinello molecular dynamics with centroid molecular dynamics. The first technique allows the forces on the atoms to be obtained from ab initio electronic structure. The second technique, given the forces on the atoms, allows one to calculate an approximate quantum time evolution for the nuclei. The combination of the two, therefore, represents the first feasible approach to simulating the fully quantum dynamics of a many-body system. An application to excess proton translocation along a model water wire will be presented.

  17. A method for clustering of miRNA sequences using fragmented programming.

    PubMed

    Ivashchenko, Anatoly; Pyrkova, Anna; Niyazova, Raigul

    2016-01-01

    Clustering of miRNA sequences is an important problem in molecular genetics associated cellular biology. Thousands of such sequences are known today through advancement in sophisticated molecular tools, sequencing techniques, computational resources and rule based mathematical models. Analysis of such large-scale miRNA sequences for inferring patterns towards deducing cellular function is a great challenge in modern molecular biology. Therefore, it is of interest to develop mathematical models specific for miRNA sequences. The process is to group (cluster) such miRNA sequences using well-defined known features. We describe a method for clustering of miRNA sequences using fragmented programming. Subsequently, we illustrated the utility of the model using a dendrogram (a tree diagram) for publically known A.thaliana miRNA nucleotide sequences towards the inference of observed conserved patterns. PMID:27212839

  18. A method for clustering of miRNA sequences using fragmented programming

    PubMed Central

    Ivashchenko, Anatoly; Pyrkova, Anna; Niyazova, Raigul

    2016-01-01

    Clustering of miRNA sequences is an important problem in molecular genetics associated cellular biology. Thousands of such sequences are known today through advancement in sophisticated molecular tools, sequencing techniques, computational resources and rule based mathematical models. Analysis of such large-scale miRNA sequences for inferring patterns towards deducing cellular function is a great challenge in modern molecular biology. Therefore, it is of interest to develop mathematical models specific for miRNA sequences. The process is to group (cluster) such miRNA sequences using well-defined known features. We describe a method for clustering of miRNA sequences using fragmented programming. Subsequently, we illustrated the utility of the model using a dendrogram (a tree diagram) for publically known A.thaliana miRNA nucleotide sequences towards the inference of observed conserved patterns PMID:27212839

  19. Eigenfunction-expansion method for solving the quantum-wire problem: Formulation

    NASA Astrophysics Data System (ADS)

    Baraff, G. A.; Gershoni, D.

    1991-02-01

    We present a method of formulating the multiband-envelope-function equations for a quantum structure whose internal interfaces are perpendicular planes. The method can be used for quantum wells, quantum wires, or quantum dots (one-, two-, or three-dimensional confinement of the electronic wave function), as well as for periodic repetitions (superlattices) of these elementary structures. The technique used is expansion of the multiband envelope functions in a Fourier series for each of the coordinates x, y, and z. Special attention is paid to formulating interface-matching conditions that impose Hermiticity on the resulting systems of equations. This demand leads to the usual condition that the normal component of the current must be continuous across each internal interface. The method we have devised is similar to the one used by Altarelli for the quantum-well problem in that it leads to a secular equation that is solved by diagonalizing an energy-independent matrix. It differs in that here, the envelope functions are expanded in smooth continuous functions using the same expansion coefficients in all regions of the structure. Using this method, one can now calculate the optical absorption, its frequency, and polarization dependence, with the same amount of detail that has previously been possible only for confinement in one dimension, namely, in the quantum well and one-dimensional superlattice.

  20. The structure of the hydrated electron. Part 2. A mixed quantum/classical molecular dynamics embedded cluster density functional theory: single-excitation configuration interaction study.

    PubMed

    Shkrob, Ilya A; Glover, William J; Larsen, Ross E; Schwartz, Benjamin J

    2007-06-21

    Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Ax18 Ax18 A matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer (approximately 18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not allow for mixing of the excess

  1. Study of methods to increase cluster/dislocation loop densities in electrodes

    NASA Astrophysics Data System (ADS)

    Yang, Xiaoling; Miley, George H.

    2009-03-01

    Recent research has developed a technique for imbedding ultra-high density deuterium ``clusters'' (50 to 100 atoms per cluster) in various metals such as Palladium (Pd), Beryllium (Be) and Lithium (Li). It was found the thermally dehydrogenated PdHx retained the clusters and exhibited up to 12 percent lower resistance compared to the virginal Pd samplesootnotetextA. G. Lipson, et al. Phys. Solid State. 39 (1997) 1891. SQUID measurements showed that in Pd these condensed matter clusters approach metallic conditions, exhibiting superconducting propertiesootnotetextA. Lipson, et al. Phys. Rev. B 72, 212507 (2005ootnotetextA. G. Lipson, et al. Phys. Lett. A 339, (2005) 414-423. If the fabrication methods under study are successful, a large packing fraction of nuclear reactive clusters can be developed in the electrodes by electrolyte or high pressure gas loading. This will provide a much higher low-energy-nuclear- reaction (LENR) rate than achieved with earlier electrodeootnotetextCastano, C.H., et al. Proc. ICCF-9, Beijing, China 19-24 May, 2002..

  2. A comprehensive comparison of different clustering methods for reliability analysis of microarray data.

    PubMed

    Kafieh, Rahele; Mehridehnavi, Alireza

    2013-01-01

    In this study, we considered some competitive learning methods including hard competitive learning and soft competitive learning with/without fixed network dimensionality for reliability analysis in microarrays. In order to have a more extensive view, and keeping in mind that competitive learning methods aim at error minimization or entropy maximization (different kinds of function optimization), we decided to investigate the abilities of mixture decomposition schemes. Therefore, we assert that this study covers the algorithms based on function optimization with particular insistence on different competitive learning methods. The destination is finding the most powerful method according to a pre-specified criterion determined with numerical methods and matrix similarity measures. Furthermore, we should provide an indication showing the intrinsic ability of the dataset to form clusters before we apply a clustering algorithm. Therefore, we proposed Hopkins statistic as a method for finding the intrinsic ability of a data to be clustered. The results show the remarkable ability of Rayleigh mixture model in comparison with other methods in reliability analysis task.

  3. A Comprehensive Comparison of Different Clustering Methods for Reliability Analysis of Microarray Data

    PubMed Central

    Kafieh, Rahele; Mehridehnavi, Alireza

    2013-01-01

    In this study, we considered some competitive learning methods including hard competitive learning and soft competitive learning with/without fixed network dimensionality for reliability analysis in microarrays. In order to have a more extensive view, and keeping in mind that competitive learning methods aim at error minimization or entropy maximization (different kinds of function optimization), we decided to investigate the abilities of mixture decomposition schemes. Therefore, we assert that this study covers the algorithms based on function optimization with particular insistence on different competitive learning methods. The destination is finding the most powerful method according to a pre-specified criterion determined with numerical methods and matrix similarity measures. Furthermore, we should provide an indication showing the intrinsic ability of the dataset to form clusters before we apply a clustering algorithm. Therefore, we proposed Hopkins statistic as a method for finding the intrinsic ability of a data to be clustered. The results show the remarkable ability of Rayleigh mixture model in comparison with other methods in reliability analysis task. PMID:24083134

  4. Quantum-Classical Nonadiabatic Dynamics: Coupled- vs Independent-Trajectory Methods.

    PubMed

    Agostini, Federica; Min, Seung Kyu; Abedi, Ali; Gross, E K U

    2016-05-10

    Trajectory-based mixed quantum-classical approaches to coupled electron-nuclear dynamics suffer from well-studied problems such as the lack of (or incorrect account for) decoherence in the trajectory surface hopping method and the inability of reproducing the spatial splitting of a nuclear wave packet in Ehrenfest-like dynamics. In the context of electronic nonadiabatic processes, these problems can result in wrong predictions for quantum populations and in unphysical outcomes for the nuclear dynamics. In this paper, we propose a solution to these issues by approximating the coupled electronic and nuclear equations within the framework of the exact factorization of the electron-nuclear wave function. We present a simple quantum-classical scheme based on coupled classical trajectories and test it against the full quantum mechanical solution from wave packet dynamics for some model situations which represent particularly challenging problems for the above-mentioned traditional methods. PMID:27030209

  5. Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods.

    PubMed

    Li, Jilai; Farrokhnia, Maryam; Rulíšek, Lubomír; Ryde, Ulf

    2015-07-01

    We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular, the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerization reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site. PMID:26039490

  6. Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods.

    PubMed

    Li, Jilai; Farrokhnia, Maryam; Rulíšek, Lubomír; Ryde, Ulf

    2015-07-01

    We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular, the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerization reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site.

  7. Vibrational anharmonicity of small gold and silver clusters using the VSCF method.

    PubMed

    Mancera, Luis A; Benoit, David M

    2016-01-01

    We study the vibrational spectra of small neutral gold (Au2-Au10) and silver (Ag2-Au5) clusters using the vibrational self-consistent field method (VSCF) in order to account for anharmonicity. We report harmonic, VSCF, and correlation-corrected VSCF calculations obtained using a vibrational configuration interaction approach (VSCF/VCI). Our implementation of the method is based on an efficient calculation of the potential energy surfaces (PES), using periodic density functional theory (DFT) with a plane-wave pseudopotential basis. In some cases, we use an efficient technique (fast-VSCF) assisted by the Voter-Chen potential in order to get an efficient reduction of the number of pair-couplings between modes. This allows us to efficiently reduce the computing time of 2D-PES without degrading the accuracy. We found that anharmonicity of the gold clusters is very small with maximum rms deviations of about 1 cm(-1), although for some particular modes anharmonicity reaches values slightly larger than 2 cm(-1). Silver clusters show slightly larger anharmonicity. In both cases, large differences between calculated and experimental vibrational frequencies (when available) stem more likely from the quality of the electronic structure method used than from vibrational anharmonicity. We show that noble gas embedding often affects the vibrational properties of these clusters more than anharmonicity, and discuss our results in the context of experimental studies. PMID:26619274

  8. Smoothed Particle Inference: A Kilo-Parametric Method for X-ray Galaxy Cluster Modeling

    SciTech Connect

    Peterson, John R.; Marshall, P.J.; Andersson, K.; /Stockholm U. /SLAC

    2005-08-05

    We propose an ambitious new method that models the intracluster medium in clusters of galaxies as a set of X-ray emitting smoothed particles of plasma. Each smoothed particle is described by a handful of parameters including temperature, location, size, and elemental abundances. Hundreds to thousands of these particles are used to construct a model cluster of galaxies, with the appropriate complexity estimated from the data quality. This model is then compared iteratively with X-ray data in the form of adaptively binned photon lists via a two-sample likelihood statistic and iterated via Markov Chain Monte Carlo. The complex cluster model is propagated through the X-ray instrument response using direct sampling Monte Carlo methods. Using this approach the method can reproduce many of the features observed in the X-ray emission in a less assumption-dependent way that traditional analyses, and it allows for a more detailed characterization of the density, temperature, and metal abundance structure of clusters. Multi-instrument X-ray analyses and simultaneous X-ray, Sunyaev-Zeldovich (SZ), and lensing analyses are a straight-forward extension of this methodology. Significant challenges still exist in understanding the degeneracy in these models and the statistical noise induced by the complexity of the models.

  9. A New Multistage Medical Segmentation Method Based on Superpixel and Fuzzy Clustering

    PubMed Central

    Wei, Benzheng; Yu, Zhen; Yang, Gongping; Yin, Yilong

    2014-01-01

    The medical image segmentation is the key approach of image processing for brain MRI images. However, due to the visual complex appearance of image structures and the imaging characteristic, it is still challenging to automatically segment brain MRI image. A new multi-stage segmentation method based on superpixel and fuzzy clustering (MSFCM) is proposed to achieve the good brain MRI segmentation results. The MSFCM utilizes the superpixels as the clustering objects instead of pixels, and it can increase the clustering granularity and overcome the influence of noise and bias effectively. In the first stage, the MRI image is parsed into several atomic areas, namely, superpixels, and a further parsing step is adopted for the areas with bigger gray variance over setting threshold. Subsequently, designed fuzzy clustering is carried out to the fuzzy membership of each superpixel, and an iterative broadcast method based on the Butterworth function is used to redefine their classifications. Finally, the segmented image is achieved by merging the superpixels which have the same classification label. The simulated brain database from BrainWeb site is used in the experiments, and the experimental results demonstrate that MSFCM method outperforms the traditional FCM algorithm in terms of segmentation accuracy and stability for MRI image. PMID:24734117

  10. Application of attribute weighting method based on clustering centers to discrimination of linearly non-separable medical datasets.

    PubMed

    Polat, Kemal

    2012-08-01

    In this paper, attribute weighting method based on the cluster centers with aim of increasing the discrimination between classes has been proposed and applied to nonlinear separable datasets including two medical datasets (mammographic mass dataset and bupa liver disorders dataset) and 2-D spiral dataset. The goals of this method are to gather the data points near to cluster center all together to transform from nonlinear separable datasets to linear separable dataset. As clustering algorithm, k-means clustering, fuzzy c-means clustering, and subtractive clustering have been used. The proposed attribute weighting methods are k-means clustering based attribute weighting (KMCBAW), fuzzy c-means clustering based attribute weighting (FCMCBAW), and subtractive clustering based attribute weighting (SCBAW) and used prior to classifier algorithms including C4.5 decision tree and adaptive neuro-fuzzy inference system (ANFIS). To evaluate the proposed method, the recall, precision value, true negative rate (TNR), G-mean1, G-mean2, f-measure, and classification accuracy have been used. The results have shown that the best attribute weighting method was the subtractive clustering based attribute weighting with respect to classification performance in the classification of three used datasets. PMID:21611787

  11. Quantum critical point of Dirac fermions studied using efficient continuous-time projector quantum Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Iazzi, Mauro; Corboz, Philippe; Troyer, Matthias

    2015-03-01

    Quantum phase transition (QPT) of Dirac fermions is a fascinating topic both in condensed matter and in high energy physics. Besides its immediate connection to fundamental problems like mass generation and exotic phases of matter, it provides a common playground where state of the art numerical simulations can be crosschecked with various effective field theory predictions, thus deepen our understanding of both fields. The universality class of the QPT is fundamentally different from the usual bosonic field theory because of the coupling to the gapless fermionic mode at the critical point. We study lattice models with spinless and multi-flavor Dirac fermions using the newly developed efficient continuous-time projector quantum Monte Carlo method. Besides eliminating the Trotter error, the method also enables us to directly calculate derivative observables in a continuous range of interaction strengths, thus greatly enhancing the resolution of the quantum critical region. Compatible results are also obtained from infinite projected entangled-pair states calculations. We compare these numerical results with predictions of the Gross-Neveu theory and discuss their physical implications.

  12. Stepwise Threshold Clustering: A New Method for Genotyping MHC Loci Using Next-Generation Sequencing Technology

    PubMed Central

    Stutz, William E.; Bolnick, Daniel I.

    2014-01-01

    Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms.Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems:1) a “gray zone” where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2) a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci – Stepwise Threshold Clustering (STC) – that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus) samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications. PMID

  13. A comparison of cluster and systematic sampling methods for measuring crude mortality.

    PubMed Central

    Rose, Angela M. C.; Grais, Rebecca F.; Coulombier, Denis; Ritter, Helga

    2006-01-01

    OBJECTIVE: To compare the results of two different survey sampling techniques (cluster and systematic) used to measure retrospective mortality on the same population at about the same time. METHODS: Immediately following a cluster survey to assess mortality retrospectively in a town in North Darfur, Sudan in 2005, we conducted a systematic survey on the same population and again measured mortality retrospectively. This was only possible because the geographical layout of the town, and the availability of a good previous estimate of the population size and distribution, were conducive to the systematic survey design. RESULTS: Both the cluster and the systematic survey methods gave similar results below the emergency threshold for crude mortality (0.80 versus 0.77 per 10,000/day, respectively). The results for mortality in children under 5 years old (U5MR) were different (1.16 versus 0.71 per 10,000/day), although this difference was not statistically significant. The 95% confidence intervals were wider in each case for the cluster survey, especially for the U5MR (0.15-2.18 for the cluster versus 0.09-1.33 for the systematic survey). CONCLUSION: Both methods gave similar age and sex distributions. The systematic survey, however, allowed for an estimate of the town's population size, and a smaller sample could have been used. This study was conducted in a purely operational, rather than a research context. A research study into alternative methods for measuring retrospective mortality in areas with mortality significantly above the emergency threshold is needed, and is planned for 2006. PMID:16628302

  14. THE IMPACT OF ENHANCED He AND CNONa ABUNDANCES ON GLOBULAR CLUSTER RELATIVE AGE-DATING METHODS

    SciTech Connect

    MarIn-Franch, Antonio; Aparicio, Antonio; Cassisi, Santi; Pietrinferni, Adriano E-mail: antapaj@iac.e E-mail: pietrinferni@oa-teramo.inaf.i

    2010-05-10

    The impact that unrecognized differences in the chemical patterns of Galactic globular clusters (GGCs) have on their relative age determinations is studied. The two most widely used relative age-dating methods, horizontal and vertical, together with the more recent relative MS-fitting method, were carefully analyzed on a purely theoretical basis. The BaSTI library was adopted to perform the present analysis. We find that relative ages derived using the horizontal and vertical methods are largely dependent on the initial He content and heavy element distribution. Unrecognized cluster-to-cluster chemical abundance differences can lead to an error in the derived relative ages as large as {approx}0.5 (or {approx}6 Gyr if an age of 12.8 Gyr is adopted for normalization) and even larger for some extreme cases. It is shown that the relative MS-fitting method is by far the age-dating technique for which undetected cluster-to-cluster differences in the He abundance have less impact. Present results are used in order to pose constraints on the maximum possible spread in the He and CNONa elements abundances on the basis of the estimates-taken from the literature-of the GGCs relative age dispersion obtained with the various relative age-dating techniques. Finally, it is shown that the age-metallicity relation found for young GGCs by the GC Treasury program is a real age sequence and cannot be produced by variations in the He and/or heavy element distribution.

  15. An accurate potential energy surface for the F + H2 → HF + H reaction by the coupled-cluster method

    NASA Astrophysics Data System (ADS)

    Chen, Jun; Sun, Zhigang; Zhang, Dong H.

    2015-01-01

    A three dimensional potential energy surface for the F + H2 → HF + H reaction has been computed by the spin unrestricted coupled cluster method with singles, doubles, triples, and perturbative quadruples [UCCSDT(2)Q] using the augmented correlation-consistent polarised valence quadruple zeta basis set for the fluorine atom and the correlation-consistent polarised valence quadruple zeta basis set for the hydrogen atom. All the calculations are based on the restricted open-shell Hartree-Fock orbitals, together with the frozen core approximations, and the UCCSD(T)/complete basis set (CBS) correction term was included. The global potential energy surface was calculated by fitting the sampled ab initio points without any scaling factor for the correlation energy part using a neutral network function method. Extensive dynamics calculations have been carried out on the potential energy surface. The reaction rate constants, integral cross sections, product rotational states distribution, and forward and backward scattering as a function of collision energy of the F + HD → HF + D, F + HD → DF + H, and F + H2 reaction, were calculated by the time-independent quantum dynamics scattering theory using the new surface. The satisfactory agreement with the reported experimental observations previously demonstrates the accuracy of the new potential energy surface.

  16. An accurate potential energy surface for the F + H2 → HF + H reaction by the coupled-cluster method.

    PubMed

    Chen, Jun; Sun, Zhigang; Zhang, Dong H

    2015-01-14

    A three dimensional potential energy surface for the F + H2 → HF + H reaction has been computed by the spin unrestricted coupled cluster method with singles, doubles, triples, and perturbative quadruples [UCCSDT(2)Q] using the augmented correlation-consistent polarised valence quadruple zeta basis set for the fluorine atom and the correlation-consistent polarised valence quadruple zeta basis set for the hydrogen atom. All the calculations are based on the restricted open-shell Hartree-Fock orbitals, together with the frozen core approximations, and the UCCSD(T)/complete basis set (CBS) correction term was included. The global potential energy surface was calculated by fitting the sampled ab initio points without any scaling factor for the correlation energy part using a neutral network function method. Extensive dynamics calculations have been carried out on the potential energy surface. The reaction rate constants, integral cross sections, product rotational states distribution, and forward and backward scattering as a function of collision energy of the F + HD → HF + D, F + HD → DF + H, and F + H2 reaction, were calculated by the time-independent quantum dynamics scattering theory using the new surface. The satisfactory agreement with the reported experimental observations previously demonstrates the accuracy of the new potential energy surface.

  17. Spin-orbit interactions in electronic structure quantum Monte Carlo methods

    NASA Astrophysics Data System (ADS)

    Melton, Cody A.; Zhu, Minyi; Guo, Shi; Ambrosetti, Alberto; Pederiva, Francesco; Mitas, Lubos

    2016-04-01

    We develop generalization of the fixed-phase diffusion Monte Carlo method for Hamiltonians which explicitly depends on particle spins such as for spin-orbit interactions. The method is formulated in a zero-variance manner and is similar to the treatment of nonlocal operators in commonly used static-spin calculations. Tests on atomic and molecular systems show that it is very accurate, on par with the fixed-node method. This opens electronic structure quantum Monte Carlo methods to a vast research area of quantum phenomena in which spin-related interactions play an important role.

  18. Strengths and weaknesses of weak-strong cluster problems: A detailed overview of state-of-the-art classical heuristics versus quantum approaches

    NASA Astrophysics Data System (ADS)

    Mandrà, Salvatore; Zhu, Zheng; Wang, Wenlong; Perdomo-Ortiz, Alejandro; Katzgraber, Helmut G.

    2016-08-01

    To date, a conclusive detection of quantum speedup remains elusive. Recently, a team by Google Inc. [V. S. Denchev et al., Phys. Rev. X 6, 031015 (2016), 10.1103/PhysRevX.6.031015] proposed a weak-strong cluster model tailored to have tall and narrow energy barriers separating local minima, with the aim to highlight the value of finite-range tunneling. More precisely, results from quantum Monte Carlo simulations as well as the D-Wave 2X quantum annealer scale considerably better than state-of-the-art simulated annealing simulations. Moreover, the D-Wave 2X quantum annealer is ˜108 times faster than simulated annealing on conventional computer hardware for problems with approximately 103 variables. Here, an overview of different sequential, nontailored, as well as specialized tailored algorithms on the Google instances is given. We show that the quantum speedup is limited to sequential approaches and study the typical complexity of the benchmark problems using insights from the study of spin glasses.

  19. Applying clustering approach in predictive uncertainty estimation: a case study with the UNEEC method

    NASA Astrophysics Data System (ADS)

    Dogulu, Nilay; Solomatine, Dimitri; Lal Shrestha, Durga

    2014-05-01

    Within the context of flood forecasting, assessment of predictive uncertainty has become a necessity for most of the modelling studies in operational hydrology. There are several uncertainty analysis and/or prediction methods available in the literature; however, most of them rely on normality and homoscedasticity assumptions for model residuals occurring in reproducing the observed data. This study focuses on a statistical method analyzing model residuals without having any assumptions and based on a clustering approach: Uncertainty Estimation based on local Errors and Clustering (UNEEC). The aim of this work is to provide a comprehensive evaluation of the UNEEC method's performance in view of clustering approach employed within its methodology. This is done by analyzing normality of model residuals and comparing uncertainty analysis results (for 50% and 90% confidence level) with those obtained from uniform interval and quantile regression methods. An important part of the basis by which the methods are compared is analysis of data clusters representing different hydrometeorological conditions. The validation measures used are PICP, MPI, ARIL and NUE where necessary. A new validation measure linking prediction interval to the (hydrological) model quality - weighted mean prediction interval (WMPI) - is also proposed for comparing the methods more effectively. The case study is Brue catchment, located in the South West of England. A different parametrization of the method than its previous application in Shrestha and Solomatine (2008) is used, i.e. past error values in addition to discharge and effective rainfall is considered. The results show that UNEEC's notable characteristic in its methodology, i.e. applying clustering to data of predictors upon which catchment behaviour information is encapsulated, contributes increased accuracy of the method's results for varying flow conditions. Besides, classifying data so that extreme flow events are individually

  20. Determination of the transmission coefficients for quantum structures using FDTD method.

    PubMed

    Peng, Yangyang; Wang, Xiaoying; Sui, Wenquan

    2011-12-01

    The purpose of this work is to develop a simple method to incorporate quantum effect in traditional finite-difference time-domain (FDTD) simulators. Witch could make it possible to co-simulate systems include quantum structures and traditional components. In this paper, tunneling transmission coefficient is calculated by solving time-domain Schrödinger equation with a developed FDTD technique, called FDTD-S method. To validate the feasibility of the method, a simple resonant tunneling diode (RTD) structure model has been simulated using the proposed method. The good agreement between the numerical and analytical results proves its accuracy. The effectness and accuracy of this approach makes it a potential method for analysis and design of hybrid systems includes quantum structures and traditional components. PMID:22409063

  1. Determination of the transmission coefficients for quantum structures using FDTD method.

    PubMed

    Peng, Yangyang; Wang, Xiaoying; Sui, Wenquan

    2011-12-01

    The purpose of this work is to develop a simple method to incorporate quantum effect in traditional finite-difference time-domain (FDTD) simulators. Witch could make it possible to co-simulate systems include quantum structures and traditional components. In this paper, tunneling transmission coefficient is calculated by solving time-domain Schrödinger equation with a developed FDTD technique, called FDTD-S method. To validate the feasibility of the method, a simple resonant tunneling diode (RTD) structure model has been simulated using the proposed method. The good agreement between the numerical and analytical results proves its accuracy. The effectness and accuracy of this approach makes it a potential method for analysis and design of hybrid systems includes quantum structures and traditional components.

  2. Towards spectral geometric methods for Euclidean quantum gravity

    NASA Astrophysics Data System (ADS)

    Panine, Mikhail; Kempf, Achim

    2016-04-01

    The unification of general relativity with quantum theory will also require a coming together of the two quite different mathematical languages of general relativity and quantum theory, i.e., of differential geometry and functional analysis, respectively. Of particular interest in this regard is the field of spectral geometry, which studies to which extent the shape of a Riemannian manifold is describable in terms of the spectra of differential operators defined on the manifold. Spectral geometry is hard because it is highly nonlinear, but linearized spectral geometry, i.e., the task to determine small shape changes from small spectral changes, is much more tractable and may be iterated to approximate the full problem. Here, we generalize this approach, allowing, in particular, nonequal finite numbers of shape and spectral degrees of freedom. This allows us to study how well the shape degrees of freedom are encoded in the eigenvalues. We apply this strategy numerically to a class of planar domains and find that the reconstruction of small shape changes from small spectral changes is possible if enough eigenvalues are used. While isospectral nonisometric shapes are known to exist, we find evidence that generically shaped isospectral nonisometric shapes, if existing, are exceedingly rare.

  3. AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application

    PubMed Central

    Hoinka, Jan; Berezhnoy, Alexey; Sauna, Zuben E.; Przytycka, Teresa M.

    2014-01-01

    Systematic Evolution of Ligands by EXponential Enrichment (SELEX) is a well established experimental procedure to identify aptamers - synthetic single-stranded (ribo)nucleic molecules that bind to a given molecular target. Recently, new sequencing technologies have revolutionized the SELEX protocol by allowing for deep sequencing of the selection pools after each cycle. The emergence of High Throughput SELEX (HT-SELEX) has opened the field to new computational opportunities and challenges that are yet to be addressed. To aid the analysis of the results of HT-SELEX and to advance the understanding of the selection process itself, we developed AptaCluster. This algorithm allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets. We performed HT-SELEX with Interleukin 10 receptor alpha chain (IL-10RA) as the target molecule and used AptaCluster to analyze the resulting sequences. AptaCluster allowed for the first survey of the relationships between sequences in different selection rounds and revealed previously not appreciated properties of the SELEX protocol. As the first tool of this kind, AptaCluster enables novel ways to analyze and to optimize the HT-SELEX procedure. Our AptaCluster algorithm is available as a very fast multiprocessor implementation upon request. PMID:25558474

  4. Two-Step Nucleation and Growth of InP Quantum Dots via Magic-Sized Cluster Intermediates

    SciTech Connect

    Gary, Dylan C.; Terban, Maxwell W.; Billinge, Simon J. L.; Cossairt, Brandi M.

    2015-01-30

    We report on the role of magic-sized clusters (MSCs) as key intermediates in the synthesis of indium phosphide quantum dots (InP QDs) from molecular precursors. These observations suggest that previous efforts to control nucleation and growth by tuning precursor reactivity have been undermined by formation of these kinetically persistent MSCs prior to QD formation. The thermal stability of InP MSCs is influenced by the presence of exogenous bases as well as choice of the anionic ligand set. Addition of a primary amine, a common additive in previous InP QD syntheses, to carboxylate terminated MSCs was found to bypass the formation of MSCs, allowing for homogeneous growth of InP QDs through a continuum of isolable sizes. Substitution of the carboxylate ligand set for a phosphonate ligand set increased the thermal stability of one particular InP MSC to 400°C. The structure and optical properties of the MSCs with both carboxylate and phosphonate ligand sets were studied by UV-Vis absorption spectroscopy, powder XRD analysis, and solution ³¹P{¹H} and ¹H NMR spectroscopy. Finally, the carboxylate terminated MSCs were identified as effective single source precursors (SSPs) for the synthesis of high quality InP QDs. Employing InP MSCs as SSPs for QDs effectively decouples the formation of MSCs from the subsequent second nucleation event and growth of InP QDs. The concentration dependence of this SSP reaction, as well as the shape uniformity of particles observed by TEM suggests that the stepwise growth from MSCs directly to QDs proceeds via a second nucleation event rather than an aggregative growth mechanism.

  5. Two-Step Nucleation and Growth of InP Quantum Dots via Magic-Sized Cluster Intermediates

    DOE PAGES

    Gary, Dylan C.; Terban, Maxwell W.; Billinge, Simon J. L.; Cossairt, Brandi M.

    2015-01-30

    We report on the role of magic-sized clusters (MSCs) as key intermediates in the synthesis of indium phosphide quantum dots (InP QDs) from molecular precursors. These observations suggest that previous efforts to control nucleation and growth by tuning precursor reactivity have been undermined by formation of these kinetically persistent MSCs prior to QD formation. The thermal stability of InP MSCs is influenced by the presence of exogenous bases as well as choice of the anionic ligand set. Addition of a primary amine, a common additive in previous InP QD syntheses, to carboxylate terminated MSCs was found to bypass the formationmore » of MSCs, allowing for homogeneous growth of InP QDs through a continuum of isolable sizes. Substitution of the carboxylate ligand set for a phosphonate ligand set increased the thermal stability of one particular InP MSC to 400°C. The structure and optical properties of the MSCs with both carboxylate and phosphonate ligand sets were studied by UV-Vis absorption spectroscopy, powder XRD analysis, and solution ³¹P{¹H} and ¹H NMR spectroscopy. Finally, the carboxylate terminated MSCs were identified as effective single source precursors (SSPs) for the synthesis of high quality InP QDs. Employing InP MSCs as SSPs for QDs effectively decouples the formation of MSCs from the subsequent second nucleation event and growth of InP QDs. The concentration dependence of this SSP reaction, as well as the shape uniformity of particles observed by TEM suggests that the stepwise growth from MSCs directly to QDs proceeds via a second nucleation event rather than an aggregative growth mechanism.« less

  6. a Three-Step Spatial-Temporal Clustering Method for Human Activity Pattern Analysis

    NASA Astrophysics Data System (ADS)

    Huang, W.; Li, S.; Xu, S.

    2016-06-01

    How people move in cities and what they do in various locations at different times form human activity patterns. Human activity pattern plays a key role in in urban planning, traffic forecasting, public health and safety, emergency response, friend recommendation, and so on. Therefore, scholars from different fields, such as social science, geography, transportation, physics and computer science, have made great efforts in modelling and analysing human activity patterns or human mobility patterns. One of the essential tasks in such studies is to find the locations or places where individuals stay to perform some kind of activities before further activity pattern analysis. In the era of Big Data, the emerging of social media along with wearable devices enables human activity data to be collected more easily and efficiently. Furthermore, the dimension of the accessible human activity data has been extended from two to three (space or space-time) to four dimensions (space, time and semantics). More specifically, not only a location and time that people stay and spend are collected, but also what people "say" for in a location at a time can be obtained. The characteristics of these datasets shed new light on the analysis of human mobility, where some of new methodologies should be accordingly developed to handle them. Traditional methods such as neural networks, statistics and clustering have been applied to study human activity patterns using geosocial media data. Among them, clustering methods have been widely used to analyse spatiotemporal patterns. However, to our best knowledge, few of clustering algorithms are specifically developed for handling the datasets that contain spatial, temporal and semantic aspects all together. In this work, we propose a three-step human activity clustering method based on space, time and semantics to fill this gap. One-year Twitter data, posted in Toronto, Canada, is used to test the clustering-based method. The results show that the

  7. Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

    PubMed

    Li, Hongzhi; Fajer, Mikolai; Yang, Wei

    2007-01-14

    A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.

  8. An Energy-Efficient Cluster-Based Vehicle Detection on Road Network Using Intention Numeration Method

    PubMed Central

    Devasenapathy, Deepa; Kannan, Kathiravan

    2015-01-01

    The traffic in the road network is progressively increasing at a greater extent. Good knowledge of network traffic can minimize congestions using information pertaining to road network obtained with the aid of communal callers, pavement detectors, and so on. Using these methods, low featured information is generated with respect to the user in the road network. Although the existing schemes obtain urban traffic information, they fail to calculate the energy drain rate of nodes and to locate equilibrium between the overhead and quality of the routing protocol that renders a great challenge. Thus, an energy-efficient cluster-based vehicle detection in road network using the intention numeration method (CVDRN-IN) is developed. Initially, sensor nodes that detect a vehicle are grouped into separate clusters. Further, we approximate the strength of the node drain rate for a cluster using polynomial regression function. In addition, the total node energy is estimated by taking the integral over the area. Finally, enhanced data aggregation is performed to reduce the amount of data transmission using digital signature tree. The experimental performance is evaluated with Dodgers loop sensor data set from UCI repository and the performance evaluation outperforms existing work on energy consumption, clustering efficiency, and node drain rate. PMID:25793221

  9. Adapting interrelated two-way clustering method for quantitative structure-activity relationship (QSAR) modeling of mutagenicity/non- mutagenicity of a diverse set of chemicals.

    PubMed

    Majumdar, Subhabrata; Basak, Subhash C; Grunwald, Gregory D

    2013-12-01

    Interrelated Two-way Clustering (ITC) is an unsupervised clustering method developed to divide samples into two groups in gene expression data obtained through microarrays, selecting important genes simultaneously in the process. This has been found to be a better approach than conventional clustering methods like K-means or selforganizing map for the scenarios when number of samples is much smaller than number of variables (n«p). In this paper we used the ITC approach for classification of a diverse set of 508 chemicals regarding mutagenicity. A large number of topological indices (TIs), 3-dimensional, and quantum chemical descriptors, as well as atom pairs (APs) has been used as explanatory variables. In this paper, ITC has been used only for predictor selection, after which ridge regression is employed to build the final predictive model. The proper leave-one-out (LOO) method of cross-validation in this scenario is to take as holdout each of the 508 compounds before predictor thinning and compare the predicted values with the experimental data. ITC based results obtained here are comparable to those developed earlier.

  10. Health state evaluation of shield tunnel SHM using fuzzy cluster method

    NASA Astrophysics Data System (ADS)

    Zhou, Fa; Zhang, Wei; Sun, Ke; Shi, Bin

    2015-04-01

    Shield tunnel SHM is in the path of rapid development currently while massive monitoring data processing and quantitative health grading remain a real challenge, since multiple sensors belonging to different types are employed in SHM system. This paper addressed the fuzzy cluster method based on fuzzy equivalence relationship for the health evaluation of shield tunnel SHM. The method was optimized by exporting the FSV map to automatically generate the threshold value. A new holistic health score(HHS) was proposed and its effectiveness was validated by conducting a pilot test. A case study on Nanjing Yangtze River Tunnel was presented to apply this method. Three types of indicators, namely soil pressure, pore pressure and steel strain, were used to develop the evaluation set U. The clustering results were verified by analyzing the engineering geological conditions; the applicability and validity of the proposed method was also demonstrated. Besides, the advantage of multi-factor evaluation over single-factor model was discussed by using the proposed HHS. This investigation indicated the fuzzy cluster method and HHS is capable of characterizing the fuzziness of tunnel health, and it is beneficial to clarify the tunnel health evaluation uncertainties.

  11. Threshold selection for classification of MR brain images by clustering method

    NASA Astrophysics Data System (ADS)

    Moldovanu, Simona; Obreja, Cristian; Moraru, Luminita

    2015-12-01

    Given a grey-intensity image, our method detects the optimal threshold for a suitable binarization of MR brain images. In MR brain image processing, the grey levels of pixels belonging to the object are not substantially different from the grey levels belonging to the background. Threshold optimization is an effective tool to separate objects from the background and further, in classification applications. This paper gives a detailed investigation on the selection of thresholds. Our method does not use the well-known method for binarization. Instead, we perform a simple threshold optimization which, in turn, will allow the best classification of the analyzed images into healthy and multiple sclerosis disease. The dissimilarity (or the distance between classes) has been established using the clustering method based on dendrograms. We tested our method using two classes of images: the first consists of 20 T2-weighted and 20 proton density PD-weighted scans from two healthy subjects and from two patients with multiple sclerosis. For each image and for each threshold, the number of the white pixels (or the area of white objects in binary image) has been determined. These pixel numbers represent the objects in clustering operation. The following optimum threshold values are obtained, T = 80 for PD images and T = 30 for T2w images. Each mentioned threshold separate clearly the clusters that belonging of the studied groups, healthy patient and multiple sclerosis disease.

  12. Threshold selection for classification of MR brain images by clustering method

    SciTech Connect

    Moldovanu, Simona; Obreja, Cristian; Moraru, Luminita

    2015-12-07

    Given a grey-intensity image, our method detects the optimal threshold for a suitable binarization of MR brain images. In MR brain image processing, the grey levels of pixels belonging to the object are not substantially different from the grey levels belonging to the background. Threshold optimization is an effective tool to separate objects from the background and further, in classification applications. This paper gives a detailed investigation on the selection of thresholds. Our method does not use the well-known method for binarization. Instead, we perform a simple threshold optimization which, in turn, will allow the best classification of the analyzed images into healthy and multiple sclerosis disease. The dissimilarity (or the distance between classes) has been established using the clustering method based on dendrograms. We tested our method using two classes of images: the first consists of 20 T2-weighted and 20 proton density PD-weighted scans from two healthy subjects and from two patients with multiple sclerosis. For each image and for each threshold, the number of the white pixels (or the area of white objects in binary image) has been determined. These pixel numbers represent the objects in clustering operation. The following optimum threshold values are obtained, T = 80 for PD images and T = 30 for T2w images. Each mentioned threshold separate clearly the clusters that belonging of the studied groups, healthy patient and multiple sclerosis disease.

  13. Foliated Quantum Error-Correcting Codes.

    PubMed

    Bolt, A; Duclos-Cianci, G; Poulin, D; Stace, T M

    2016-08-12

    We show how to construct a large class of quantum error-correcting codes, known as Calderbank-Steane-Shor codes, from highly entangled cluster states. This becomes a primitive in a protocol that foliates a series of such cluster states into a much larger cluster state, implementing foliated quantum error correction. We exemplify this construction with several familiar quantum error-correction codes and propose a generic method for decoding foliated codes. We numerically evaluate the error-correction performance of a family of finite-rate Calderbank-Steane-Shor codes known as turbo codes, finding that they perform well over moderate depth foliations. Foliated codes have applications for quantum repeaters and fault-tolerant measurement-based quantum computation. PMID:27563942

  14. Foliated Quantum Error-Correcting Codes

    NASA Astrophysics Data System (ADS)

    Bolt, A.; Duclos-Cianci, G.; Poulin, D.; Stace, T. M.

    2016-08-01

    We show how to construct a large class of quantum error-correcting codes, known as Calderbank-Steane-Shor codes, from highly entangled cluster states. This becomes a primitive in a protocol that foliates a series of such cluster states into a much larger cluster state, implementing foliated quantum error correction. We exemplify this construction with several familiar quantum error-correction codes and propose a generic method for decoding foliated codes. We numerically evaluate the error-correction performance of a family of finite-rate Calderbank-Steane-Shor codes known as turbo codes, finding that they perform well over moderate depth foliations. Foliated codes have applications for quantum repeaters and fault-tolerant measurement-based quantum computation.

  15. Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors

    SciTech Connect

    Kamiya, Muneaki; Hirata, So; Valiev, Marat

    2008-02-19

    Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly-interacting molecular clusters [Hirata et al. Mol. Phys. 103, 2255 (2005)] have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine–water clusters with an excellent result for an initial performance assessment. Our original method included up to two- or three-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the dipole–dipole approximation. In this work, the dipole moments are replaced by atom-centered point charges determined so that they reproduce the electrostatic potentials of the cluster subunits as closely as possible and also self-consistently with one another in the cluster environment. They have been shown to lead to dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits like zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSE) known to plague direct evaluation of weak interactions have been eliminated by com-bining the Valiron–Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method in an economical fashion (quadratic scaling n2 with respect to the number of subunits n when n is small and linear scaling when n is large). A new variant of VMFC has also been proposed in which three-body and all higher-order Coulomb effects on BSSE are estimated approximately. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results of conventional electron correlation calculations within 0.1 kcal/mol. The proposed method is significantly more accurate and also efficient than conventional correlation methods uncorrected of BSSE.

  16. Validation tests of an improved kernel density estimation method for identifying disease clusters

    SciTech Connect

    Cai, Qiang; Rushton, Gerald; Bhaduri, Budhendra L

    2011-01-01

    The spatial filter method, which belongs to the class of kernel density estimation methods, has been used to make morbidity and mortality maps in several recent studies. We propose improvements in the method that include a spatial basis of support designed to give a constant standard error for the standardized mortality/morbidity rate; a stair-case weight method for weighting observations to reduce estimation bias; and a method for selecting parameters to control three measures of performance of the method: sensitivity, specificity and false discovery rate. We test the performance of the method using Monte Carlo simulations of hypothetical disease clusters over a test area of four counties in Iowa. The simulations include different types of spatial disease patterns and high resolution population distribution data. Results confirm that the new features of the spatial filter method do substantially improve its performance in realistic situations comparable to those where the method is likely to be used.

  17. Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

    PubMed

    Dreuw, Andreas

    2006-11-13

    With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.

  18. Time-Sliced Thawed Gaussian Propagation Method for Simulations of Quantum Dynamics.

    PubMed

    Kong, Xiangmeng; Markmann, Andreas; Batista, Victor S

    2016-05-19

    A rigorous method for simulations of quantum dynamics is introduced on the basis of concatenation of semiclassical thawed Gaussian propagation steps. The time-evolving state is represented as a linear superposition of closely overlapping Gaussians that evolve in time according to their characteristic equations of motion, integrated by fourth-order Runge-Kutta or velocity Verlet. The expansion coefficients of the initial superposition are updated after each semiclassical propagation period by implementing the Husimi Transform analytically in the basis of closely overlapping Gaussians. An advantage of the resulting time-sliced thawed Gaussian (TSTG) method is that it allows for full-quantum dynamics propagation without any kind of multidimensional integral calculation, or inversion of overlap matrices. The accuracy of the TSTG method is demonstrated as applied to simulations of quantum tunneling, showing quantitative agreement with benchmark calculations based on the split-operator Fourier transform method. PMID:26845486

  19. Research on Quantum Authentication Methods for the Secure Access Control Among Three Elements of Cloud Computing

    NASA Astrophysics Data System (ADS)

    Dong, Yumin; Xiao, Shufen; Ma, Hongyang; Chen, Libo

    2016-08-01

    Cloud computing and big data have become the developing engine of current information technology (IT) as a result of the rapid development of IT. However, security protection has become increasingly important for cloud computing and big data, and has become a problem that must be solved to develop cloud computing. The theft of identity authentication information remains a serious threat to the security of cloud computing. In this process, attackers intrude into cloud computing services through identity authentication information, thereby threatening the security of data from multiple perspectives. Therefore, this study proposes a model for cloud computing protection and management based on quantum authentication, introduces the principle of quantum authentication, and deduces the quantum authentication process. In theory, quantum authentication technology can be applied in cloud computing for security protection. This technology cannot be cloned; thus, it is more secure and reliable than classical methods.

  20. PSII manganese cluster: protonation of W2, O5, O4 and His337 in the S1 state explored by combined quantum chemical and electrostatic energy computations.

    PubMed

    Robertazzi, Arturo; Galstyan, Artur; Knapp, Ernst Walter

    2014-08-01

    Photosystem II (PSII) is a membrane-bound protein complex that oxidizes water to produce energized protons, which are used to built up a proton gradient across the thylakoidal membrane in the leafs of plants. This light-driven reaction is catalyzed by withdrawing electrons from the Mn₄CaO₅-cluster (Mn-cluster) in four discrete oxidation steps [S₁-(S₄/S₀)] characterized in the Kok-cycle. In order to understand in detail the proton release events and the subsequent translocation of such energized protons, the protonation pattern of the Mn-cluster need to be elucidated. The new high-resolution PSII crystal structure from Umena, Kawakami, Shen, and Kamiya is an excellent basis to make progress in solving this problem. Following our previous work on oxidation and protonation states of the Mn-cluster, in this work, quantum chemical/electrostatic calculations were performed in order to estimate the pKa of different protons of relevant groups and atoms of the Mn-cluster such as W2, O4, O5 and His337. In broad agreement with previous experimental and theoretical work, our data suggest that W2 and His337 are likely to be in hydroxyl and neutral form, respectively, O5 and O4 to be unprotonated. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy. PMID:24721390

  1. A Numerical Method to Study Highly Correlated Nanostructures: The Logarithmic Discretization Embedded Cluster Approximation

    NASA Astrophysics Data System (ADS)

    Anda, E.; Chiappe, G.; Busser, C.; Davidovich, M.; Martins, G.; H-Meisner, F.; Dagotto, E.

    2008-03-01

    A numerical algorithm to study transport properties of highly correlated local structures is proposed. The method, dubbed the Logarithmic Discretization Embedded Cluster Approximation (LDECA), consists of diagonalizing a finite cluster containing the many-body terms of the Hamiltonian and embedding it into the rest of the system, combined with Wilson's ideas of a logarithmic discretization of the representation of the Hamiltonian. LDECA's rapid convergence eliminates finite-size effects commonly present in the embedding cluster approximation (ECA) method. The physics associated with both one embedded dot and a string of two dots side-coupled to leads is discussed. In the former case, our results accurately agree with Bethe ansatz (BA) data, while in the latter, the results are framed in the conceptual background of a two-stage Kondo problem. A diagrammatic expansion provides the theoretical foundation for the method. It is argued that LDECA allows for the study of complex problems that are beyond the reach of currently available numerical methods.

  2. The IMACS Cluster Building Survey. I. Description of the Survey and Analysis Methods

    NASA Technical Reports Server (NTRS)

    Oemler Jr., Augustus; Dressler, Alan; Gladders, Michael G.; Rigby, Jane R.; Bai, Lei; Kelson, Daniel; Villanueva, Edward; Fritz, Jacopo; Rieke, George; Poggianti, Bianca M.; Vulcani, Benedetta

    2013-01-01

    The IMACS Cluster Building Survey uses the wide field spectroscopic capabilities of the IMACS spectrograph on the 6.5 m Baade Telescope to survey the large-scale environment surrounding rich intermediate-redshift clusters of galaxies. The goal is to understand the processes which may be transforming star-forming field galaxies into quiescent cluster members as groups and individual galaxies fall into the cluster from the surrounding supercluster. This first paper describes the survey: the data taking and reduction methods. We provide new calibrations of star formation rates (SFRs) derived from optical and infrared spectroscopy and photometry. We demonstrate that there is a tight relation between the observed SFR per unit B luminosity, and the ratio of the extinctions of the stellar continuum and the optical emission lines.With this, we can obtain accurate extinction-corrected colors of galaxies. Using these colors as well as other spectral measures, we determine new criteria for the existence of ongoing and recent starbursts in galaxies.

  3. THE IMACS CLUSTER BUILDING SURVEY. I. DESCRIPTION OF THE SURVEY AND ANALYSIS METHODS

    SciTech Connect

    Oemler, Augustus Jr.; Dressler, Alan; Kelson, Daniel; Villanueva, Edward; Gladders, Michael G.; Rigby, Jane R.; Bai Lei; Fritz, Jacopo; Rieke, George; Poggianti, Bianca M.; Vulcani, Benedetta

    2013-06-10

    The IMACS Cluster Building Survey uses the wide field spectroscopic capabilities of the IMACS spectrograph on the 6.5 m Baade Telescope to survey the large-scale environment surrounding rich intermediate-redshift clusters of galaxies. The goal is to understand the processes which may be transforming star-forming field galaxies into quiescent cluster members as groups and individual galaxies fall into the cluster from the surrounding supercluster. This first paper describes the survey: the data taking and reduction methods. We provide new calibrations of star formation rates (SFRs) derived from optical and infrared spectroscopy and photometry. We demonstrate that there is a tight relation between the observed SFR per unit B luminosity, and the ratio of the extinctions of the stellar continuum and the optical emission lines. With this, we can obtain accurate extinction-corrected colors of galaxies. Using these colors as well as other spectral measures, we determine new criteria for the existence of ongoing and recent starbursts in galaxies.

  4. Linear-response theory for Mukherjee's multireference coupled-cluster method: Excitation energies

    NASA Astrophysics Data System (ADS)

    Jagau, Thomas-C.; Gauss, Jürgen

    2012-07-01

    The recently presented linear-response function for Mukherjee's multireference coupled-cluster method (Mk-MRCC) [T.-C. Jagau and J. Gauss, J. Chem. Phys. 137, 044115 (2012)], 10.1063/1.4734308 is employed to determine vertical excitation energies within the singles and doubles approximation (Mk-MRCCSD-LR) for ozone as well as for o-benzyne, m-benzyne, and p-benzyne, which display increasing multireference character in their ground states. In order to assess the impact of a multireference ground-state wavefunction on excitation energies, we compare all our results to those obtained at the single-reference coupled-cluster level of theory within the singles and doubles as well as within the singles, doubles, and triples approximation. Special attention is paid to the artificial splitting of certain excited states which arises from the redundancy intrinsic to Mk-MRCC theory and hinders the straightforward application of the Mk-MRCC-LR method.

  5. Geometry-dependent lifetime of Interatomic coulombic decay using equation-of-motion coupled cluster method

    SciTech Connect

    Ghosh, Aryya; Vaval, Nayana

    2014-12-21

    Electronically excited atom or molecule in an environment can relax via transferring its excess energy to the neighboring atoms or molecules. The process is called Interatomic or Intermolecular coulombic decay (ICD). The ICD is a fast decay process in environment. Generally, the ICD mechanism predominates in weakly bound clusters. In this paper, we have applied the complex absorbing potential approach/equation-of-motion coupled cluster (CAP/EOMCCSD) method which is a combination of CAP and EOMCC approach to study the lifetime of ICD at various geometries of the molecules. We have applied this method to calculate the lifetime of ICD in Ne-X; X = Ne, Mg, Ar, systems. We compare our results with other theoretical and experimental results available in literature.

  6. Segmentation of bone pixels from EROI Image using clustering method for bone age assessment

    NASA Astrophysics Data System (ADS)

    Bakthula, Rajitha; Agarwal, Suneeta

    2016-03-01

    The bone age of a human can be identified using carpal and epiphysis bones ossification, which is limited to teen age. The accurate age estimation depends on best separation of bone pixels and soft tissue pixels in the ROI image. The traditional approaches like canny, sobel, clustering, region growing and watershed can be applied, but these methods requires proper pre-processing and accurate initial seed point estimation to provide accurate results. Therefore this paper proposes new approach to segment the bone from soft tissue and background pixels. First pixels are enhanced using BPE and the edges are identified by HIPI. Later a K-Means clustering is applied for segmentation. The performance of the proposed approach has been evaluated and compared with the existing methods.

  7. A new artefacts resistant method for automatic lineament extraction using Multi-Hillshade Hierarchic Clustering (MHHC)

    NASA Astrophysics Data System (ADS)

    Šilhavý, Jakub; Minár, Jozef; Mentlík, Pavel; Sládek, Ján

    2016-07-01

    This paper presents a new method of automatic lineament extraction which includes the removal of the 'artefacts effect' which is associated with the process of raster based analysis. The core of the proposed Multi-Hillshade Hierarchic Clustering (MHHC) method incorporates a set of variously illuminated and rotated hillshades in combination with hierarchic clustering of derived 'protolineaments'. The algorithm also includes classification into positive and negative lineaments. MHHC was tested in two different territories in Bohemian Forest and Central Western Carpathians. The original vector-based algorithm was developed for comparison of the individual lineaments proximity. Its use confirms the compatibility of manual and automatic extraction and their similar relationships to structural data in the study areas.

  8. Template method for nano-order positioning and dense packing of quantum dots for optoelectronic device application

    NASA Astrophysics Data System (ADS)

    Mukai, Kohki; Hirota, Akinobu; Shimizu, Yuta; Nakashima, Seisuke

    2015-04-01

    In this paper, we present recent progress of our researches on positioning of quantum dot in the field of optoelectronics. The first research is aimed at quantum information device application. As a technology for production of quantum devices, we developed the method for positioning of a single colloidal quantum dot. Oxide lines on a Si substrate drawn by a scanning probe microscope were used as a negative etching mask with controlling their cross section in order to create a nanohole for trapping of a single quantum dot. The other research is aimed at solar cell application. It has been predicted that quantum-dot superlattice solar cell will achieve photoelectric conversion efficiency of more than 70%. After the sedimentation of the colloidal quantum dots into the pyramidal holes processed by anisotropic wet etching on a Si substrate, we observed characteristic photoluminescence from the quantum-dot sheet.

  9. 2D Quantum Simulation of MOSFET Using the Non Equilibrium Green's Function Method

    NASA Technical Reports Server (NTRS)

    Svizhenko, Alexel; Anantram, M. P.; Govindan, T. R.; Yan, Jerry (Technical Monitor)

    2000-01-01

    The objectives this viewgraph presentation summarizes include: (1) the development of a quantum mechanical simulator for ultra short channel MOSFET simulation, including theory, physical approximations, and computer code; (2) explore physics that is not accessible by semiclassical methods; (3) benchmarking of semiclassical and classical methods; and (4) study other two-dimensional devices and molecular structure, from discretized Hamiltonian to tight-binding Hamiltonian.

  10. Quantum mechanical method of fragment's angular and energy distribution calculation for binary and ternary fission

    SciTech Connect

    Kadmensky, S. G. Titova, L. V.; Pen'kov, N. V.

    2006-08-15

    In the framework of quantum-mechanical fission theory, the method of calculation for partial fission width amplitudes and asymptotic behavior of the fissile nucleus wave function with strong channel coupling taken into account has been suggested. The method allows one to solve the calculation problem of angular and energy distribution countation for binary and ternary fission.

  11. Molecular orbital calculations of octahedral molybdenum cluster complexes with the DV-X{alpha} method

    SciTech Connect

    Imoto, Hideo; Saito, Taro; Adachi, Hirohiko

    1995-04-26

    Discrete variational-{Chi}{alpha} molecular orbital methods were applied to octahedral cluster complexes, [Mo{sub 6}X{sub 8}-(PH{sub 3}){sub 6}](X = S and Se). This structure is of interest due to its role in superconductivity of Chevrel plates. Level energies are discussed and factors contributing to their separations are categorized. Agreement with empirical XPS data is excellent.

  12. Various methods of optimizing control pulses for quantum systems with decoherence

    NASA Astrophysics Data System (ADS)

    Pawela, Łukasz; Sadowski, Przemysław

    2016-05-01

    We design control setting that allows the implementation of an approximation of an unitary operation of a quantum system under decoherence using various quantum system layouts and numerical algorithms. We focus our attention on the possibility of adding ancillary qubits which help to achieve a desired quantum map on the initial system. Furthermore, we use three methods of optimizing the control pulses: genetic optimization, approximate evolution method and approximate gradient method. To model the noise in the system we use the Lindblad equation. We obtain results showing that applying the control pulses to the ancilla allows one to successfully implement unitary operation on a target system in the presence of noise, which is not possible which control field applied to the system qubits.

  13. Torsional diffusion Monte Carlo: A method for quantum simulations of proteins

    NASA Astrophysics Data System (ADS)

    Clary, David C.

    2001-06-01

    The quantum diffusion Monte Carlo (DMC) method is extended to the treatment of coupled torsional motions in proteins. A general algorithm and computer program has been developed by interfacing this torsional-DMC method with all-atom force-fields for proteins. The method gives the zero-point energy and atomic coordinates averaged over the coupled torsional motions in the quantum ground state of the protein. Application of the new algorithm is made to the proteins gelsolin (356 atoms and 142 torsions) and gp41-HIV (1101 atoms and 452 torsions). The results indicate that quantum-dynamical effects are important for the energies and geometries of typical proteins such as these.

  14. Method and apparatus for detecting and/or imaging clusters of small scattering centers in the body

    DOEpatents

    Perez-Mendez, V.; Sommer, F.G.

    1982-07-13

    An ultrasonic method and apparatus are provided for detecting and imaging clusters of small scattering centers in the breast wherein periodic pulses are applied to an ultrasound emitting transducer and projected into the body, thereafter being received by at least one receiving transducer positioned to receive scattering from the scattering center clusters. The signals are processed to provide an image showing cluster extent and location. 6 figs.

  15. Method and apparatus for detecting and/or imaging clusters of small scattering centers in the body

    DOEpatents

    Perez-Mendez, Victor; Sommer, Frank G.

    1982-01-01

    An ultrasonic method and apparatus are provided for detecting and imaging clusters of small scattering centers in the breast wherein periodic pulses are applied to an ultrasound emitting transducer and projected into the body, thereafter being received by at least one receiving transducer positioned to receive scattering from the scattering center clusters. The signals are processed to provide an image showing cluster extent and location.

  16. Comparison of the completely renormalized equation-of-motion coupled-cluster and Quantum Monte Carlo results for the low-lying electronic states of methylene

    NASA Astrophysics Data System (ADS)

    Gour, Jeffrey R.; Piecuch, Piotr; Włoch, Marta

    2010-10-01

    The left-eigenstate completely renormalized (CR) equation-of-motion (EOM) coupled-cluster (CC) method with singles, doubles, and non-iterative triples, abbreviated as CR-EOMCC(2,3) [M. Włoch et al., Mol. Phys. 104, 2149 (2006); P. Piecuch et al., Int. J. Quantum Chem. 109, 3268 (2009)], and the companion ground-state CR-CC(2,3) methodology [P. Piecuch and M. Włoch, J. Chem. Phys. 123, 224105 (2005); P. Piecuch et al., Chem. Phys. Lett. 418, 467 (2006)] are used to determine the total electronic and adiabatic excitation energies corresponding to the ground and lowest three excited states of methylene. The emphasis is on comparing the CR-CC(2,3)/CR-EOMCC(2,3) results obtained with the large correlation-consistent basis sets of the aug-cc-pCV xZ (x = T, Q, 5) quality and the corresponding complete basis set (CBS) limits with the recently published variational and diffusion Quantum Monte Carlo (QMC) data [P. Zimmerman et al., J. Chem. Phys. 131, 124103 (2009)]. It is demonstrated that the CBS CR-CC(2,3)/CR-EOMCC(2,3) results are in very good agreement with the best QMC, i.e. diffusion MC (DMC) data, with errors in the total and adiabatic excitation energies of all calculated states on the order of a few millihartree and less than 0.1 eV, respectively, even for the challenging, strongly multi-reference C 1 A 1 state for which the basic EOMCC approach with singles and doubles completely fails. The agreement between the CBS CR-CC(2,3)/CR-EOMCC(2,3) and variational MC (VMC) results for the total energies is not as good as in the DMC case, but the excitation energies resulting from the CBS CR-CC(2,3)/CR-EOMCC(2,3) and VMC calculations agree very well.

  17. Semiclassical modeling of quantum-mechanical multiparticle systems using parallel particle-in-cell methods

    NASA Astrophysics Data System (ADS)

    Dauger, Dean Edward

    2001-08-01

    We are successful in building a code that models many particle dynamic quantum systems by combining a semiclassical approximation of Feynman path integrals with parallel computing techniques (particle-in-cell) and numerical methods developed for simulating plasmas, establishing this approach as a viable technique for multiparticle time-dependent quantum mechanics. Run on high-performance parallel computers, this code applies semiclassical methods to simulate the time evolution of wavefunctions of many particles. We describe the analytical derivation and computational implementation of these techniques in detail. We present a study to thoroughly demonstrate the code's fidelity to quantum mechanics, resulting in innovative visualization and analysis techniques. We introduce and exhibit a method to address fermion particle statistics. We present studies of two quantum-mechanical problems: a two-electron, one- dimensional atom, resulting in high-quality extractions of one- and two-electron eigenstates, and electrostatic quasi-modes due to quantum effects in a hot electron plasma, relevant for predictions about stellar evolution. We supply discussions of alternative derivations, alternative implementations of the derivations, and an exploration of their consequences. Source code is shown throughout this dissertation. Finally, we present an extensive discussion of applications and extrapolations of this work, with suggestions for future direction.

  18. [Calculation method of absolute quantum yields in photocatalytic slurry reactor based on cylindrical light].

    PubMed

    Shen, Xun-wei; Yuan, Chun-wei

    2005-01-01

    Heterogeneous photocatalysis in slurry reactors have the particular characteristic that the catalyst particles not only absorb but also scatter photons so the radiation scattering can not be neglected. However, it is very difficult in mathematics to obtain the rigorous solution of the radiative transfer equation. Consequently present methods, in which the apparent quantum yields can be calculated by employing the incident radiation intensity, always underestimate quantum yields calculations. In this paper, a method is developed to produce absolute values of photocatalytic quantum yields in slurry reactor based on cylindrical UV light source. In a typical laboratory reactor (diameter equal to 5.6 cm and length equal to 10 cm) the values for the photocatalytic degradation of phenol are reported under precisely defined conditions. The true value of the local volumetric rate of photon absorption (LVRPA) can be obtained. It was shown that apparent quantum yields differ from true quantum yields 7.08% and that for the same geometric arrangement, vanishing fraction accounts for 1.1% of the incident radiation. The method can be used to compare reactivity of different catalysts or, for a given catalyst, reactivity with different model compounds and as a principle to design a reactor.

  19. NMR quantum computing: applying theoretical methods to designing enhanced systems.

    PubMed

    Mawhinney, Robert C; Schreckenbach, Georg

    2004-10-01

    Density functional theory results for chemical shifts and spin-spin coupling constants are presented for compounds currently used in NMR quantum computing experiments. Specific design criteria were examined and numerical guidelines were assessed. Using a field strength of 7.0 T, protons require a coupling constant of 4 Hz with a chemical shift separation of 0.3 ppm, whereas carbon needs a coupling constant of 25 Hz for a chemical shift difference of 10 ppm, based on the minimal coupling approximation. Using these guidelines, it was determined that 2,3-dibromothiophene is limited to only two qubits; the three qubit system bromotrifluoroethene could be expanded to five qubits and the three qubit system 2,3-dibromopropanoic acid could also be used as a six qubit system. An examination of substituent effects showed that judiciously choosing specific groups could increase the number of available qubits by removing rotational degeneracies in addition to introducing specific conformational preferences that could increase (or decrease) the magnitude of the couplings. The introduction of one site of unsaturation can lead to a marked improvement in spectroscopic properties, even increasing the number of active nuclei.

  20. Nanothermodynamics of large iron clusters by means of a flat histogram Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Basire, M.; Soudan, J.-M.; Angelié, C.

    2014-09-01

    The thermodynamics of iron clusters of various sizes, from 76 to 2452 atoms, typical of the catalyst particles used for carbon nanotubes growth, has been explored by a flat histogram Monte Carlo (MC) algorithm (called the σ-mapping), developed by Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. This method provides the classical density of states, gp(Ep) in the configurational space, in terms of the potential energy of the system, with good and well controlled convergence properties, particularly in the melting phase transition zone which is of interest in this work. To describe the system, an iron potential has been implemented, called "corrected EAM" (cEAM), which approximates the MEAM potential of Lee et al. [Phys. Rev. B 64, 184102 (2001)] with an accuracy better than 3 meV/at, and a five times larger computational speed. The main simplification concerns the angular dependence of the potential, with a small impact on accuracy, while the screening coefficients Sij are exactly computed with a fast algorithm. With this potential, ergodic explorations of the clusters can be performed efficiently in a reasonable computing time, at least in the upper half of the solid zone and above. Problems of ergodicity exist in the lower half of the solid zone but routes to overcome them are discussed. The solid-liquid (melting) phase transition temperature Tm is plotted in terms of the cluster atom number Nat. The standard N_{at}^{-1/3} linear dependence (Pawlow law) is observed for Nat >300, allowing an extrapolation up to the bulk metal at 1940 ±50 K. For Nat <150, a strong divergence is observed compared to the Pawlow law. The melting transition, which begins at the surface, is stated by a Lindemann-Berry index and an atomic density analysis. Several new features are obtained for the thermodynamics of cEAM clusters, compared to the Rydberg pair potential clusters studied in Paper I.

  1. Renyi entanglement entropy of interacting fermions calculated using the continuous-time quantum Monte Carlo method.

    PubMed

    Wang, Lei; Troyer, Matthias

    2014-09-12

    We present a new algorithm for calculating the Renyi entanglement entropy of interacting fermions using the continuous-time quantum Monte Carlo method. The algorithm only samples the interaction correction of the entanglement entropy, which by design ensures the efficient calculation of weakly interacting systems. Combined with Monte Carlo reweighting, the algorithm also performs well for systems with strong interactions. We demonstrate the potential of this method by studying the quantum entanglement signatures of the charge-density-wave transition of interacting fermions on a square lattice.

  2. Calculating work in adiabatic two-level quantum Markovian master equations: a characteristic function method.

    PubMed

    Liu, Fei

    2014-09-01

    We present a characteristic function method to calculate the probability density functions of the inclusive work in adiabatic two-level quantum Markovian master equations. These systems are steered by some slowly varying parameters and the dissipations may depend on time. Our theory is based on the interpretation of the quantum jump for the master equations. In addition to the calculation, we also find that the fluctuation properties of the work can be described by the symmetry of the characteristic functions, which is exactly the same as in the case of isolated systems. A periodically driven two-level model is used to demonstrate the method. PMID:25314409

  3. Cluster analysis of European Y-chromosomal STR haplotypes using the discrete Laplace method.

    PubMed

    Andersen, Mikkel Meyer; Eriksen, Poul Svante; Morling, Niels

    2014-07-01

    The European Y-chromosomal short tandem repeat (STR) haplotype distribution has previously been analysed in various ways. Here, we introduce a new way of analysing population substructure using a new method based on clustering within the discrete Laplace exponential family that models the probability distribution of the Y-STR haplotypes. Creating a consistent statistical model of the haplotypes enables us to perform a wide range of analyses. Previously, haplotype frequency estimation using the discrete Laplace method has been validated. In this paper we investigate how the discrete Laplace method can be used for cluster analysis to further validate the discrete Laplace method. A very important practical fact is that the calculations can be performed on a normal computer. We identified two sub-clusters of the Eastern and Western European Y-STR haplotypes similar to results of previous studies. We also compared pairwise distances (between geographically separated samples) with those obtained using the AMOVA method and found good agreement. Further analyses that are impossible with AMOVA were made using the discrete Laplace method: analysis of the homogeneity in two different ways and calculating marginal STR distributions. We found that the Y-STR haplotypes from e.g. Finland were relatively homogeneous as opposed to the relatively heterogeneous Y-STR haplotypes from e.g. Lublin, Eastern Poland and Berlin, Germany. We demonstrated that the observed distributions of alleles at each locus were similar to the expected ones. We also compared pairwise distances between geographically separated samples from Africa with those obtained using the AMOVA method and found good agreement.

  4. A study of several CAD methods for classification of clustered microcalcifications

    NASA Astrophysics Data System (ADS)

    Wei, Liyang; Yang, Yongyi; Nishikawa, Robert M.; Jiang, Yulei

    2005-04-01

    In this paper we investigate several state-of-the-art machine-learning methods for automated classification of clustered microcalcifications (MCs), aimed to assisting radiologists for more accurate diagnosis of breast cancer in a computer-aided diagnosis (CADx) scheme. The methods we consider include: support vector machine (SVM), kernel Fisher discriminant (KFD), and committee machines (ensemble averaging and AdaBoost), most of which have been developed recently in statistical learning theory. We formulate differentiation of malignant from benign MCs as a supervised learning problem, and apply these learning methods to develop the classification algorithms. As input, these methods use image features automatically extracted from clustered MCs. We test these methods using a database of 697 clinical mammograms from 386 cases, which include a wide spectrum of difficult-to-classify cases. We use receiver operating characteristic (ROC) analysis to evaluate and compare the classification performance by the different methods. In addition, we also investigate how to combine information from multiple-view mammograms of the same case so that the best decision can be made by a classifier. In our experiments, the kernel-based methods (i.e., SVM, KFD) yield the best performance, significantly outperforming a well-established CADx approach based on neural network learning.

  5. A Novel Method for Analyzing and Interpreting GCM Results Using Clustered Climate Regimes

    NASA Astrophysics Data System (ADS)

    Hoffman, F. M.; Hargrove, W. W.; Erickson, D. J.; Oglesby, R. J.

    2003-12-01

    A high-performance parallel clustering algorithm has been developed for analyzing and comparing climate model results and long time series climate measurements. Designed to identify biases and detect trends in disparate climate change data sets, this tool combines and simplifies large temporally-varying data sets from atmospheric measurements to multi-century climate model output. Clustering is a statistical procedure which provides an objective method for grouping multivariate conditions into a set of states or regimes within a given level of statistical tolerance. The groups or clusters--statistically defined across space and through time--possess centroids which represent the synoptic conditions of observations or model results contained in each state no matter when or where they occurred. The clustering technique was applied to five business-as-usual (BAU) scenarios from the Parallel Climate Model (PCM). Three fields of significance (surface temperature, precipitation, and soil moisture) were clustered from 2000 through 2098. Our analysis shows an increase in spatial area occupied by the cluster or climate regime which typifies desert regions (i.e., an increase in desertification) and a decrease in the spatial area occupied by the climate regime typifying winter-time high latitude perma-frost regions. The same analysis subsequently applied to the ensemble as a whole demonstrates the consistency and variability of trends from each ensemble member. The patterns of cluster changes can be used to show predicted variability in climate on global and continental scales. Novel three-dimensional phase space representations of these climate regimes show the portion of this phase space occupied by the land surface at all points in space and time. Any single spot on the globe will exist in one of these climate regimes at any single point in time, and by incrementing time, that same spot will trace out a trajectory or orbit among these climate regimes in phase space. When a

  6. Blinking correlation in nanocrystal quantum dots probed with novel laser scanning confocal microscopy methods

    NASA Astrophysics Data System (ADS)

    Hefti, Ryan Alf

    Semiconductor quantum dots have a vast array of applications: as fluorescent labels in biological systems, as physical or chemical sensors, as components in photovoltaic technology, and in display devices. An attribute of nearly every quantum dot is its blinking, or fluorescence intermittency, which tends to be a disadvantage in most applications. Despite the fact that blinking has been a nearly universal phenomenon among all types of fluorescent constructs, it is more prevalent in quantum dots than in traditional fluorophores. Furthermore, no unanimously accepted model of quantum dot blinking yet exists. The work encompassed by this dissertation began with an in-depth study of molecular motor protein dynamics in a variety of environments using two specially developed techniques, both of which feature applicability to live cell systems. Parked-beam confocal microscopy was utilized to increase temporal resolution of molecular motor motion dynamics by an order of magnitude over other popular methods. The second technique, fast-scanning confocal microscopy (FSCM), was used for long range observation of motor proteins. While using FSCM on motor protein assays, we discovered an unusual phenomenon. Single quantum dots seemingly communicated with neighboring quantum dots, indicated by a distinct correlation in their blinking patterns. In order to explain this novel correlation phenomenon, the majority of blinking models developed thus far would suggest a dipole-dipole interaction or a Coulomb interaction between singly charged quantum dots. However, our results indicate that the interaction energy is higher than supported by current models, thereby prompting a renewed examination. We propose that the blinking correlation we observed is due to a Coulomb interaction on the order of 3-4 elementary charges per quantum dot and that multiple charging of individual quantum dots may be required to plunge them into a non-emissive state. As a result of charging, charge carriers are

  7. Heats of formation of phosphorus compounds determined by current methods of computational quantum chemistry

    NASA Astrophysics Data System (ADS)

    Haworth, Naomi L.; Bacskay, George B.

    2002-12-01

    The heats of formation of a range of phosphorus containing molecules (P2, P4, PH, PH2, PH3, P2H2, P2H4, PO, PO2, PO3, P2O, P2O2, HPO, HPOH, H2POH, H3PO, HOPO, and HOPO2) have been determined by high level quantum chemical calculations. The equilibrium geometries and vibrational frequencies were computed via density functional theory, utilizing the B3LYP/6-31G(2df,p) functional and basis set. Atomization energies were obtained by the application of ab initio coupled cluster theory with single and double excitations from (spin)-restricted Hartree-Fock reference states with perturbative correction for triples [CCSD(T)], in conjunction with cc-pVnZ basis sets (n=T, Q, 5) which include an extra d function on the phosphorus atoms and diffuse functions on the oxygens, as recommended by Bauschlicher [J. Phys. Chem. A 103, 11126 (1999)]. The valence correlated atomization energies were extrapolated to the complete basis limit and corrected for core-valence (CV) correlation and scalar relativistic effects, as well as for basis set superposition errors (BSSE) in the CV terms. This methodology is effectively the same as the one adopted by Bauschlicher in his study of PO, PO2, PO3, HPO, HOPO, and HOPO2. Consequently, for these molecules the results of this work closely match Bauschlicher's computed values. The theoretical heats of formation, whose accuracy is estimated as ranging from ±1.0 to ±2.5 kcal mol-1, are consistent with the available experimental data. The current set of theoretical data represent a convenient benchmark, against which the results of other computational procedures, such as G3, G3X, and G3X2, can be compared. Despite the fact that G3X2 [which is an approximation to the quadratic CI procedure QCISD(T,Full)/G3Xlarge] is a formally higher level theory than G3X, the heats of formation obtained by these two methods are found to be of comparable accuracy. Both reproduce the benchmark heats of formation on the average to within ±2 kcal mol-1 and, for these

  8. A Novel Clustering Method Curbing the Number of States in Reinforcement Learning

    NASA Astrophysics Data System (ADS)

    Kotani, Naoki; Nunobiki, Masayuki; Taniguchi, Kenji

    We propose an efficient state-space construction method for a reinforcement learning. Our method controls the number of categories with improving the clustering method of Fuzzy ART which is an autonomous state-space construction method. The proposed method represents weight vector as the mean value of input vectors in order to curb the number of new categories and eliminates categories whose state values are low to curb the total number of categories. As the state value is updated, the size of category becomes small to learn policy strictly. We verified the effectiveness of the proposed method with simulations of a reaching problem for a two-link robot arm. We confirmed that the number of categories was reduced and the agent achieved the complex task quickly.

  9. Pump and Probe Spectroscopy of CH_3F-({ortho}-H_2){n} Clusters in Solid Parahydrogen by Using Two Cw-Ir Quantum Cascade Lasers

    NASA Astrophysics Data System (ADS)

    Kawasaki, Hiroyuki; Mizoguchi, Asao; Kanamori, Hideto

    2016-06-01

    The absorption spectrum of the ν3 (C-F stretching) mode of CH_3F in solid {para}-H_2 by FTIR showed a series of equal interval peaks Their interpretation was that the {n}-th peak of this series was due to CH_3F-({ortho}-H_2){n} clusters which were formed CH_3F and {n}'s {ortho}-H_2 in first nearest neighbor sites of the {para}-H_2 crystal with {hcp} structure. In order to understand this system in more detail, we have studied these peaks, especially {n} = 0 - 3 corresponding to 1037 - 1041 wn, by using high-resolution and high-sensitive infrared quantum cascade laser (QCL) spectroscopy. Before now, we have observed photochromic phenomena of these peaks by taking an advantage of the high brightness of the laser. However, it has not been revealed what kind of mechanism is undergoing in these processes. In order to solve this problem we introduced two cw-IR QCLs for pump and prove experiment. While the pumping laser is breaching a certain peak with high power, the probing laser is monitoring the increase of other peaks by rapid scan method. The time resolution of this spectroscopy is 5 msec. The new precise kinetic information will help us to understand the molecular interaction in solid {para}-H_2. K. Yoshioka and D. T. Anderson, J. Chem. Phys. 119 (2003) 4731-4742 A. R. W. McKellar, A. Mizoguchi, and H. Kanamori, Phys. Chem. Chem. Phys. 13 (2011) 11587-11589

  10. Dynamic Cluster Quantum Monte Carlo Simulations of a Two-Dimensional Hubbard Model with Stripelike Charge-Density-Wave Modulations: Interplay between Inhomogeneities and the Superconducting State

    SciTech Connect

    Maier, Thomas A; Alvarez, Gonzalo; Summers, Michael Stuart; Schulthess, Thomas C

    2010-01-01

    Using dynamic cluster quantum Monte Carlo simulations, we study the superconducting behavior of a 1=8 doped two-dimensional Hubbard model with imposed unidirectional stripelike charge-density-wave modulation. We find a significant increase of the pairing correlations and critical temperature relative to the homogeneous system when the modulation length scale is sufficiently large. With a separable form of the irreducible particle-particle vertex, we show that optimized superconductivity is obtained for a moderate modulation strength due to a delicate balance between the modulation enhanced pairing interaction, and a concomitant suppression of the bare particle-particle excitations by a modulation reduction of the quasiparticle weight.

  11. An adaptive quantum mechanics/molecular mechanics method for the infrared spectrum of water: incorporation of the quantum effect between solute and solvent.

    PubMed

    Watanabe, Hiroshi C; Banno, Misa; Sakurai, Minoru

    2016-03-14

    Quantum effects in solute-solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase. For accurate spectrum evaluation, the surrounding solvent molecules, in addition to the solute of interest, should be treated using a quantum mechanical method. However, conventional quantum mechanics/molecular mechanics (QM/MM) methods cannot handle free QM solvent molecules during molecular dynamics (MD) simulation because of the diffusion problem. To deal with this problem, we have previously proposed an adaptive QM/MM "size-consistent multipartitioning (SCMP) method". In the present study, as the first application of the SCMP method, we demonstrate the reproduction of the infrared spectrum of liquid-phase water, and evaluate the quantum effect in comparison with conventional QM/MM simulations.

  12. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics.

    PubMed

    John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D

    2016-04-01

    We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems. PMID:27176426

  13. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

    2016-04-01

    We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

  14. Hierarchical clustering method for improved prostate cancer imaging in diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Kavuri, Venkaiah C.; Liu, Hanli

    2013-03-01

    We investigate the feasibility of trans-rectal near infrared (NIR) based diffuse optical tomography (DOT) for early detection of prostate cancer using a transrectal ultrasound (TRUS) compatible imaging probe. For this purpose, we designed a TRUS-compatible, NIR-based image system (780nm), in which the photo diodes were placed on the trans-rectal probe. DC signals were recorded and used for estimating the absorption coefficient. We validated the system using laboratory phantoms. For further improvement, we also developed a hierarchical clustering method (HCM) to improve the accuracy of image reconstruction with limited prior information. We demonstrated the method using computer simulations laboratory phantom experiments.

  15. Formation of fragments in heavy-ion collisions using a modified clusterization method

    SciTech Connect

    Goyal, Supriya; Puri, Rajeev K.

    2011-04-15

    We study the formation and stability of the fragments by extending the minimum spanning tree method (MST) for clusterization. In this extension, each fragment is subjected to a binding-energy check calculated using the modified Bethe-Weizsaecker formula. Earlier, a constant binding-energy cut of 4 MeV/nucleon was imposed. Our results for {sup 197}Au+{sup 197}Au collisions are compared with ALADiN data and also with the calculations based on the simulated annealing technique. We shall show that the present modified version improves the agreement compared to the MST method.

  16. Consumers' Kansei Needs Clustering Method for Product Emotional Design Based on Numerical Design Structure Matrix and Genetic Algorithms

    PubMed Central

    Chen, Deng-kai; Gu, Rong; Gu, Yu-feng; Yu, Sui-huai

    2016-01-01

    Consumers' Kansei needs reflect their perception about a product and always consist of a large number of adjectives. Reducing the dimension complexity of these needs to extract primary words not only enables the target product to be explicitly positioned, but also provides a convenient design basis for designers engaging in design work. Accordingly, this study employs a numerical design structure matrix (NDSM) by parameterizing a conventional DSM and integrating genetic algorithms to find optimum Kansei clusters. A four-point scale method is applied to assign link weights of every two Kansei adjectives as values of cells when constructing an NDSM. Genetic algorithms are used to cluster the Kansei NDSM and find optimum clusters. Furthermore, the process of the proposed method is presented. The details of the proposed approach are illustrated using an example of electronic scooter for Kansei needs clustering. The case study reveals that the proposed method is promising for clustering Kansei needs adjectives in product emotional design.

  17. Consumers' Kansei Needs Clustering Method for Product Emotional Design Based on Numerical Design Structure Matrix and Genetic Algorithms

    PubMed Central

    Chen, Deng-kai; Gu, Rong; Gu, Yu-feng; Yu, Sui-huai

    2016-01-01

    Consumers' Kansei needs reflect their perception about a product and always consist of a large number of adjectives. Reducing the dimension complexity of these needs to extract primary words not only enables the target product to be explicitly positioned, but also provides a convenient design basis for designers engaging in design work. Accordingly, this study employs a numerical design structure matrix (NDSM) by parameterizing a conventional DSM and integrating genetic algorithms to find optimum Kansei clusters. A four-point scale method is applied to assign link weights of every two Kansei adjectives as values of cells when constructing an NDSM. Genetic algorithms are used to cluster the Kansei NDSM and find optimum clusters. Furthermore, the process of the proposed method is presented. The details of the proposed approach are illustrated using an example of electronic scooter for Kansei needs clustering. The case study reveals that the proposed method is promising for clustering Kansei needs adjectives in product emotional design. PMID:27630709

  18. Solving the inverse Ising problem by mean-field methods in a clustered phase space with many states.

    PubMed

    Decelle, Aurélien; Ricci-Tersenghi, Federico

    2016-07-01

    In this work we explain how to properly use mean-field methods to solve the inverse Ising problem when the phase space is clustered, that is, many states are present. The clustering of the phase space can occur for many reasons, e.g., when a system undergoes a phase transition, but also when data are collected in different regimes (e.g., quiescent and spiking regimes in neural networks). Mean-field methods for the inverse Ising problem are typically used without taking into account the eventual clustered structure of the input configurations and may lead to very poor inference (e.g., in the low-temperature phase of the Curie-Weiss model). In this work we explain how to modify mean-field approaches when the phase space is clustered and we illustrate the effectiveness of our method on different clustered structures (low-temperature phases of Curie-Weiss and Hopfield models). PMID:27575082

  19. Solving the inverse Ising problem by mean-field methods in a clustered phase space with many states

    NASA Astrophysics Data System (ADS)

    Decelle, Aurélien; Ricci-Tersenghi, Federico

    2016-07-01

    In this work we explain how to properly use mean-field methods to solve the inverse Ising problem when the phase space is clustered, that is, many states are present. The clustering of the phase space can occur for many reasons, e.g., when a system undergoes a phase transition, but also when data are collected in different regimes (e.g., quiescent and spiking regimes in neural networks). Mean-field methods for the inverse Ising problem are typically used without taking into account the eventual clustered structure of the input configurations and may lead to very poor inference (e.g., in the low-temperature phase of the Curie-Weiss model). In this work we explain how to modify mean-field approaches when the phase space is clustered and we illustrate the effectiveness of our method on different clustered structures (low-temperature phases of Curie-Weiss and Hopfield models).

  20. Consumers' Kansei Needs Clustering Method for Product Emotional Design Based on Numerical Design Structure Matrix and Genetic Algorithms.

    PubMed

    Yang, Yan-Pu; Chen, Deng-Kai; Gu, Rong; Gu, Yu-Feng; Yu, Sui-Huai

    2016-01-01

    Consumers' Kansei needs reflect their perception about a product and always consist of a large number of adjectives. Reducing the dimension complexity of these needs to extract primary words not only enables the target product to be explicitly positioned, but also provides a convenient design basis for designers engaging in design work. Accordingly, this study employs a numerical design structure matrix (NDSM) by parameterizing a conventional DSM and integrating genetic algorithms to find optimum Kansei clusters. A four-point scale method is applied to assign link weights of every two Kansei adjectives as values of cells when constructing an NDSM. Genetic algorithms are used to cluster the Kansei NDSM and find optimum clusters. Furthermore, the process of the proposed method is presented. The details of the proposed approach are illustrated using an example of electronic scooter for Kansei needs clustering. The case study reveals that the proposed method is promising for clustering Kansei needs adjectives in product emotional design.

  1. Consumers' Kansei Needs Clustering Method for Product Emotional Design Based on Numerical Design Structure Matrix and Genetic Algorithms.

    PubMed

    Yang, Yan-Pu; Chen, Deng-Kai; Gu, Rong; Gu, Yu-Feng; Yu, Sui-Huai

    2016-01-01

    Consumers' Kansei needs reflect their perception about a product and always consist of a large number of adjectives. Reducing the dimension complexity of these needs to extract primary words not only enables the target product to be explicitly positioned, but also provides a convenient design basis for designers engaging in design work. Accordingly, this study employs a numerical design structure matrix (NDSM) by parameterizing a conventional DSM and integrating genetic algorithms to find optimum Kansei clusters. A four-point scale method is applied to assign link weights of every two Kansei adjectives as values of cells when constructing an NDSM. Genetic algorithms are used to cluster the Kansei NDSM and find optimum clusters. Furthermore, the process of the proposed method is presented. The details of the proposed approach are illustrated using an example of electronic scooter for Kansei needs clustering. The case study reveals that the proposed method is promising for clustering Kansei needs adjectives in product emotional design. PMID:27630709

  2. An iterative finite difference method for solving the quantum hydrodynamic equations of motion

    SciTech Connect

    Kendrick, Brian K

    2010-01-01

    The quantum hydrodynamic equations of motion associated with the de Broglie-Bohm description of quantum mechanics describe a time evolving probability density whose 'fluid' elements evolve as a correlated ensemble of particle trajectories. These equations are intuitively appealing due to their similarities with classical fluid dynamics and the appearance of a generalized Newton's equation of motion in which the total force contains both a classical and quantum contribution. However, the direct numerical solution of the quantum hydrodynamic equations (QHE) is fraught with challenges: the probability 'fluid' is highly-compressible, it has zero viscosity, the quantum potential ('pressure') is non-linear, and if that weren't enough the quantum potential can also become singular during the course of the calculations. Collectively these properties are responsible for the notorious numerical instabilities associated with a direct numerical solution of the QHE. The most successful and stable numerical approach that has been used to date is based on the Moving Least Squares (MLS) algorithm. The improved stability of this approach is due to the repeated local least squares fitting which effectively filters or reduces the numerical noise which tends to accumulate with time. However, this method is also subject to instabilities if it is pushed too hard. In addition, the stability of the MLS approach often comes at the expense of reduced resolution or fidelity of the calculation (i.e., the MLS filtering eliminates the higher-frequency components of the solution which may be of interest). Recently, a promising new solution method has been developed which is based on an iterative solution of the QHE using finite differences. This method (referred to as the Iterative Finite Difference Method or IFDM) is straightforward to implement, computationally efficient, stable, and its accuracy and convergence properties are well understood. A brief overview of the IFDM will be presented

  3. Comparing methods of analysing datasets with small clusters: case studies using four paediatric datasets.

    PubMed

    Marston, Louise; Peacock, Janet L; Yu, Keming; Brocklehurst, Peter; Calvert, Sandra A; Greenough, Anne; Marlow, Neil

    2009-07-01

    Studies of prematurely born infants contain a relatively large percentage of multiple births, so the resulting data have a hierarchical structure with small clusters of size 1, 2 or 3. Ignoring the clustering may lead to incorrect inferences. The aim of this study was to compare statistical methods which can be used to analyse such data: generalised estimating equations, multilevel models, multiple linear regression and logistic regression. Four datasets which differed in total size and in percentage of multiple births (n = 254, multiple 18%; n = 176, multiple 9%; n = 10 098, multiple 3%; n = 1585, multiple 8%) were analysed. With the continuous outcome, two-level models produced similar results in the larger dataset, while generalised least squares multilevel modelling (ML GLS 'xtreg' in Stata) and maximum likelihood multilevel modelling (ML MLE 'xtmixed' in Stata) produced divergent estimates using the smaller dataset. For the dichotomous outcome, most methods, except generalised least squares multilevel modelling (ML GH 'xtlogit' in Stata) gave similar odds ratios and 95% confidence intervals within datasets. For the continuous outcome, our results suggest using multilevel modelling. We conclude that generalised least squares multilevel modelling (ML GLS 'xtreg' in Stata) and maximum likelihood multilevel modelling (ML MLE 'xtmixed' in Stata) should be used with caution when the dataset is small. Where the outcome is dichotomous and there is a relatively large percentage of non-independent data, it is recommended that these are accounted for in analyses using logistic regression with adjusted standard errors or multilevel modelling. If, however, the dataset has a small percentage of clusters greater than size 1 (e.g. a population dataset of children where there are few multiples) there appears to be less need to adjust for clustering.

  4. Prediction of CpG-island function: CpG clustering vs. sliding-window methods

    PubMed Central

    2010-01-01

    Background Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence. Results We compare sliding-window to clustering (i.e. CpGcluster) predictions by applying new ways to detect putative functionality of CpG islands. Analyzing the co-localization with several genomic regions as a function of window size vs. statistical significance (p-value), CpGcluster shows a higher overlap with promoter regions and highly conserved elements, at the same time showing less overlap with Alu retrotransposons. The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by CpGcluster. Many of these islets seem to be functional, as they are unmethylated, highly conserved and/or located within the promoter region. Finally, we show that window-based islands can spuriously overlap several, differentially regulated promoters as well as different methylation domains, which might indicate a wrong merge of several CpG islands into a single, very long island. The shorter CpGcluster islands seem to be much more specific when concerning the overlap with alternative transcription start sites or the detection of homogenous methylation domains. Conclusions The main difference between sliding-window approaches and clustering methods is the length of the predicted islands. Short islands, often differentially methylated, are almost exclusively predicted by CpGcluster. This suggests that CpGcluster may be the algorithm of choice to explore the function of these short, but putatively functional CpG islands. PMID:20500903

  5. Vibronic coupling in molecular crystals: A Franck-Condon Herzberg-Teller model of H-aggregate fluorescence based on quantum chemical cluster calculations

    SciTech Connect

    Wykes, M. Parambil, R.; Gierschner, J.; Beljonne, D.

    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.

  6. Quantum Communication

    NASA Astrophysics Data System (ADS)

    Weinfurter, Harald; Zeilinger, Anton

    Quantum entanglement lies at the heart of the new field of quantum communication and computation. For a long time, entanglement was seen just as one of those fancy features which make quantum mechanics so counterintuitive. But recently, quantum information theory has shown the tremendous importance of quantum correlations for the formulation of new methods of information transfer and for algorithms exploiting the capabilities of quantum computers.This chapter describes the first experimental realizations of quantum communication schemes using entangled photon pairs. We show how to make communication secure against eavesdropping using entanglement-based quantum cryptography, how to increase the information capacity of a quantum channel by quantum dense coding and, finally, how to communicate quantum information itself in the process of quantum teleportation.

  7. Comparative analysis of codeword representation by clustering methods for the classification of histological tissue types

    NASA Astrophysics Data System (ADS)

    Saygili, Ahmet; Uysal, Gunalp; Bilgin, Gokhan

    2015-12-01

    In this study, the classification of several histological tissue types, i.e., muscles, nerves, connective and epithelial tissue cells, is studied in high resolutional histological images. In the feature extraction step, bag of features method is utilized to reveal distinguishing features of each tissue cell types. Local small blocks of sub-images/patches are extracted to find discriminative patterns for followed strategy. For detecting points of interest in local patches, Harris corner detection method is applied. Afterwards, discriminative features are extracted using the scale invariant feature transform method using these points of interests. Several code word representations are obtained by clustering approach (using k-means fuzzy c-means, expectation maximization method, Gaussian mixture models) and evaluated in comparative manner. In the last step, the classification of the tissue cells data are performed using k-nearest neighbor and support vector machines methods.

  8. A new sparse Bayesian learning method for inverse synthetic aperture radar imaging via exploiting cluster patterns

    NASA Astrophysics Data System (ADS)

    Fang, Jun; Zhang, Lizao; Duan, Huiping; Huang, Lei; Li, Hongbin

    2016-05-01

    The application of sparse representation to SAR/ISAR imaging has attracted much attention over the past few years. This new class of sparse representation based imaging methods present a number of unique advantages over conventional range-Doppler methods, the basic idea behind these works is to formulate SAR/ISAR imaging as a sparse signal recovery problem. In this paper, we propose a new two-dimensional pattern-coupled sparse Bayesian learning(SBL) method to capture the underlying cluster patterns of the ISAR target images. Based on this model, an expectation-maximization (EM) algorithm is developed to infer the maximum a posterior (MAP) estimate of the hyperparameters, along with the posterior distribution of the sparse signal. Experimental results demonstrate that the proposed method is able to achieve a substantial performance improvement over existing algorithms, including the conventional SBL method.

  9. Improved transfer matrix methods for calculating quantum transmission coefficient.

    PubMed

    Biswas, Debabrata; Kumar, Vishal

    2014-07-01

    Methods for calculating the transmission coefficient are proposed, all of which arise from improved nonreflecting WKB boundary conditions at the edge of the computational domain in one-dimensional geometries. In the first, the Schrödinger equation is solved numerically, while the second is a transfer matrix (TM) algorithm where the potential is approximated by steps, but with the first and last matrix modified to reflect the new boundary condition. Both methods give excellent results with first-order WKB boundary conditions. The third uses the transfer matrix method with third-order WKB boundary conditions. For the parabolic potential, the average error for the modified third-order TM method reduces by factor of 4100 over the unmodified TM method.

  10. Application of statistics filter method and clustering analysis in fault diagnosis of roller bearings

    NASA Astrophysics Data System (ADS)

    Song, L. Y.; Wang, H. Q.; Gao, J. J.; Yang, J. F.; Liu, W. B.; Chen, P.

    2012-05-01

    Condition diagnosis of roller bearings depends largely on the feature analysis of vibration signals. Spectrum statistics filter (SSF) method could adaptively reduce the noise. This method is based on hypothesis testing in the frequency domain to eliminate the identical component between the reference signal and the primary signal. This paper presents a statistical parameter namely similarity factor to evaluate the filtering performance. The performance of the method is compared with the classical method, band pass filter (BPF). Results show that statistics filter is preferable to BPF in vibration signal processing. Moreover, the significance level awould be optimized by genetic algorithms. However, it is very difficult to identify fault states only from time domain waveform or frequency spectrum when the effect of the noise is so strong or fault feature is not obvious. Pattern recognition is then applied to fault diagnosis in this study through system clustering method. This paper processes experiment rig data that after statistics filter, and the accuracy of clustering analysis increases substantially.

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

    DOEpatents

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

    2012-05-29

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

  12. Benchmark calculations on the nuclear quadrupole-coupling parameters for open-shell molecules using non-relativistic and scalar-relativistic coupled-cluster methods

    SciTech Connect

    Cheng, Lan

    2015-08-14

    Quantum-chemical computations of nuclear quadrupole-coupling parameters for 24 open-shell states of small molecules based on non-relativistic and spin-free exact two-component (SFX2C) relativistic equation-of-motion coupled-cluster (EOM-CC) as well as spin-orbital-based restricted open-shell Hartree-Fock coupled-cluster (ROHF-CC) methods are reported. Relativistic effects, the performance of the EOM-CC and ROHF-CC methods for treating electron correlation, as well as basis-set convergence have been carefully analyzed. Consideration of relativistic effects is necessary for accurate calculations on systems containing third-row (K-Kr) and heavier elements, as expected, and the SFX2C approach is shown to be a useful cost-effective option here. Further, it is demonstrated that the EOM-CC methods constitute flexible and accurate alternatives to the ROHF-CC methods in the calculations of nuclear quadrupole-coupling parameters for open-shell states.

  13. Exploring Quantum Many-Body Spin Dynamics with Truncated Wigner Methods

    NASA Astrophysics Data System (ADS)

    Schachenmayer, Johannes

    Recent experiments in atomic, molecular, and optical physics offer controlled and clean environments to experimentally study non-equilibrium dynamics of large many-body quantum spin-models with variable range interactions. Thus, efficient computation of such dynamics is of great importance. While in one dimension, time-dependent density matrix renormalization group methods (t-DMRG) have proven effective under certain conditions, computing dynamics in higher dimensional systems remains an outstanding challenge. Recently we formulated the discrete truncated Wigner approximation (DTWA), a semiclassical method based on the truncated Wigner approximation (TWA) that has been proven to be surprisingly accurate in predicting quench dynamics in high-dimensional lattices with up to tens of thousands of quantum spins. Here, we introduce the DTWA and show how it can compute time-evolution of quantum states in experiments that engineer spin-models with polar molecules in optical lattices or with ions in two-dimensional Penning traps. We show, how the DTWA can provide results for the time-evolution of classical and quantum correlations in quench experiments in regimes where other numerical methods are generally unreliable. We report on progress of how to incorporate higher order corrections to the method, and how to adapt it to systems with both spin and bosonic degrees of freedom.

  14. On the Methods for Constructing Meson-Baryon Reaction Models within Relativistic Quantum Field Theory

    SciTech Connect

    B. Julia-Diaz, H. Kamano, T.-S. H. Lee, A. Matsuyama, T. Sato, N. Suzuki

    2009-04-01

    Within the relativistic quantum field theory, we analyze the differences between the $\\pi N$ reaction models constructed from using (1) three-dimensional reductions of Bethe-Salpeter Equation, (2) method of unitary transformation, and (3) time-ordered perturbation theory. Their relations with the approach based on the dispersion relations of S-matrix theory are dicusssed.

  15. Teaching Basic Quantum Mechanics in Secondary School Using Concepts of Feynman Path Integrals Method

    ERIC Educational Resources Information Center

    Fanaro, Maria de los Angeles; Otero, Maria Rita; Arlego, Marcelo

    2012-01-01

    This paper discusses the teaching of basic quantum mechanics in high school. Rather than following the usual formalism, our approach is based on Feynman's path integral method. Our presentation makes use of simulation software and avoids sophisticated mathematical formalism. (Contains 3 figures.)

  16. Meiofaunal community analysis by high-throughput sequencing: comparison of extraction, quality filtering, and clustering methods.

    PubMed

    Brannock, Pamela M; Halanych, Kenneth M

    2015-10-01

    Using molecular tools to examine community composition of meiofauna, animals 45μm to 1mm in size living between sediment grains in aquatic environments, is relatively new in comparison to bacterial and archaeal microbial studies. Although high-throughput molecular approaches are starting to be applied to these ccommunities, effectiveness of different approaches for nucleic acid extraction from meiofauna is poorly known and bioinformatic pipelines vary between studies. Given this situation, there is a need for protocols to be developed that promote consistency in sample collection and processing, sequence quality filtering, and Operational Taxonomic Unit (OTU) clustering methods. Herein, we assess different approaches used for DNA extraction (DNA extracted directly from sediment versus elutriated material retained on a 45μm sieve) as well as how different quality filtering methods of sequences and OTU clustering algorithms impact genetic assessment of meiofauna community composition. DNA extracted directly from sediment resulted in higher presence of non-metazoan eukaryotic taxa; in contrast, an elutriation (resuspension with decanting) approach increased meiofauna abundance and enriched metazoan OTUs. In regards to bioinformatics analyses, the number of overall OTUs varied by clustering algorithm, primarily due to the applied method of sequence quality filtering. However, alpha and beta diversity analyses showed similar trends regardless of bioinformatics pipeline utilized. Based on our results, we recommend studies of meiofauna communities first elutriate samples prior to DNA extraction and include multiple biological replicates to account for variation in community-level composition. The quality filtering method should be carefully considered as this step accounted for large discrepancy in the number of OTUs inferred.

  17. a Fully Quantum Method of Determination of Penetrability and Reflection Coefficients in Quantum FRW Model with Radiation

    NASA Astrophysics Data System (ADS)

    Maydanyuk, Sergei P.

    In the paper the closed Friedmann-Robertson-Walker model with quantization in the presence of the positive cosmological constant and radiation is studied. For analysis of tunneling probability for birth of an asymptotically de Sitter, inflationary universe as a function of the radiation energy, a new definition of a "free" wave propagating inside strong fields is proposed. On such a basis, tunneling boundary condition is corrected, penetrability and reflection relative to the barrier are calculated in fully quantum stationary approach. For the first time nonzero interference between the incident and reflected waves has been taken into account which turns out to play important role inside cosmological potentials and could be explained by non-locality of barriers in quantum mechanics. Inside the whole region of radiation energy the tunneling probability for the birth of the inflationary universe is found to be close to its value obtained in the semiclassical approach. The reflection from the barrier is determined for the first time (which differs essentially on 1 at the energy of radiation close to the barrier height). The proposed method could be easily generalized on the cosmological models with barriers of arbitrary shape, as demonstrated for the FRW model with included Chaplygin gas. The result is stable for variations of the studied barriers, accuracy is found to be 11-18 digits for all coefficients and energies below the barrier height.

  18. A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm.

    PubMed

    de Brito, Daniel M; Maracaja-Coutinho, Vinicius; de Farias, Savio T; Batista, Leonardo V; do Rêgo, Thaís G

    2016-01-01

    Genomic Islands (GIs) are regions of bacterial genomes that are acquired from other organisms by the phenomenon of horizontal transfer. These regions are often responsible for many important acquired adaptations of the bacteria, with great impact on their evolution and behavior. Nevertheless, these adaptations are usually associated with pathogenicity, antibiotic resistance, degradation and metabolism. Identification of such regions is of medical and industrial interest. For this reason, different approaches for genomic islands prediction have been proposed. However, none of them are capable of predicting precisely the complete repertory of GIs in a genome. The difficulties arise due to the changes in performance of different algorithms in the face of the variety of nucleotide distribution in different species. In this paper, we present a novel method to predict GIs that is built upon mean shift clustering algorithm. It does not require any information regarding the number of clusters, and the bandwidth parameter is automatically calculated based on a heuristic approach. The method was implemented in a new user-friendly tool named MSGIP--Mean Shift Genomic Island Predictor. Genomes of bacteria with GIs discussed in other papers were used to evaluate the proposed method. The application of this tool revealed the same GIs predicted by other methods and also different novel unpredicted islands. A detailed investigation of the different features related to typical GI elements inserted in these new regions confirmed its effectiveness. Stand-alone and user-friendly versions for this new methodology are available at http://msgip.integrativebioinformatics.me. PMID:26731657

  19. A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm

    PubMed Central

    de Brito, Daniel M.; Maracaja-Coutinho, Vinicius; de Farias, Savio T.; Batista, Leonardo V.; do Rêgo, Thaís G.

    2016-01-01

    Genomic Islands (GIs) are regions of bacterial genomes that are acquired from other organisms by the phenomenon of horizontal transfer. These regions are often responsible for many important acquired adaptations of the bacteria, with great impact on their evolution and behavior. Nevertheless, these adaptations are usually associated with pathogenicity, antibiotic resistance, degradation and metabolism. Identification of such regions is of medical and industrial interest. For this reason, different approaches for genomic islands prediction have been proposed. However, none of them are capable of predicting precisely the complete repertory of GIs in a genome. The difficulties arise due to the changes in performance of different algorithms in the face of the variety of nucleotide distribution in different species. In this paper, we present a novel method to predict GIs that is built upon mean shift clustering algorithm. It does not require any information regarding the number of clusters, and the bandwidth parameter is automatically calculated based on a heuristic approach. The method was implemented in a new user-friendly tool named MSGIP—Mean Shift Genomic Island Predictor. Genomes of bacteria with GIs discussed in other papers were used to evaluate the proposed method. The application of this tool revealed the same GIs predicted by other methods and also different novel unpredicted islands. A detailed investigation of the different features related to typical GI elements inserted in these new regions confirmed its effectiveness. Stand-alone and user-friendly versions for this new methodology are available at http://msgip.integrativebioinformatics.me. PMID:26731657

  20. A hierarchy of local coupled cluster singles and doubles response methods for ionization potentials.

    PubMed

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

    2016-02-28

    We present a hierarchy of local coupled cluster (CC) linear response (LR) methods to calculate ionization potentials (IPs), i.e., excited states with one electron annihilated relative to a ground state reference. The time-dependent perturbation operator V(t), as well as the operators related to the first-order (with respect to V(t)) amplitudes and multipliers, thus are not number conserving and have half-integer particle rank m. Apart from calculating IPs of neutral molecules, the method offers also the possibility to study ground and excited states of neutral radicals as ionized states of closed-shell anions. It turns out that for comparable accuracy IPs require a higher-order treatment than excitation energies; an IP-CC LR method corresponding to CC2 LR or the algebraic diagrammatic construction scheme through second order performs rather poorly. We therefore systematically extended the order with respect to the fluctuation potential of the IP-CC2 LR Jacobian up to IP-CCSD LR, keeping the excitation space of the first-order (with respect to V(t)) cluster operator restricted to the m=½⊕3/2 subspace and the accuracy of the zero-order (ground-state) amplitudes at the level of CC2 or MP2. For the more expensive diagrams beyond the IP-CC2 LR Jacobian, we employ local approximations. The implemented methods are capable of treating large molecular systems with hundred atoms or more.