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Sample records for coupled channels calculation

  1. Dynamical coupled channels calculation of pion and omega meson production

    SciTech Connect

    Paris, Mark W.

    2009-02-15

    The dynamical coupled-channels approach developed at the Excited Baryon Analysis Center is extended to include the {omega}N channel to study {pi}- and {omega}-meson production induced by scattering pions and photons from the proton. Six intermediate channels, including {pi}N, {eta}N, {pi}{delta}, {sigma}N, {rho}N, and {omega}N, are employed to describe unpolarized and polarized data. Bare parameters in an effective hadronic Lagrangian are determined in a fit to the data for {pi}N{yields}{pi}N, {gamma}N{yields}{pi}N, {pi}{sup -}p{yields}{omega}n, and {gamma}p{yields}{omega}p reactions at center-of-mass energies from threshold to W<2.0 GeV. The T matrix determined in these fits is used to calculate the photon beam asymmetry for {omega}-meson production and the {omega}N{yields}{omega}N total cross section and {omega}N-scattering lengths. The calculated beam asymmetry is in good agreement with the observed in the range of energies near threshold to W < or approx. 2.0 GeV.

  2. Coupled channels calculation of a piLAMBDAN quasibound state

    SciTech Connect

    Garcilazo, H.; Gal, A.

    2010-05-15

    We extend the study of a J{sup P}=2{sup +},I=3/2, piLAMBDAN quasibound state [Phys. Rev. D 78, 014013 (2008)] by solving nonrelativistic Faddeev equations, using {sup 3}S{sub 1}-{sup 3}D{sub 1}, LAMBDAN-SIGMAN coupled channels chiral quark model local interactions, and piN and coupled piLAMBDA-piSIGMA separable interactions fitted to the position and decay parameters of the DELTA(1232) and SIGMA(1385) resonances, respectively. The results exhibit a strong sensitivity to the p-wave pion-hyperon interaction, with a piLAMBDAN quasibound state persisting over a wide range of acceptable parametrizations.

  3. Four-body continuum-discretized coupled-channels calculations

    SciTech Connect

    Rodriguez-Gallardo, M.; Arias, J. M.; Moro, A. M.; Gomez-Camacho, J.; Thompson, I. J.; Tostevin, J. A.

    2009-11-15

    The development of a continuum-bin scheme of discretization for three-body projectiles is necessary for studies of reactions of Borromean nuclei such as {sup 6}He within the continuum-discretized coupled-channels approach. Such a procedure, for constructing bin states on selected continuum energy intervals, is formulated and applied for the first time to reactions of a three-body projectile. The continuum representation uses the eigenchannel expansion of the three-body S matrix. The method is applied to the challenging case of the {sup 6}He+{sup 208}Pb reaction at 22 MeV, where an accurate treatment of both the Coulomb and the nuclear interactions with the target is necessary.

  4. Calculation of nuclear reaction cross sections on excited nuclei with the coupled-channels method

    SciTech Connect

    Kawano, T.; Talou, P.; Lynn, J. E.; Chadwick, M. B.; Madland, D. G.

    2009-08-15

    We calculate nuclear cross sections on excited nuclei in the fast neutron energy range. We partition the whole process into two contributions: the direct reaction part and the compound nuclear reactions. A coupled-channels method is used for calculating the direct transition of the nucleus from the initial excited state, which is a member of the ground-state rotational band, to the final ground and excited low-lying levels. This process is strongly affected by the channel coupling. The compound nuclear reactions on the excited state are calculated with the statistical Hauser-Feshbach model, with the transmission coefficients obtained from the coupled-channels calculation. The calculations are performed for a strongly deformed nucleus {sup 169}Tm, and selected cross sections for the ground and first excited states are compared. The calculation is also made for actinides to investigate possible modification to the fission cross section when the target is excited. It is shown that both the level coupling for the entrance channel, and the different target spin, change the fission cross section.

  5. Four-body continuum-discretized coupled-channels calculations using a transformed harmonic oscillator basis

    SciTech Connect

    Rodriguez-Gallardo, M.; Arias, J. M.; Gomez-Camacho, J.; Moro, A. M.; Johnson, R. C.; Tostevin, J. A.; Thompson, I. J.

    2008-06-15

    The scattering of a weakly bound three-body system by a target is discussed. A transformed harmonic oscillator basis is used to provide an appropriate discrete and finite basis for treating the continuum part of the spectrum of the projectile. The continuum-discretized coupled-channels framework is used for the scattering calculations. The formalism is applied to different reactions, {sup 6}He+{sup 12}C at 229.8 MeV, {sup 6}He+{sup 64}Zn at 10 and 13.6 MeV, and {sup 6}He+{sup 208}Pb at 22 MeV, induced by the Borromean nucleus {sup 6}He. Both the Coulomb and nuclear interactions with a target are taken into account.

  6. Analytical transformed harmonic oscillator basis for continuum discretized coupled channels calculations

    SciTech Connect

    Moro, A. M.; Arias, J. M.; Gomez-Camacho, J.; Perez-Bernal, F.

    2009-11-15

    A new method for continuum discretization in continuum-discretized coupled-channels calculations is proposed. The method is based on an analytic local-scale transformation of the harmonic-oscillator wave functions proposed for other purposes in a recent work [Karatagladis et al., Phys. Rev. C 71, 064601 (2005)]. The new approach is compared with the standard method of continuum discretization in terms of energy bins for the reactions d+{sup 58}Ni at 80 MeV, {sup 6}Li+{sup 40}Ca at 156 MeV, and {sup 6}He+{sup 208}Pb at 22 MeV and 240 MeV/nucleon. In all cases very good agreement between both approaches is found.

  7. A Partial Width Calculation of OZI-Allowed Charmonium Decays in a Coupled Channel Framework

    NASA Astrophysics Data System (ADS)

    Sakai, M.; Matsuda, Y.; Hirano, M.; Katō, K.

    2009-09-01

    Okubo-Zweig-Iizuka-allowed partial decay widths, masses, and total decay width of charmonium states are studied in a nonrelativistic coupled-channel framework based on microscopic effective quark interactions. With the help of the complex scale transformation, the coupled channel equation is easily solved under the proper boundary condition for resonances. The obtained result as a whole is very successful and encouraging for the traditional charmonium states including ψ(4040) whose features of mass and partial decay widths have been argued historically. The coupling mechanisms of these states are investigated by reducing artificially the channel coupling strengths little by little and finally turning the coupling off. The situations turn out to be quite different from what we would have naively supposed. Other solutions than the traditional charmonium states were obatined at the same time. Some of them are discussed in relation with new particles observed recently.

  8. Markov chain models of coupled intracellular calcium channels: Kronecker structured representations and benchmark stationary distribution calculations.

    PubMed

    Deremigio, Hilary; Kemper, Peter; Lamar, M Drew; Smith, Gregory D

    2008-01-01

    Mathematical models of calcium release sites derived from Markov chain models of intracellular calcium channels exhibit collective gating reminiscent of the experimentally observed phenomenon of stochastic calcium excitability (i.e., calcium puffs and sparks). We present a Kronecker structured representation for calcium release site models and perform benchmark stationary distribution calculations using numerical iterative solution techniques that leverage this structure. In this context we find multi-level methods and certain preconditioned projection methods superior to simple Gauss-Seidel type iterations. Response measures such as the number of channels in a particular state converge more quickly using these numerical iterative methods than occupation measures calculated via Monte Carlo simulation.

  9. Two-dimensional coupled fluid and electrodynamic calculations for a MHD DCW channel with slag layers

    NASA Astrophysics Data System (ADS)

    Liu, B. L.

    1982-01-01

    A fully coupled, two dimensional numerical method of modeling linear, coal-fired MHD generators is developed for the case of a plasma flow bounded by a slag layer on the channel walls. The governing partial differential equations for the plasma flow, slag layer and electrodynamics are presented and their coupling discussed. An iterative, numerical procedure employing non-uniform computational meshes and appropriate tridiagonal matrix solution schemes for the equations is presented. The method permits the investigation of the mutual plasma flow-slag layer development for prescribed wall temperatures, electrode geometry, slag properties and channel loading. In particular, the slag layer-plasma interface properties which require prior specification in an uncoupled analysis comprise part of the solution in the present approach. Results are presented for a short diagonally connected generator channel and include contour plots of the electric potential and current stream function as well as transverse and axial profiles of pertinent plasma properties. The results indicate that a thin electrode slag layer can be maintained in the presence of reasonable current density levels.

  10. Comparison of the coupled-channel calculation with the WKB method for α-decay fine structure

    NASA Astrophysics Data System (ADS)

    Ni, Dongdong; Ren, Zhongzhou

    2013-05-01

    The α-decay fine structures in heavy deformed even-even and odd-mass nuclei are investigated using the newly developed multichannel cluster model (MCCM) and the WKB barrier penetration formalism. The MCCM is based on the coupled-channel Schrödinger equation with outgoing wave boundary conditions. For even-even nuclei, the two methods yield comparable results concerning the branching ratios for 0+ and 2+ states but the WKB formula fails in reproducing the branching ratios for excited 4+ states. For odd-mass nuclei, it is hard to use the WKB formula to interpret the unexpected behavior BRI+1 >BRI while the MCCM succeeds. These emphasize that the coupling effects of decay channels cannot be ignored in describing the α-decay fine structure.

  11. S2 in planetary atmospheres: a coupled-channel Schrödinger equation calculation of the B 3Σ u^- - X 3Σ g^- transition

    NASA Astrophysics Data System (ADS)

    Gibson, S. T.; Cavanagh, S. J.; Lewis, B. R.; Stark, G.; Smith, P. L.

    2003-05-01

    Diatomic sulfur (S2) has been observed in absorption, via the strong ultraviolet B 3Σu^- - X 3Σg^- system, in the atmospheres of Jupiter and Io. The determinations of S2 abundances and temperatures from its ultraviolet absorption signature are hindered by the very large uncertainties associated with the fundamental spectroscopic parameters of the molecule. Oscillator strengths, line widths and line shapes are, to date, poorly determined. As part of a combined program of calculations and laboratory measurements, we present preliminary model calculations of the S2 B - X absorption spectrum. From limited spectroscopic information, it is known that the B 3Σ u^- state is heavily perturbed by B'' 3Πu, 1Πu and 5Σu^-(5Πu) predissociating states (Wheeler et al. 1998) which yield an apparently complex spectrum. In contrast, the analogous B - X transition in molecular oxygen (O2), responsible for the Schumann-Runge bands, has been studied extensively in the laboratory. The apparent complexities of this spectrum are readily understood, in terms of a coupled-channel Schrödinger equation (CSE) model (Lewis et al. 2001). We apply a CSE model developed for the B 3Σ u^- - X 3Σg^- transition of O2 to the analogous S2 spectrum, employing the potential energy curves and coupling scheme of Wheeler et al., as a starting point.The CSE calculations provide valuable insight into the photodissociation spectrum, demonstrating complex interference effects that are more pronounced than for O2 and hence of significance to planetary photochemical models. These calculations will guide planned measurements of the strengths and lineshapes of the B-X system. References: M. D. Wheeler, S. M. Newman, and A. J. Orr-Ewing, J. Chem. Phys. 108, 6594-6605 (1998); B. R. Lewis, S. T. Gibson, F. T. Hawes, and L. W. Torop, Phys. Chem. Earth (C) 26, 519-526 (2001).

  12. Hyperspherical coupled channel calculations of energy and structure of 4He-4He-Li+ and its isotopic combinations

    NASA Astrophysics Data System (ADS)

    Liu, Min-min; Wu, Meng-Shan; Han, Hui-li; Shi, Ting-yun

    2016-07-01

    The ground state vibrational energy and spatial features of 4He-4He-Li+ and its triatomic isotopic complexes are studied using the slow variable discretization (SVD) method in the hyperspherical coordinates for the zero total angular momentum. Our results show that the dominant structure of the system is an isosceles triangle with the shorter side associated with the two Li+-He distances using the sum-of-potential approximation. Corrections caused by the induced dipole-induced dipole interactions on the He atoms are also investigated. The effects are seen to be small and have a minor influence on the binding energy and the structure of present system. The results are also compared with the full ab initio calculations including all the three-body interactions and information of three-body corrections is obtained.

  13. Four-body continuum-discretized coupled-channels calculations: Application to {sup 6}He+{sup 64}Zn at 13.6 MeV

    SciTech Connect

    Rodriguez-Gallardo, M.; Arias, J. M.; Moro, A. M.; Gomez-Camacho, J.; Thompson, I. J.; Tostevin, J. A.

    2010-04-26

    The recently developed four-body continuum-discretized coupled-channels (CDCC) method, making use of the binning procedure, is applied to the reaction {sup 6}He+{sup 64}Zn at 13.6 MeV (around the Coulomb barrier). Excellent agreement with available elastic data is found.

  14. Coupled channel model of the scalar isovector meson photoproduction

    NASA Astrophysics Data System (ADS)

    Bibrzycki, Ł.; Kamiński, R.

    2017-03-01

    We present the coupled channel model of the scalar isovector resonance photoproduction including the πη, KK̅ and πη' channels and calculate resulting mass distribution and the cross section in the πη channel. We show that the shape of this mass distribution, is strongly affected by the phase of background amplitude. We also discuss the effect of inclusion the πη' channel on the overall isovector photoproduction process.

  15. Nonadiabatic quantum dynamics of C(1D)+H2→CH+H: coupled-channel calculations including Renner-Teller and Coriolis terms.

    PubMed

    Defazio, Paolo; Bussery-Honvault, Béatrice; Honvault, Pascal; Petrongolo, Carlo

    2011-09-21

    The Renner-Teller (RT) coupled-channel dynamics for the C((1)D)+H(2)(X(1)Σ(g) (+))→CH(X(2)Π)+H((2)S) reaction has been investigated for the first time, considering the first two singlet states ã̃(1)A' and b(1)A'' of CH(2) dissociating into the products and RT couplings, evaluated through the ab initio matrix elements of the electronic angular momentum. We have obtained initial-state-resolved probabilities, cross sections and thermal rate constants via the real wavepacket method for both coupled electronic states. In contrast to the N((2)D)+H(2)(X(1)Σ(g)(+)) system, RT effects tend to reduce probabilities, cross sections, and rate constants in the low energy range compared to Born-Oppenheimer (BO) ones, due to the presence of a repulsive RT barrier in the effective potentials and to long-lived resonances. Furthermore, contrary to BO results, the rate constants have a positive temperature dependence in the 100-400 K range. The two-state RT rate constant at 300 K, lower than the BO one, remains inside the error bars of the experimental value.

  16. Coupled-channel scattering on a torus

    SciTech Connect

    Guo, Peng; Dudek, Jozef Jon; Edwards, Robert G.; Szczepaniak, Adam Pawel

    2013-07-01

    Based on the Hamiltonian formalism approach, a generalized Luscher's formula for two particle scattering in both the elastic and coupled-channel cases in moving frames is derived from a relativistic Lippmann-Schwinger equation. Some strategies for extracting scattering amplitudes for a coupled-channel system from the discrete finite-volume spectrum are discussed and illustrated with a toy model of two-channel resonant scattering. This formalism will, in the near future, be used to extract information about hadron scattering from lattice QCD computations.

  17. Coupled-channel scattering on a torus

    DOE PAGES

    Guo, Peng; Dudek, Jozef Jon; Edwards, Robert G.; ...

    2013-07-01

    Based on the Hamiltonian formalism approach, a generalized Luscher's formula for two particle scattering in both the elastic and coupled-channel cases in moving frames is derived from a relativistic Lippmann-Schwinger equation. Some strategies for extracting scattering amplitudes for a coupled-channel system from the discrete finite-volume spectrum are discussed and illustrated with a toy model of two-channel resonant scattering. This formalism will, in the near future, be used to extract information about hadron scattering from lattice QCD computations.

  18. Dynamical coupled channel approach to omega meson production

    SciTech Connect

    Mark Paris

    2007-09-10

    The dynamical coupled channel approach of Matsuyama, Sato, and Lee is used to study the $\\omega$--meson production induced by pions and photons scattering from the proton. The parameters of the model are fixed in a two-channel (\\omega N,\\pi N) calculation for the non-resonant and resonant contributions to the $T$ matrix by fitting the available unpolarized differential cross section data. The polarized photon beam asymmetry is predicted and compared to existing data.

  19. Integral dependent spin couplings in CI calculations

    NASA Astrophysics Data System (ADS)

    Iberle, K.; Davidson, E. R.

    1982-06-01

    Although the number of ways to combine Slater determinants to form spin eigenfunctions increases rapidly with the number of open shells, most of these spin couplings will make only a small contribution to a given state, provided the spin coupling is chosen judiciously. The technique of limiting calculations to the interacting subspace pioneered by Bunge (1970) was employed by Munch and Davidson (1975) to the vanadium atom. The use of an interacting space looses its advantage in more complex cases. However, the problem can always be reduced to only one interacting spin coupling by making the coefficients integral dependent. The present investigation is concerned with the performance of integral dependent interacting couplings, taking into account the results of three test calculations.

  20. Integral dependent spin couplings in CI calculations

    NASA Technical Reports Server (NTRS)

    Iberle, K.; Davidson, E. R.

    1982-01-01

    Although the number of ways to combine Slater determinants to form spin eigenfunctions increases rapidly with the number of open shells, most of these spin couplings will make only a small contribution to a given state, provided the spin coupling is chosen judiciously. The technique of limiting calculations to the interacting subspace pioneered by Bunge (1970) was employed by Munch and Davidson (1975) to the vanadium atom. The use of an interacting space looses its advantage in more complex cases. However, the problem can always be reduced to only one interacting spin coupling by making the coefficients integral dependent. The present investigation is concerned with the performance of integral dependent interacting couplings, taking into account the results of three test calculations.

  1. Continuum channel coupling of shape resonances in N2

    NASA Astrophysics Data System (ADS)

    Poliakoff, E. D.; Kakar, Sandeep; Rosenberg, R. A.

    1992-02-01

    We have measured vibrational branching ratios for 2σ-1u photoionization of N2 in an effort to elucidate fundamental aspects of continuum channel coupling. Calculations have shown that photoejection of a 2σu electron from N2 should be influenced by a shape resonance in the 3σg →ɛσu photoionization channel and that this continuum channel coupling can result in deviations from Franck-Condon behavior for the resulting N+2(B 2Σ+u) ion. In the present study, the N2 molecules are ionized by monochromatic synchrotron radiation (25coupling between the 2σ-1u and 3σ-1g ionization channels. However, our results exhibit significant discrepancies with theory. The areas of agreement and disagreement suggest useful avenues of further study to clarify the nature of continuum channel coupling in molecular photoionization.

  2. Coupled-channel analysis for ϕ photoproduction with Λ(1520)

    NASA Astrophysics Data System (ADS)

    Ozaki, S.; Hosaka, A.; Nagahiro, H.; Scholten, O.

    2009-09-01

    We investigate photoproduction of ϕ mesons off protons within a coupled-channel effective-Lagrangian method which is based on the K-matrix approach. Since the threshold energy of the KΛ(1520) channel is close to that of ϕN, the contribution of this channel to ϕ photoproduction near the threshold energy region may give rise to some unexpected structures. In the transition amplitude KΛ(1520)→ϕN, the kinematics allows an intermediate kaon to be on-shell. This happens in the energy region where a peak structure has been observed in ϕ photoproduction. In our calculations, the on-shell kaon effect indeed reproduces a peak structure, though with a magnitude that is far too small to explain the observed effect. As a following step, we introduce a nucleon resonance in our model. The coupling of the resonance to the KΛ(1520) and ϕN channels is not suppressed by the Okubo-Zweig-Iizuka (OZI) rule if the resonance contains a dominant hidden strangeness component. We find that the resonance can reproduce a peak structure of the correct magnitude at the right energy. We also investigate the effects of coupled channels and the resonance on the angular distribution and the spin-density matrices for ϕ photoproduction.

  3. Extracting Effective Higgs Couplings in the Golden Channel

    DOE PAGES

    Chen, Yi; Vega-Morales, Roberto

    2014-04-08

    Kinematic distributions in Higgs decays to four charged leptons, the so called ‘golden channel, are a powerful probe of the tensor structure of its couplings to neutral electroweak gauge bosons. In this study we construct the first part of a comprehensive analysis framework designed to maximize the information contained in this channel in order to perform direct extraction of the various possible Higgs couplings. We first complete an earlier analytic calculation of the leading order fully differential cross sections for the golden channel signal and background to include the 4e and 4μ final states with interference between identical final states.more » We also examine the relative fractions of the different possible combinations of scalar-tensor couplings by integrating the fully differential cross section over all kinematic variables as well as show various doubly differential spectra for both the signal and background. From these analytic expressions we then construct a ‘generator level’ analysis framework based on the maximum likelihood method. Then, we demonstrate the ability of our framework to perform multi-parameter extractions of all the possible effective couplings of a spin-0 scalar to pairs of neutral electroweak gauge bosons including any correlations. Furthermore, this framework provides a powerful method for study of these couplings and can be readily adapted to include the relevant detector and systematic effects which we demonstrate in an accompanying study to follow.« less

  4. Extracting Effective Higgs Couplings in the Golden Channel

    SciTech Connect

    Chen, Yi; Vega-Morales, Roberto

    2014-04-08

    Kinematic distributions in Higgs decays to four charged leptons, the so called ‘golden channel, are a powerful probe of the tensor structure of its couplings to neutral electroweak gauge bosons. In this study we construct the first part of a comprehensive analysis framework designed to maximize the information contained in this channel in order to perform direct extraction of the various possible Higgs couplings. We first complete an earlier analytic calculation of the leading order fully differential cross sections for the golden channel signal and background to include the 4e and 4μ final states with interference between identical final states. We also examine the relative fractions of the different possible combinations of scalar-tensor couplings by integrating the fully differential cross section over all kinematic variables as well as show various doubly differential spectra for both the signal and background. From these analytic expressions we then construct a ‘generator level’ analysis framework based on the maximum likelihood method. Then, we demonstrate the ability of our framework to perform multi-parameter extractions of all the possible effective couplings of a spin-0 scalar to pairs of neutral electroweak gauge bosons including any correlations. Furthermore, this framework provides a powerful method for study of these couplings and can be readily adapted to include the relevant detector and systematic effects which we demonstrate in an accompanying study to follow.

  5. Benchmarking Calculations of Excitonic Couplings between Bacteriochlorophylls.

    PubMed

    Kenny, Elise P; Kassal, Ivan

    2016-01-14

    Excitonic couplings between (bacterio)chlorophyll molecules are necessary for simulating energy transport in photosynthetic complexes. Many techniques for calculating the couplings are in use, from the simple (but inaccurate) point-dipole approximation to fully quantum-chemical methods. We compared several approximations to determine their range of applicability, noting that the propagation of experimental uncertainties poses a fundamental limit on the achievable accuracy. In particular, the uncertainty in crystallographic coordinates yields an uncertainty of about 20% in the calculated couplings. Because quantum-chemical corrections are smaller than 20% in most biologically relevant cases, their considerable computational cost is rarely justified. We therefore recommend the electrostatic TrEsp method across the entire range of molecular separations and orientations because its cost is minimal and it generally agrees with quantum-chemical calculations to better than the geometric uncertainty. Understanding these uncertainties can guard against striving for unrealistic precision; at the same time, detailed benchmarks can allow important qualitative questions-which do not depend on the precise values of the simulation parameters-to be addressed with greater confidence about the conclusions.

  6. Quantum biological channel modeling and capacity calculation.

    PubMed

    Djordjevic, Ivan B

    2012-12-10

    Quantum mechanics has an important role in photosynthesis, magnetoreception, and evolution. There were many attempts in an effort to explain the structure of genetic code and transfer of information from DNA to protein by using the concepts of quantum mechanics. The existing biological quantum channel models are not sufficiently general to incorporate all relevant contributions responsible for imperfect protein synthesis. Moreover, the problem of determination of quantum biological channel capacity is still an open problem. To solve these problems, we construct the operator-sum representation of biological channel based on codon basekets (basis vectors), and determine the quantum channel model suitable for study of the quantum biological channel capacity and beyond. The transcription process, DNA point mutations, insertions, deletions, and translation are interpreted as the quantum noise processes. The various types of quantum errors are classified into several broad categories: (i) storage errors that occur in DNA itself as it represents an imperfect storage of genetic information, (ii) replication errors introduced during DNA replication process, (iii) transcription errors introduced during DNA to mRNA transcription, and (iv) translation errors introduced during the translation process. By using this model, we determine the biological quantum channel capacity and compare it against corresponding classical biological channel capacity. We demonstrate that the quantum biological channel capacity is higher than the classical one, for a coherent quantum channel model, suggesting that quantum effects have an important role in biological systems. The proposed model is of crucial importance towards future study of quantum DNA error correction, developing quantum mechanical model of aging, developing the quantum mechanical models for tumors/cancer, and study of intracellular dynamics in general.

  7. Quantum Biological Channel Modeling and Capacity Calculation

    PubMed Central

    Djordjevic, Ivan B.

    2012-01-01

    Quantum mechanics has an important role in photosynthesis, magnetoreception, and evolution. There were many attempts in an effort to explain the structure of genetic code and transfer of information from DNA to protein by using the concepts of quantum mechanics. The existing biological quantum channel models are not sufficiently general to incorporate all relevant contributions responsible for imperfect protein synthesis. Moreover, the problem of determination of quantum biological channel capacity is still an open problem. To solve these problems, we construct the operator-sum representation of biological channel based on codon basekets (basis vectors), and determine the quantum channel model suitable for study of the quantum biological channel capacity and beyond. The transcription process, DNA point mutations, insertions, deletions, and translation are interpreted as the quantum noise processes. The various types of quantum errors are classified into several broad categories: (i) storage errors that occur in DNA itself as it represents an imperfect storage of genetic information, (ii) replication errors introduced during DNA replication process, (iii) transcription errors introduced during DNA to mRNA transcription, and (iv) translation errors introduced during the translation process. By using this model, we determine the biological quantum channel capacity and compare it against corresponding classical biological channel capacity. We demonstrate that the quantum biological channel capacity is higher than the classical one, for a coherent quantum channel model, suggesting that quantum effects have an important role in biological systems. The proposed model is of crucial importance towards future study of quantum DNA error correction, developing quantum mechanical model of aging, developing the quantum mechanical models for tumors/cancer, and study of intracellular dynamics in general. PMID:25371271

  8. Optimized coordinates in vibrational coupled cluster calculations

    SciTech Connect

    Thomsen, Bo; Christiansen, Ove; Yagi, Kiyoshi

    2014-04-21

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

  9. Coupled-channel scattering in 1 + 1 dimensional lattice model

    SciTech Connect

    Guo, Peng

    2013-07-01

    Based on the Lippmann-Schwinger equation approach, a generalized Lüscher’s formula in 1+1 dimensions for two particles scattering in both the elastic and coupled-channel cases in moving frames is derived. A two-dimensional coupled-channel scattering lattice model is presented, which represents a two-coupled-channel resonant scattering scalars system. The Monte Carlo simulation is performed on finite lattices and in various moving frames. The two-dimensional generalized Lüscher’s formula is used to extract the scattering amplitudes for the coupled-channel system from the discrete finite-volume spectrum.

  10. Calculation of the axion magnetoelectric coupling

    NASA Astrophysics Data System (ADS)

    Coh, Sinisa; Vanderbilt, David; Malashevich, Andrei; Souza, Ivo

    2010-03-01

    Recently it was shown [X.-L. Qi et al., PRB 78, 195424 (2008); A.M. Essin et al., PRL 102, 146805 (2009)] that there exists a purely isotropic (``axionic'') component θ to the magnetoelectric coupling (MEC). Furthermore, this θ arises only from the electron orbital motion, and in strong Z2 topological insulators it is unusually large and equals exactly half a quantum (θ=π). Experimental observation of this large MEC would require some peculiar breaking of the time-reversal (T) symmetry at the surfaces, but θ might be observed in normal insulators that have T already broken in the bulk. Since there are by now several examples of strong Z2 topological insulators having θ=π, we believe there is no strong reason why θ should necessarily be small in a normal insulator with broken T. For this reason, we have used density-functional theory to calculate θ in various materials. We first consider Cr2O3, a widely studied magnetoelectric material, but we find θ to be very small there. We attribute this to a weak spin-orbit effect in Cr (and to the fact that even a strong spin-orbit effect by itself does not guarantee a large θ). To calculate θ we express it in terms of well localized Wannier functions to ensure smoothness of the gauge and also to allow for decomposition of contributions to θ coming from various electronic bands. The calculation of θ for BiFeO3 and other materials is currently ongoing.

  11. Transfer/Breakup Channel Couplings in Sub-barrier Fusion Reactions

    NASA Astrophysics Data System (ADS)

    Beck, C.

    2013-03-01

    With the recent availability of state-of-the-art radioactive ion beams, there has been a renew interest in the investigation of nuclear reactions with heavy ions near the Coulomb barrier. The role of inelastic and transfer channel couplings in fusion reactions induced by stable heavy ions can be revisited. Detailed analysis of recent experimental fusion cross sections by using standard coupled-channel calculations is first discussed. Multi-neutron transfer effects are introduced in the fusion process below the Coulomb barrier by analyzing 32S+90,96Zr as benchmark reactions. The enhancement of fusion cross sections for 32S+96Zr is well reproduced at sub-barrier energies by NTFus code calculations including the coupling of the neutrontransfer channels following the Zagrebaev semi-classical model. Similar effects for 40Ca+90Zr and 40Ca+96Zr fusion excitation functions are found. The breakup coupling in both the elastic scattering and in the fusion process induced by weakly bound stable projectiles is also shown to be crucial. In the second part of this work, full coupled-channel calculations of the fusion excitation functions are performed by using the breakup coupling for the more neutron-rich reaction and for the more weakly bound projectiles. We clearly demonstrate that Continuum-Discretized Coupled-Channel calculations are capable to reproduce the fusion enhancement from the breakup coupling in 6Li+59Co.

  12. Coupled-Channel Effects in Collisions Between Heavy Ions Near the Coulomb Barrier

    NASA Astrophysics Data System (ADS)

    Beck, C.

    With the recent availability of state-of-the-art heavy-ion stable and radioactive beams, there has been a renew interest in the investigation of nuclear reactions with heavy ions. I first present the role of inelastic and transfer channel couplings in fusion reactions induced by stable heavy ions. Analysis of experimental fusion cross sections by using standard coupled-channel calculations is discussed. The role of multi-neutron transfer is investigated in the fusion process below the Coulomb barrier by analyzing ^{32}S+{^{90,96}}{Zr} as benchmark reactions. The enhancement of fusion cross sections for ^{32}S+{^{96}}{Zr} is well reproduced at sub-barrier energies by NTFus code calculations including the coupling of the neutron-transfer channels following the Zagrebaev semi-classical model. Similar effects for ^{40}{Ca}+{^{90}}{Zr} and ^{40}{Ca}+ {^{96}}{Zr} fusion excitation functions are found. The breakup coupling in both the elastic scattering and in the fusion process induced by weakly bound stable projectiles is also shown to be crucial. In this lecture, full coupled-channel calculations of the fusion excitation functions are performed by using the breakup coupling for the more neutron-rich reaction and for the more weakly bound projectiles. I clearly demonstrate that Continuum-Discretized Coupled-Channel calculations are capable to reproduce the fusion enhancement from the breakup coupling in 6{Li}+{^{59}}{Co}.

  13. Fully converged iterative method for coupled channel problems

    NASA Astrophysics Data System (ADS)

    Shu, Di; Simbotin, I.; Côté, R.

    2016-05-01

    We implemented a numerical method using a distorted-wave perturbative approach for coupled-channel scattering problems. Our new method provides a way to avoid costly computations for the propagation of the full solutions in coupled-channel problems to large distances for slowly vanishing couplings. Thus, instead of dealing with large matrices, all computations are performed in a channel by channel fashion. The distorted wavefunction for each channel is initialized with the appropriate solution (which includes the diagonal element of the coupling potential matrix). We then solve single-channel inhomogeneous radial equations which contain the (off-diagonal) couplings as a perturbation, and we iterate until desired accuracy is achieved. We tested for stability by continuing to iterate even after convergence has been achieved, e.g., for a total of 75 iterations. Partial support from the US Army Research Office (ARO-MURI W911NF-14-1-0378), and from NSF (Grant No. PHY-1415560).

  14. Calculated Coupling Efficiency Between an Elliptical-Core Optical Fiber and a Silicon Oxynitride Rib Waveguide [Corrected Copy

    NASA Technical Reports Server (NTRS)

    Tuma, Margaret L.; Beheim, Glenn

    1995-01-01

    The effective-index method and Marcatili's technique were utilized independently to calculate the electric field profile of a rib channel waveguide. Using the electric field profile calculated from each method, the theoretical coupling efficiency between a single-mode optical fiber and a rib waveguide was calculated using the overlap integral. Perfect alignment was assumed and the coupling efficiency calculated. The coupling efficiency calculation was then repeated for a range of transverse offsets.

  15. Calculating Conductance of Ion Channels - Linking Molecular Dynamics and Electrophysiology

    NASA Astrophysics Data System (ADS)

    Wilson, Michael A.; Pohorille, Andrew

    2015-01-01

    Molecular dynamics computer simulations were combined with an electrodiffusion model to compute conduction of simple ion channels. The main assumptions of the model, and the consistency, efficiency and accuracy of the ion current calculations were tested and found satisfactory. The calculated current-voltage dependence for a synthetic peptide channel is in agreement with experiments and correctly captures the asymmetry of current with respect to applied field.

  16. High-Fidelity Coupled Monte-Carlo/Thermal-Hydraulics Calculations

    NASA Astrophysics Data System (ADS)

    Ivanov, Aleksandar; Sanchez, Victor; Ivanov, Kostadin

    2014-06-01

    Monte Carlo methods have been used as reference reactor physics calculation tools worldwide. The advance in computer technology allows the calculation of detailed flux distributions in both space and energy. In most of the cases however, those calculations are done under the assumption of homogeneous material density and temperature distributions. The aim of this work is to develop a consistent methodology for providing realistic three-dimensional thermal-hydraulic distributions by coupling the in-house developed sub-channel code SUBCHANFLOW with the standard Monte-Carlo transport code MCNP. In addition to the innovative technique of on-the fly material definition, a flux-based weight-window technique has been introduced to improve both the magnitude and the distribution of the relative errors. Finally, a coupled code system for the simulation of steady-state reactor physics problems has been developed. Besides the problem of effective feedback data interchange between the codes, the treatment of temperature dependence of the continuous energy nuclear data has been investigated.

  17. Coupled-Channels Study of α-DECAY Rates for Deformed Nuclei

    NASA Astrophysics Data System (ADS)

    Ni, Dongdong; Ren, Zhongzhou

    The generalized density-dependent cluster model is devoted to calculate α-decay half-lives of spherical and deformed nuclei. The multi-channel cluster model is developed to describe the α-decay fine structure in heavy deformed nuclei, including half-lives and branching ratios. After a brief review of these two models, special cases of the α-decay fine structure are presented. Calculations are separately performed using the coupled-channels and WKB approaches.

  18. Nonscaling calculation of the effective diffusion coefficient in periodic channels

    NASA Astrophysics Data System (ADS)

    Kalinay, Pavol

    2017-01-01

    An algorithm calculating the effective diffusion coefficient D(x) in 2D and 3D channels with periodically varying cross section along the longitudinal coordinate x is presented. Unlike other methods, it is not based on scaling of the transverse coordinates, or the smallness of the width of the channel. The result is expressed as an integral of specific contributions to D(x) coming from the positions neighboring to x. The method avoids the hierarchy of derivatives of the channel shaping function h(x), so it is also suitable for the channels with cusps or jumps of their width. The method describes correctly D(x) in wide channels, giving the expected behavior in the limit of infinite width (no confinement).

  19. Electrostatic calculations for an ion channel. I. Energy and potential profiles and interactions between ions.

    PubMed Central

    Levitt, D G

    1978-01-01

    The electrostatic energy profile of one, two, or three ions in an aqueous channel through a lipid membrane is calculated. It is shown that the previous solution to this problem (based on the assumption that the channel is infinitely long) significantly overestimates the electrostatic energy barrier. For example, for a 3-A radius pore, the energy is 16 kT for the infinite channel and 6.7 kT for an ion in the center of a channel 25 A long. The energy as a function of the position of the ion is also determined. With this energy profile, the rate of crossing the membrane (using the Nernst-Planck equation) was estimated and found to be compatible with the maximum conductance observed for the gramicidin A channel. The total electrostatic energy (as a function of position) required to place two or three ions in the channel is also calculated. The electrostatic interaction is small for two ions at opposite ends of the channel and large for any positioning of the three ions. Finally, the gradient through the channel of an applied potential is calculated. The solution to these problems is based on solving an equivalent problem in which an appropriate surface charge is placed on the boundary between the lipid and aqueous regions. The magnitude of the surface charge is obtained from the numerical solution for a system of coupled integral equations. PMID:656542

  20. Bit error probability of trellis-coded quadrature amplitude modulation over cross-coupled multidimensional channels

    NASA Astrophysics Data System (ADS)

    Kavehrad, Mohsen; Sundberg, Carl-Erik W.

    1987-04-01

    Average bit error probabilities for M-ary quadrature amplitude modulation (MQAM) systems are evaluated using a truncated union bound to calculate an approximate upper bound on the average bit error probability. Coded BPSK and QSPK are studied in a dual-polarized channel with and without an interference compensator. Trellis-coded MQAM signals are also examined. A new technique, dual-channel polarization hopping, which provides diversity gains when applied to coded cross-coupled channels is proposed. Average bit error probabilities for convolutionally coded QAM schemes in cross-coupled interference channels are derived. It is concluded that trellis-coded QAM schemes give larger coding gains in cross-coupled interference channels than in Gaussian noise and the choice of optimum code for the trellis-coded QAM scheme depends on the expected interference level.

  1. Coupled channel approach to the structure of the X(3872)

    SciTech Connect

    Ortega, P. G.; Segovia, J.; Entem, D. R.; Fernandez, F.

    2010-03-01

    We have performed a coupled channel calculation of the 1{sup ++} cc sector including qq and DD* molecular configurations. The calculation was done within a constituent quark model which successfully describes the meson spectrum, in particular, the cc 1{sup --} sector. Two and four-quark configurations are coupled using the {sup 3}P{sub 0} model. The elusive X(3872) meson appears as a new state with a high probability for the DD* molecular component. When the mass difference between neutral and charged states is included, a large D{sup 0}D*{sup 0} component is found which dominates for large distances and breaks isospin symmetry in the physical state. The original cc(2{sup 3}P{sub 1}) state acquires a sizable DD* component and can be identified with the X(3940). We study the B{yields}K{pi}{sup +{pi}-}J/{psi} and B{yields}KD{sup 0}D*{sup 0} decays, finding a good agreement with Belle and BABAR experimental data.

  2. An effective field theory for coupled-channel scattering

    NASA Astrophysics Data System (ADS)

    Cohen, Thomas D.; Gelman, Boris A.; van Kolck, U.

    2004-05-01

    The problem of describing low-energy two-body scattering for systems with two open channels with different thresholds is addressed in the context of an effective field theory. In particular, the problem where the threshold is unnaturally small and the cross section at low energy is unnaturally large is considered. It is shown that the lowest-order point coupling associated with the mixing of the channels scales as Λ-2 rather than Λ-1 (the scaling of the same-channel coupling and the scaling in a single-channel case) where Λ is the ultraviolet cutoff. The renormalization of the theory at lowest order is given explicitly. The treatment of higher orders is straightforward. The potential implications for systems with deep open channels are discussed.

  3. Coupling a mechanosensitive channel with a vesicle under shear flow

    NASA Astrophysics Data System (ADS)

    Pak, On Shun; Young, Yuan Nan; Veerapaneni, Shravan; Stone, Howard

    2014-11-01

    Mechanosensitive channels enable cells to respond to their local environment. Continuum mechanical models have been proposed to describe how bilayer deformation induced by the transmembrane protein and the membrane tension influence the free energy of channel gating under static conditions. The dynamics of mechanosensitive channels under flow conditions however remains largely unexplored. Cells under flow display interesting features not observed under static environments. Here we present a model coupling a mechanosensitive channel with the dynamics of a vesicle under shear flow to investigate how the channel gating responds to hydrodynamic stress. The model could be used to investigate the release of signaling molecules, transport of ions or drugs across cell membranes under flow in biological systems, as well as the design and control of channel gating in synthetic cells.

  4. Amplitude death of coupled hair bundles with stochastic channel noise

    NASA Astrophysics Data System (ADS)

    Kim, Kyung-Joong; Ahn, Kang-Hun

    2014-04-01

    Hair cells conduct auditory transduction in vertebrates. In lower vertebrates such as frogs and turtles, due to the active mechanism in hair cells, hair bundles (stereocilia) can be spontaneously oscillating or quiescent. Recently an amplitude death phenomenon has been proposed [K.-H. Ahn, J. R. Soc. Interface, 10, 20130525 (2013)] as a mechanism for auditory transduction in frog hair-cell bundles, where sudden cessation of the oscillations arises due to the coupling between nonidentical hair bundles. The gating of the ion channel is intrinsically stochastic due to the stochastic nature of the configuration change of the channel. The strength of the noise due to the channel gating can be comparable to the thermal Brownian noise of hair bundles. Thus, we perform stochastic simulations of the elastically coupled hair bundles. In spite of stray noisy fluctuations due to its stochastic dynamics, our simulation shows the transition from collective oscillation to amplitude death as interbundle coupling strength increases. In its stochastic dynamics, the formation of the amplitude death state of coupled hair bundles can be seen as a sudden suppression of the displacement fluctuation of the hair bundles as the coupling strength increases. The enhancement of the signal-to-noise ratio through the amplitude death phenomenon is clearly seen in the stochastic dynamics. Our numerical results demonstrate that the multiple number of transduction channels per hair bundle is an important factor to the amplitude death phenomenon, because the phenomenon may disappear for a small number of transduction channels due to strong gating noise.

  5. Coupled Dynamics for Superfluid (4) {He} 4 He in a Channel

    NASA Astrophysics Data System (ADS)

    Khomenko, D.; Mishra, P.; Pomyalov, A.

    2017-06-01

    We study the coupled dynamics of normal and superfluid components of superfluid ^4{He} in a channel considering the counterflow turbulence with laminar normal component. In particular, we calculated profiles of the normal velocity, the mutual friction, the vortex line density and other flow properties and compared them to the case where the dynamic of the normal component is "frozen." We have found that the coupling between the normal and superfluid components leads to flattening of the normal velocity profile, increasingly more pronounced with temperature, as the mutual friction, and therefore, coupling becomes stronger. The commonly measured flow properties also change when the coupling between the two components is taken into account.

  6. Point kinetics calculations with fully coupled thermal fluids reactivity feedback

    SciTech Connect

    Zhang, H.; Zou, L.; Andrs, D.; Zhao, H.; Martineau, R.

    2013-07-01

    The point kinetics model has been widely used in the analysis of the transient behavior of a nuclear reactor. In the traditional nuclear reactor system safety analysis codes such as RELAP5, the reactivity feedback effects are calculated in a loosely coupled fashion through operator splitting approach. This paper discusses the point kinetics calculations with the fully coupled thermal fluids and fuel temperature feedback implemented into the RELAP-7 code currently being developed with the MOOSE framework. (authors)

  7. Dynamical Coupled-channels Effects on Pion Photoproduction

    SciTech Connect

    Julia-Diaz, B; Lee, T -S. H.; Matsuyama, A; Sato, T; Smith, L C

    2007-12-18

    The electromagnetic pion production reactions are investigated within the dynamical coupled-channels model developed in {\\bf Physics Reports, 439, 193 (2007)}. The meson-baryon channels included in this study are $\\gamma N$, $\\pi N$, $\\eta N$, and the $\\pi\\Delta$, $\\rho N$ and $\\sigma N$ resonant components of the $\\pi\\pi N$ channel. With the hadronic parameters of the model determined in a recent study of $\\pi N$ scattering, we show that the pion photoproduction data up to the second resonance region can be described to a very large extent by only adjusting the bare $\\gamma N \\rightarrow N^*$ helicity amplitudes, while the non-resonant electromagnetic couplings are taken from previous works. It is found that the coupled-channels effects can contribute about 10 - 20 $\\%$ of the production cross sections in the $\\Delta$ (1232) resonance region, and can drastically change the magnitude and shape of the cross sections in the second resonance region. The importance of the off-shell effects in a dynamical approach is also demonstrated. The meson cloud effects as well as the coupled-channels contributions to the $\\gamma N \\rightarrow N^*$ form factors are found to be mainly in the low $Q^2$ region. For the magnetic M1 $\\gamma N \\rightarrow \\Delta$ (1232) form factor, the results are close to that of the Sato-Lee Model. Necessary improvements to the model and future developments are discussed.

  8. Improving the calculation of magnetic coupling constants in MRPT methods.

    PubMed

    Spivak, Mariano; Angeli, Celestino; Calzado, Carmen J; de Graaf, Coen

    2014-09-05

    The magnetic coupling in transition metal compounds with more than one unpaired electron per magnetic center has been studied with multiconfigurational perturbation theory. The usual shortcomings of these methodologies (severe underestimation of the magnetic coupling) have been overcome by describing the Slater determinants with a set of molecular orbitals that maximally resemble the natural orbitals of a high-level multiconfigurational reference configuration interaction calculation. These orbitals have significant delocalization tails onto the bridging ligands and largely increase the coupling strengths in the perturbative calculation. Copyright © 2014 Wiley Periodicals, Inc.

  9. Progress on the Coupling Coil for the MICE Channel

    SciTech Connect

    Green, M.A.; Li, D.; Virostek, S.P.; Lau, W.; Witte, H.; Yang,S.Q.; Drumm, P.; Ivanyushenkov, Y.

    2005-05-08

    This report describes the progress on the coupling magnet for the international Muon Ionization Cooling Experiment (MICE). MICE consists of two cells of a SFOFO cooling channel that is similar to that studied in the level 2 study of a neutrino factory. The MICE RF coupling coil module (RFCC module) consists of a 1.56 m diameter superconducting solenoid, mounted around four cells of conventional 201.25 MHz closed RF cavities. This report discusses the progress that has been made on the superconducting coupling coil that is around the center of the RF coupling module. This report describes the process by which one would cool the coupling coil using a single small 4 K cooler. In addition, the coupling magnet power system and quench protection system are also described.

  10. Structural transitions in vertically and horizontally coupled parabolic channels of Wigner crystals

    NASA Astrophysics Data System (ADS)

    Galván-Moya, J. E.; Nelissen, K.; Peeters, F. M.

    2012-11-01

    Structural phase transitions in two vertically or horizontally coupled channels of strongly interacting particles are investigated. The particles are free to move in the x direction but are confined by a parabolic potential in the y direction. They interact with each other through a screened power-law potential (r-ne-r/λ). In vertically coupled systems, the channels are stacked above each other in the direction perpendicular to the (x,y) plane, while in horizontally coupled systems both channels are aligned in the confinement direction. Using Monte Carlo (MC) simulations we obtain the ground-state configurations and the structural transitions as a function of the linear particle density and the separation between the channels. At zero temperature, the vertically coupled system exhibits a rich phase diagram with continuous and discontinuous transitions. On the other hand, the horizontally coupled system exhibits only a very limited number of phase transitions due to its symmetry. Further, we calculated the normal modes for the Wigner crystals in both cases. From MC simulations, we found that in the case of vertically coupled systems, the zigzag transition is only possible for low densities. A Ginzburg-Landau theory for the zigzag transition is presented, which predicts correctly the behavior of this transition from which we interpret the structural phase transition of the Wigner crystal through the reduction of the Brillouin zone.

  11. Mechanism of electromechanical coupling in voltage-gated potassium channels.

    PubMed

    Blunck, Rikard; Batulan, Zarah

    2012-01-01

    Voltage-gated ion channels play a central role in the generation of action potentials in the nervous system. They are selective for one type of ion - sodium, calcium, or potassium. Voltage-gated ion channels are composed of a central pore that allows ions to pass through the membrane and four peripheral voltage sensing domains that respond to changes in the membrane potential. Upon depolarization, voltage sensors in voltage-gated potassium channels (Kv) undergo conformational changes driven by positive charges in the S4 segment and aided by pairwise electrostatic interactions with the surrounding voltage sensor. Structure-function relations of Kv channels have been investigated in detail, and the resulting models on the movement of the voltage sensors now converge to a consensus; the S4 segment undergoes a combined movement of rotation, tilt, and vertical displacement in order to bring 3-4e(+) each through the electric field focused in this region. Nevertheless, the mechanism by which the voltage sensor movement leads to pore opening, the electromechanical coupling, is still not fully understood. Thus, recently, electromechanical coupling in different Kv channels has been investigated with a multitude of techniques including electrophysiology, 3D crystal structures, fluorescence spectroscopy, and molecular dynamics simulations. Evidently, the S4-S5 linker, the covalent link between the voltage sensor and pore, plays a crucial role. The linker transfers the energy from the voltage sensor movement to the pore domain via an interaction with the S6 C-termini, which are pulled open during gating. In addition, other contact regions have been proposed. This review aims to provide (i) an in-depth comparison of the molecular mechanisms of electromechanical coupling in different Kv channels; (ii) insight as to how the voltage sensor and pore domain influence one another; and (iii) theoretical predictions on the movement of the cytosolic face of the Kv channels during gating.

  12. Mechanism of Electromechanical Coupling in Voltage-Gated Potassium Channels

    PubMed Central

    Blunck, Rikard; Batulan, Zarah

    2012-01-01

    Voltage-gated ion channels play a central role in the generation of action potentials in the nervous system. They are selective for one type of ion – sodium, calcium, or potassium. Voltage-gated ion channels are composed of a central pore that allows ions to pass through the membrane and four peripheral voltage sensing domains that respond to changes in the membrane potential. Upon depolarization, voltage sensors in voltage-gated potassium channels (Kv) undergo conformational changes driven by positive charges in the S4 segment and aided by pairwise electrostatic interactions with the surrounding voltage sensor. Structure-function relations of Kv channels have been investigated in detail, and the resulting models on the movement of the voltage sensors now converge to a consensus; the S4 segment undergoes a combined movement of rotation, tilt, and vertical displacement in order to bring 3–4e+ each through the electric field focused in this region. Nevertheless, the mechanism by which the voltage sensor movement leads to pore opening, the electromechanical coupling, is still not fully understood. Thus, recently, electromechanical coupling in different Kv channels has been investigated with a multitude of techniques including electrophysiology, 3D crystal structures, fluorescence spectroscopy, and molecular dynamics simulations. Evidently, the S4–S5 linker, the covalent link between the voltage sensor and pore, plays a crucial role. The linker transfers the energy from the voltage sensor movement to the pore domain via an interaction with the S6 C-termini, which are pulled open during gating. In addition, other contact regions have been proposed. This review aims to provide (i) an in-depth comparison of the molecular mechanisms of electromechanical coupling in different Kv channels; (ii) insight as to how the voltage sensor and pore domain influence one another; and (iii) theoretical predictions on the movement of the cytosolic face of the Kv channels during

  13. Coupling Algorithms for Calculating Sensitivities of Population Balances

    SciTech Connect

    Man, P. L. W.; Kraft, M.; Norris, J. R.

    2008-09-01

    We introduce a new class of stochastic algorithms for calculating parametric derivatives of the solution of the space-homogeneous Smoluchowski's coagulation equation. Currently, it is very difficult to produce low variance estimates of these derivatives in reasonable amounts of computational time through the use of stochastic methods. These new algorithms consider a central difference estimator of the parametric derivative which is calculated by evaluating the coagulation equation at two different parameter values simultaneously, and causing variance reduction by maximising the covariance between these. The two different coupling strategies ('Single' and 'Double') have been compared to the case when there is no coupling ('Independent'). Both coupling algorithms converge and the Double coupling is the most 'efficient' algorithm. For the numerical example chosen we obtain a factor of about 100 in efficiency in the best case (small system evolution time and small parameter perturbation)

  14. Calculation of accurate channel spacing of an AWG optical demultiplexer applying proportional method

    NASA Astrophysics Data System (ADS)

    Seyringer, D.; Hodzic, E.

    2015-06-01

    We present the proportional method to correct the channel spacing between the transmitted output channels of an AWG. The developed proportional method was applied to 64-channel, 50 GHz AWG and the achieved results confirm very good correlation between designed channel spacing (50 GHz) and the channel spacing calculated from simulated AWG transmission characteristics.

  15. Potential infrared relaxation channels calculated for CO2 clathrate hydrates

    NASA Astrophysics Data System (ADS)

    Lakhlifi, Azzedine; Dahoo, Pierre Richard; Chassefière, Eric

    2017-01-01

    The infrared bar-spectrum of a single carbon dioxide molecule encapsulated in nano-cage clathrate hydrate is determined using the LD (Lakhlifi-Dahoo) extended site inclusion model successfully applied to analyze the spectra of CO2 isotopologues isolated in rare gas matrices. Trapping is energetically more favorable in clathrate structure of type sI than sII. CO2 exhibits hindered orientational motions (librational motions) around its equilibrium configurations in the small and large nano-cages. The orientation transitions are weak, and the spectra are purely vibrational. In the static field inside the cage, the doubly degenerate bending mode ν2 is blue shifted and split. From the scheme of the calculated energy levels for the different degrees of freedom, which is comparable to that of CO2 in rare gas matrices, it is conjectured that infrared excited CO2 will rather relax radiatively. Non-radiative channels can be analyzed by binary collision model.

  16. Navier-Stokes calculations with a coupled strongly implicit method. II Spline deferred-corrector solutions

    NASA Technical Reports Server (NTRS)

    Rubin, S. G.; Khosla, P. K.

    1980-01-01

    The coupled strongly implicit (CSIP) method described previously is combined with a deferred-corrector spline solver for the vorticity-stream function form of the Navier-Stokes equations. Solutions for cavity, channel and cylinder flows are obtained with the fourth-order spline 4 procedure. The strongly coupled spline corrector method converges as rapidly as the finite difference calculations and also allows for arbitrary large time increments for the Reynolds numbers considered (equal to or less than 1000). In some cases fourth-order smoothing or filtering is required in order to suppress high frequency oscillations.

  17. Coupled-channel systems in a finite volume

    NASA Astrophysics Data System (ADS)

    Davoudi, Zohreh

    2012-10-01

    In this talk I will motivate studies of two-body coupled-channel systems in a finite volume in connection with the ultimate goal of studying nuclear reactions, as well as hadronic resonances, directly from lattice QCD. I will discuss how one can determine phase shifts and mixing parameters of coupled-channels such as that of pipi-KK isosinglet system from the energy spectrum in a finite volume with periodic boundary conditions. From the energy quantization condition, the volume dependence of electroweak matrix elements of two-hadron processes can also be extracted. This is necessary for studying weak processes that mix isosinglet-isotriplet two-nucleon states, e.g. proton-proton fusion. I will show how one can obtain such transition amplitudes from lattice QCD using the formalism developed.

  18. Eikonal solutions to optical model coupled-channel equations

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Khandelwal, Govind S.; Maung, Khin M.; Townsend, Lawrence W.; Wilson, John W.

    1988-01-01

    Methods of solution are presented for the Eikonal form of the nucleus-nucleus coupled-channel scattering amplitudes. Analytic solutions are obtained for the second-order optical potential for elastic scattering. A numerical comparison is made between the first and second order optical model solutions for elastic and inelastic scattering of H-1 and He-4 on C-12. The effects of bound-state excitations on total and reaction cross sections are also estimated.

  19. How large is the contribution of excited mesons in coupled-channel effects?

    NASA Astrophysics Data System (ADS)

    Lu, Yu; Anwar, Muhammad Naeem; Zou, Bing-Song

    2017-02-01

    We study the excited B mesons' contributions to the coupled-channel effects under the framework of the 3P0 model for the bottomonium. Contrary to what has been widely accepted, the contributions of P wave B mesons are generally the largest, and to some extent, this result is independent of the potential parameters. We also push the calculation beyond B (1 P ) and carefully analyze the contributions of B (2 S ). A form factor is a key ingredient to suppress the contributions of B (2 S ) for low lying bottomonia. However, this suppression mechanism is not efficient for highly excited bottomonia, such as ϒ (5 S ) and ϒ (6 S ) . We give explanations why this difficulty happens to the 3P0 model and suggest analyzing the flux-tube breaking model for the full calculation of coupled-channel effects.

  20. Mutual coupling, channel model, and BER for curvilinear antenna arrays

    NASA Astrophysics Data System (ADS)

    Huang, Zhiyong

    This dissertation introduces a wireless communications system with an adaptive beam-former and investigates its performance with different antenna arrays. Mutual coupling, real antenna elements and channel models are included to examine the system performance. In a beamforming system, mutual coupling (MC) among the elements can significantly degrade the system performance. However, MC effects can be compensated if an accurate model of mutual coupling is available. A mutual coupling matrix model is utilized to compensate mutual coupling in the beamforming of a uniform circular array (UCA). Its performance is compared with other models in uplink and downlink beamforming scenarios. In addition, the predictions are compared with measurements and verified with results from full-wave simulations. In order to accurately investigate the minimum mean-square-error (MSE) of an adaptive array in MC, two different noise models, the environmental and the receiver noise, are modeled. The minimum MSEs with and without data domain MC compensation are analytically compared. The influence of mutual coupling on the convergence is also examined. In addition, the weight compensation method is proposed to attain the desired array pattern. Adaptive arrays with different geometries are implemented with the minimum MSE algorithm in the wireless communications system to combat interference at the same frequency. The bit-error-rate (BER) of systems with UCA, uniform rectangular array (URA) and UCA with center element are investigated in additive white Gaussian noise plus well-separated signals or random direction signals scenarios. The output SINR of an adaptive array with multiple interferers is analytically examined. The influence of the adaptive algorithm convergence on the BER is investigated. The UCA is then investigated in a narrowband Rician fading channel. The channel model is built and the space correlations are examined. The influence of the number of signal paths, number of the

  1. Towards an optical potential for rare-earths through coupled channels

    SciTech Connect

    Nobre, G. P. A.; Herman, M.; Palumbo, A.; Hoblit, S.; Brown, D.; Dietrich, F. S.

    2014-11-11

    The coupled-channel theory is a natural way of treating nonelastic channels, in particular those arising from collective excitations, defined by nuclear deformations. Proper treatment of such excitations is often essential to the accurate description of reaction experimental data. Previous works have applied different models to specific nuclei with the purpose of determining angular-integrated cross sections. In this work, we present an extensive study of the effects of collective couplings and nuclear deformations on integrated cross sections as well as on angular distributions in a consistent manner for neutron-induced reactions on nuclei in the rare-earth region. This specific subset of the nuclide chart was chosen precisely because of a clear static deformation pattern. We analyze the convergence of the coupled-channel calculations regarding the number of states being explicitly coupled. Inspired by the work done by Dietrich et al., a model for deforming the spherical Koning-Delaroche optical potential as function of quadrupole and hexadecupole deformations is also proposed. We demonstrate that the obtained results of calculations for total, elastic and inelastic cross sections, as well as elastic and inelastic angular distributions correspond to a remarkably good agreement with experimental data for scattering energies above around a few MeV.

  2. Calculation of axion-photon-photon coupling in string theory

    NASA Astrophysics Data System (ADS)

    Kim, Jihn E.

    2014-07-01

    The axion search experiments invite a plausible estimation of the axion-photon-photon coupling constant cbaraγγ in string models with phenomenologically acceptable visible sectors. We present the calculation of cbaraγγ with an exact Peccei-Quinn symmetry. In the Huh-Kim-Kyae Z12-I orbifold compactification, we obtain cbaraγγ =1123/388, and the low-temperature axion search experiments will probe the QCD corrected coupling, caγγ ≃cbaraγγ - 1.98 ≃ 0.91.

  3. Coupled-rearrangement-channel Gaussian-basis variational method for trinucleon bound states

    NASA Astrophysics Data System (ADS)

    Kameyama, H.; Kamimura, M.; Fukushima, Y.

    1989-08-01

    To the 3H and 3He ground states, we apply the coupled-rearrangement-channel variational method with Gaussian-basis functions which has successfully been used in precise calculations of muonic molecular ions, Coulomb-interacting three-body systems. The trinucleon wave function is decomposed into angular-momentum-projected three-body channels as done in the Faddeev equations method, but the interaction is fully incorporated with no partial-wave decomposition. The radial part of the channel amplitudes is expanded with a sufficient number of Gaussian-tail basis functions of the Jacobi coordinates. The Gaussian ranges are taken to be geometrical progressions which run from very short ranges through large enough ones. This ab initio variational approach is found to describe accurately both the short-range correlations and the asymptotic behavior. The Argonne V14 potential is used as an example of realistic two-nucleon interactions; for 3He, the Coulomb potential is included nonperturbatively. The calculation reproduces precisely the results of the Faddeev calculations for 3H and 3He for binding energy, probabilities of the S, S', P, and D states, and the S- and D-wave asymptotic normalization constants. Convergence of the present results is seen at a much smaller number of the three-body channels than in the Faddeev calculations. This is because the interaction is truncated in the angular momentum space in the Faddeev calculations but the full interaction is taken in the present method.

  4. Coupling of individual quantum emitters to channel plasmons

    PubMed Central

    Bermúdez-Ureña, Esteban; Gonzalez-Ballestero, Carlos; Geiselmann, Michael; Marty, Renaud; Radko, Ilya P.; Holmgaard, Tobias; Alaverdyan, Yury; Moreno, Esteban; García-Vidal, Francisco J.; Bozhevolnyi, Sergey I.; Quidant, Romain

    2015-01-01

    Efficient light-matter interaction lies at the heart of many emerging technologies that seek on-chip integration of solid-state photonic systems. Plasmonic waveguides, which guide the radiation in the form of strongly confined surface plasmon-polariton modes, represent a promising solution to manipulate single photons in coplanar architectures with unprecedented small footprints. Here we demonstrate coupling of the emission from a single quantum emitter to the channel plasmon polaritons supported by a V-groove plasmonic waveguide. Extensive theoretical simulations enable us to determine the position and orientation of the quantum emitter for optimum coupling. Concomitantly with these predictions, we demonstrate experimentally that 42% of a single nitrogen-vacancy centre emission efficiently couples into the supported modes of the V-groove. This work paves the way towards practical realization of efficient and long distance transfer of energy for integrated solid-state quantum systems. PMID:26249363

  5. Quench Protection for the MICE Cooling Channel Coupling Magnet

    SciTech Connect

    Guo, Xing Long; Xu, Feng Yu; Wang, Li; Green, Michael A.; Pan, Heng; Wu, Hong; Liu, X.K.; Jia, Lin Xiang; Amm, Kathleen

    2008-08-02

    This paper describes the passive quench protection system selected for the muon ionization cooling experiment (MICE) cooling channel coupling magnet. The MICE coupling magnet will employ two methods of quench protection simultaneously. The most important method of quench protection in the coupling magnet is the subdivision of the coil. Cold diodes and resistors are put across the subdivisions to reduce both the voltage to ground and the hot-spot temperature. The second method of quench protection is quench-back from the mandrel, which speeds up the spread of the normal region within the coils. Combining quench back with coil subdivision will reduce the hot spot temperature further. This paper explores the effect on the quench process of the number of coil sub-divisions, the quench propagation velocity within the magnet, and the shunt resistance.

  6. Calculation of anharmonic couplings and THz linewidths in crystalline PETN

    SciTech Connect

    Pereverzev, Andrey Sewell, Thomas D. Thompson, Donald L.

    2014-03-14

    We have developed a method for calculating the cubic anharmonic couplings in molecular crystals for normal modes with the zero wave vector in the framework of classical mechanics, and have applied it, combined with perturbation theory, to obtain the linewidths of all infrared absorption lines of crystalline pentaerythritol tetranitrate in the terahertz region (<100 cm{sup −1}). Contributions of the up- and down-conversion processes to the total linewidth were calculated. The computed linewidths are in qualitative agreement with experimental data and the results of molecular dynamics simulations. Quantum corrections to the linewidths in the terahertz region are shown to be negligible.

  7. Calculation of anharmonic couplings and THz linewidths in crystalline PETN

    NASA Astrophysics Data System (ADS)

    Pereverzev, Andrey; Sewell, Thomas D.; Thompson, Donald L.

    2014-03-01

    We have developed a method for calculating the cubic anharmonic couplings in molecular crystals for normal modes with the zero wave vector in the framework of classical mechanics, and have applied it, combined with perturbation theory, to obtain the linewidths of all infrared absorption lines of crystalline pentaerythritol tetranitrate in the terahertz region (<100 cm-1). Contributions of the up- and down-conversion processes to the total linewidth were calculated. The computed linewidths are in qualitative agreement with experimental data and the results of molecular dynamics simulations. Quantum corrections to the linewidths in the terahertz region are shown to be negligible.

  8. Calculation of anharmonic couplings and THz linewidths in crystalline PETN.

    PubMed

    Pereverzev, Andrey; Sewell, Thomas D; Thompson, Donald L

    2014-03-14

    We have developed a method for calculating the cubic anharmonic couplings in molecular crystals for normal modes with the zero wave vector in the framework of classical mechanics, and have applied it, combined with perturbation theory, to obtain the linewidths of all infrared absorption lines of crystalline pentaerythritol tetranitrate in the terahertz region (<100 cm(-1)). Contributions of the up- and down-conversion processes to the total linewidth were calculated. The computed linewidths are in qualitative agreement with experimental data and the results of molecular dynamics simulations. Quantum corrections to the linewidths in the terahertz region are shown to be negligible.

  9. Beam envelope calculations in general linear coupled lattices

    SciTech Connect

    Chung, Moses; Qin, Hong; Groening, Lars; Xiao, Chen; Davidson, Ronald C.

    2015-01-15

    The envelope equations and Twiss parameters (β and α) provide important bases for uncoupled linear beam dynamics. For sophisticated beam manipulations, however, coupling elements between two transverse planes are intentionally introduced. The recently developed generalized Courant-Snyder theory offers an effective way of describing the linear beam dynamics in such coupled systems with a remarkably similar mathematical structure to the original Courant-Snyder theory. In this work, we present numerical solutions to the symmetrized matrix envelope equation for β which removes the gauge freedom in the matrix envelope equation for w. Furthermore, we construct the transfer and beam matrices in terms of the generalized Twiss parameters, which enables calculation of the beam envelopes in arbitrary linear coupled systems.

  10. First Calculation of Hyperon Axial Couplings from Lattice QCD

    SciTech Connect

    Huey-Wen Lin; Konstantinos Orginos

    2007-12-06

    In this work, we report the first lattice calculation of the hyperon axial couplings, using the 2+1-flavor MILC configurations and domain-wall fermion valence quarks. Both the $\\Sigma$ and $\\Xi$ axial couplings are for the first time done in lattice QCD, and we find the numbers with greater precision than previous chiral perturbation theory and large-$N_c$ theory estimate: $g_{\\Sigma\\Sigma} = 0.450(21)_{\\rm stat}(22)_{\\rm syst}$ and $g_{\\Xi\\Xi} = -0.277(15)_{\\rm stat}(16)_{\\rm syst}$. As a side product, we also determine the low-energy chiral parameters $D$ and $F$ extracted from these coupling constants: $D=0.715(6)_{\\rm stat}(6)_{\\rm syst}$ and $F=0.453(5)_{\\rm stat}(5)_{\\rm syst}$.

  11. Finite difference time domain calculations of antenna mutual coupling

    NASA Technical Reports Server (NTRS)

    Luebbers, Raymond J.; Kunz, Karl S.

    1991-01-01

    The Finite Difference Time Domain (FDTD) technique was applied to a wide variety of electromagnetic analysis problems, including shielding and scattering. However, the method has not been exclusively applied to antennas. Here, calculations of self and mutual admittances between wire antennas are made using FDTD and compared with results obtained during the method of moments. The agreement is quite good, indicating the possibilities for FDTD application to antenna impedance and coupling.

  12. Finite difference time domain calculations of antenna mutual coupling

    NASA Technical Reports Server (NTRS)

    Luebbers, Raymond J.; Kunz, Karl S.

    1991-01-01

    The Finite Difference Time Domain (FDTD) technique has been applied to a wide variety of electromagnetic analysis problems, including shielding and scattering. However, the method has not been extensively applied to antennas. In this short paper calculations of self and mutual admittances between wire antennas are made using FDTD and compared with results obtained using the Method of Moments. The agreement is quite good, indicating the possibilities for FDTD application to antenna impedance and coupling.

  13. Calculation of NMR Spin-Spin Coupling Constants in Strychnine.

    PubMed

    Helgaker, Trygve; Jaszuński, Michał; Świder, Paweł

    2016-11-18

    We compare the NMR indirect nuclear spin-spin coupling constants in strychnine calculated using density functional theory (DFT) with the semiempirical relativistic force field (RFF) method of Kutateladze and Mukhina (KM) (J. Org. Chem. 2015, 80, 10838-10848). DFT values significantly more accurate than those obtained by KM for their comparison with RFF values can be obtained, at a lower cost, by an appropriate selection of basis set.

  14. Calculations on seismic coupling of underground explosions in salt

    SciTech Connect

    Heusinkveld, M.E.

    1981-01-20

    This report details the results of a theoretical study of seismic coupling and decoupling of underground explosions in a salt medium. A series of chemical and nuclear explosions was carried out years ago in salt domes for the Cowboy and the Dribble programs to provide experimental data on seismic coupling for both tamped explosions and explosions in cavities. The Cowboy program consisted of a series of chemical explosions, and the Dribble program consisted of the tamped nuclear Salmon event, the Sterling nuclear event in the Salmon cavity, and an associated site calibration effort. This report presents the results of extensive computer calculations, which are in satisfactory agreement with the experimental data. The calculations were extended to give general results on seismic coupling in salt. The measure of seismic coupling for most of this work was the residual reduced displacement potential (residual RDP). The decoupling associated with a shot in a cavity was expressed as the ratio of the resulting residual RDP to that of an equal-sized tamped shot.

  15. Structural basis for the coupling between activation and inactivation gates in K(+) channels.

    PubMed

    Cuello, Luis G; Jogini, Vishwanath; Cortes, D Marien; Pan, Albert C; Gagnon, Dominique G; Dalmas, Olivier; Cordero-Morales, Julio F; Chakrapani, Sudha; Roux, Benoît; Perozo, Eduardo

    2010-07-08

    The coupled interplay between activation and inactivation gating is a functional hallmark of K(+) channels. This coupling has been experimentally demonstrated through ion interaction effects and cysteine accessibility, and is associated with a well defined boundary of energetically coupled residues. The structure of the K(+) channel KcsA in its fully open conformation, in addition to four other partial channel openings, richly illustrates the structural basis of activation-inactivation gating. Here, we identify the mechanistic principles by which movements on the inner bundle gate trigger conformational changes at the selectivity filter, leading to the non-conductive C-type inactivated state. Analysis of a series of KcsA open structures suggests that, as a consequence of the hinge-bending and rotation of the TM2 helix, the aromatic ring of Phe 103 tilts towards residues Thr 74 and Thr 75 in the pore-helix and towards Ile 100 in the neighbouring subunit. This allows the network of hydrogen bonds among residues Trp 67, Glu 71 and Asp 80 to destabilize the selectivity filter, allowing entry to its non-conductive conformation. Mutations at position 103 have a size-dependent effect on gating kinetics: small side-chain substitutions F103A and F103C severely impair inactivation kinetics, whereas larger side chains such as F103W have more subtle effects. This suggests that the allosteric coupling between the inner helical bundle and the selectivity filter might rely on straightforward mechanical deformation propagated through a network of steric contacts. Average interactions calculated from molecular dynamics simulations show favourable open-state interaction-energies between Phe 103 and the surrounding residues. We probed similar interactions in the Shaker K(+) channel where inactivation was impaired in the mutant I470A. We propose that side-chain rearrangements at position 103 mechanically couple activation and inactivation in KcsA and a variety of other K(+) channels.

  16. Quantum coupled-channels model of nuclear fusion with a semiclassical consideration of neutron rearrangement

    NASA Astrophysics Data System (ADS)

    Karpov, A. V.; Rachkov, V. A.; Samarin, V. V.

    2015-12-01

    Background: Significant enhancement of sub-barrier fusion cross sections owing to neutron transfer with positive Q values was observed in many combinations of colliding nuclei. This degree of freedom has not yet been included into the rigorous quantum coupled-channels (QCC) approach. However, the empirical coupled-channels model with neutron rearrangement [Zagrebaev, Phys. Rev. C 67, 061601 (2003), 10.1103/PhysRevC.67.061601] has already been successfully used in several papers to reproduce and predict cross sections for sub-barrier fusion reactions of stable nuclei. Purpose: The objective of this study is to combine the QCC approach and the empirical model to account for additional channels of neutron rearrangement. Method: Coupling of relative motion to collective degrees of freedom (rotation of nuclei and/or their surface vibrations) are taken into account within the QCC approach. The probability of transfer of x neutrons with a given Q value is estimated semiclassically. Results: The proposed new model was successfully tested on a few combinations of fusing nuclei 40Ca+90,96Zr, 32S+96,90, and 60,64Ni+100Mo. The calculated fusion cross sections and barrier distribution functions agree well with experimental data. Conclusions: The model developed in this work confirms all the conclusions previously made within the empirical coupled-channels model with neutron rearrangement [see Rachkov et al., Phys. Rev. C 90, 014614 (2014), 10.1103/PhysRevC.90.014614]. Moreover, it has an advantage of a more reliable microscopic account for the coupling between relative motion and the collective degrees of freedom. The proposed model can also be used to reproduce the structure of the barrier distribution function. This is a step forward to a complete solution of the long-term problem of accounting for neutron transfer channels in the QCC model.

  17. Expressions for Form Factors for Inelastic Scattering and Charge Exchange in Plane-Wave, Distorted-Wave, and Coupled-Channels Reaction Formalisms

    SciTech Connect

    Dietrich, F S

    2006-09-25

    This document is intended to facilitate calculation of inelastic scattering and charge-exchange cross sections in a variety of reaction models, including the plane-wave and distorted-wave approximations and the full coupled-channels treatments. Expressions are given for the coupling potentials between the relevant channels in both coordinate and momentum space. In particular, it is expected that the plane-wave calculations should be useful as a check on the correctness of coupled-channels calculations. The Fourier transform methods used to calculate the plane-wave approximation cross sections are also intended to be used to generate the transition potentials for coupled-channels codes, using a folding model with local effective interactions. Specific expressions are given for calculating transition densities for the folding model in the random phase approximation (RPA).

  18. Coupled channel analysis of molecule picture of Pc(4380 )

    NASA Astrophysics Data System (ADS)

    Shimizu, Yuki; Suenaga, Daiki; Harada, Masayasu

    2016-06-01

    We construct a potential obtained by one-pion exchange for the coupled channel Σc*D ¯ -ΣcD¯ * and solve the coupled Schrödinger equations to determine the binding energy. We find that there exists one or two bound states with the binding energy of several MeV below the threshold of Σc* and D ¯, dominantly made from a Σc* baryon and a D ¯ meson, with the size of about 1.5 fm for a wide parameter region. We also study the pentaquark states including a b quark and/or an anti-b quark. We show that there exist pentaquarks including c b ¯, b c ¯ , and b b ¯, all of which lie at about 10 MeV below the corresponding threshold and have size of about 1.5 fm.

  19. Methodology for calculating shear stress in a meandering channel

    Treesearch

    Kyung-Seop Sin

    2010-01-01

    Shear stress in meandering channels is the key parameter to predict bank erosion and bend migration. A representative study reach of the Rio Grande River in central New Mexico has been modeled in the Hydraulics Laboratory at CSU. To determine the shear stress distribution in a meandering channel, the large scale (1:12) physical modeling study was conducted in the...

  20. Relativistic close-coupling calculations for photoionization and recombination of Ne-like Fe XVII

    NASA Astrophysics Data System (ADS)

    Zhang, Hong Lin; Nahar, Sultana N.; Pradhan, Anil K.

    2001-09-01

    Relativistic and channel coupling effects in photoionization and unified electronic recombination of Fe XVII are demonstrated with an extensive 60-level close-coupling calculation using the Breit-Pauli R-matrix method. A multiconfiguration eigenfunction expansion up to the n=3 levels of the core ion Fe XVIII is employed with five spectroscopic configurations 2s22p5,2s2p6,2s22p4 3s,3p,3d, and a number of correlation configurations. The unified e+ion recombination calculations for e+Fe XVIII-->Fe XVII include both the nonresonant and resonant recombination (``radiative'' and ``dielectronic recombination''-RR and DR). Photoionization and e+ion recombination calculations are carried out for the total and the level-specific cross sections, including the ground and several hundred excited bound levels of Fe XVII (up to fine-structure levels with n=10). The low-energy and the high-energy cross sections are compared from (i) a three-level calculation including only the 2s2p5 (2Po1/2,3/2) and 2s2p6 (2S1/2) levels of Fe XVIII, and (ii) the first 60-level calculation with Δn>0 coupled channels. Strong channel coupling effects are demonstrated throughout the energy ranges considered, in particular via giant photoexcitation-of-core (PEC) resonances due to L-M shell dipole transition arrays 2p5-->2p4 3s,3d in Fe XIII that enhance effective cross sections by orders of magnitude. Comparison is made with previous theoretical and experimental works on photoionization and recombination that considered the relatively small low-energy region (i), and the weaker Δn=0 couplings. While the simpler three-level results describe the near-threshold photoionization and recombination, they are inadequate for practical applications that also require the higher-energy cross sections for modeling ionization balance of Fe XVII in laboratory and astrophysical plasmas. The present 60-level results should provide reasonably complete and accurate datasets for both photoionization and e

  1. High-accuracy coupled cluster calculations of atomic properties

    NASA Astrophysics Data System (ADS)

    Borschevsky, A.; Yakobi, H.; Eliav, E.; Kaldor, U.

    2015-01-01

    The four-component Fock-space coupled cluster and intermediate Hamiltonian methods are implemented to evaluate atomic properties. The latter include the spectra of nobelium and lawrencium (elements 102 and 103) in the range 20000-30000 cm-1, the polarizabilities of elements 112-114 and 118, required for estimating their adsorption enthalpies on surfaces used to separate them in accelerators, and the nuclear quadrupole moments of some heavy atoms. The calculations on superheavy elements are supported by the very good agreement with experiment obtained for the lighter homologues.

  2. High-accuracy coupled cluster calculations of atomic properties

    SciTech Connect

    Borschevsky, A.; Yakobi, H.; Eliav, E.; Kaldor, U.

    2015-01-22

    The four-component Fock-space coupled cluster and intermediate Hamiltonian methods are implemented to evaluate atomic properties. The latter include the spectra of nobelium and lawrencium (elements 102 and 103) in the range 20000-30000 cm{sup −1}, the polarizabilities of elements 112-114 and 118, required for estimating their adsorption enthalpies on surfaces used to separate them in accelerators, and the nuclear quadrupole moments of some heavy atoms. The calculations on superheavy elements are supported by the very good agreement with experiment obtained for the lighter homologues.

  3. Black hole thermodynamics from calculations in strongly coupled gauge theory.

    PubMed

    Kabat, D; Lifschytz, G; Lowe, D A

    2001-02-19

    We develop an approximation scheme for the quantum mechanics of N D0-branes at finite temperature in the 't Hooft large- N limit. The entropy of the quantum mechanics calculated using this approximation agrees well with the Bekenstein-Hawking entropy of a ten-dimensional nonextremal black hole with 0-brane charge. This result is in accordance with the duality conjectured by Itzhaki, Maldacena, Sonnenschein, and Yankielowicz [Phys. Rev. D 58, 046004 (1998)]. Our approximation scheme provides a model for the density matrix which describes a black hole in the strongly coupled quantum mechanics.

  4. Formalism for determining pseudostates in modified close-coupling calculations

    NASA Astrophysics Data System (ADS)

    Coulter, Philip W.

    1980-08-01

    A formalism for determining pseudostate wave functions for use in modified close-coupling calculations is presented. Applications to low-energy electron-hydrogen scattering are discussed. The 2p― pseudostate proposed by Damburg and Karule is analyzed using this formalism and a reason for its success is given which is independent of the fact that it fully accounts for the ground-state polarizability of atomic hydrogen. The analysis suggests, in agreement with expectations of Burke and Schey and others, that short-range correlations are more important than long-range polarization in determining the best form of the pseudostates.

  5. P -wave coupled channel effects in electron-positron annihilation

    NASA Astrophysics Data System (ADS)

    Du, Meng-Lin; Meißner, Ulf-G.; Wang, Qian

    2016-11-01

    P -wave coupled channel effects arising from the D D ¯, D D¯ *+c .c . , and D*D¯* thresholds in e+e- annihilations are systematically studied. We provide an exploratory study by solving the Lippmann-Schwinger equation with short-ranged contact potentials obtained in the heavy quark limit. These contact potentials can be extracted from the P -wave interactions in the e+e- annihilations, and then be employed to investigate possible isosinglet P -wave hadronic molecules. In particular, such an investigation may provide information about exotic candidates with quantum numbers JPC=1-+ . In the mass region of the D D ¯, D D¯ *+c .c . , and D*D¯* thresholds, there are two quark model bare states, i.e. the ψ (3770 ) and ψ (4040 ), which are assigned as (13D1) and (31S1) states, respectively. By an overall fit of the cross sections of e+e-→D D ¯, D D¯ *+c .c . , D*D¯*, we determine the physical coupling constants to each channel and extract the pole positions of the ψ (3770 ) and ψ (4040 ). The deviation of the ratios from that in the heavy quark spin symmetry (HQSS) limit reflects the HQSS breaking effect due to the mass splitting between the D and the D*. Besides the two poles, we also find a pole a few MeV above the D D¯ *+c .c . threshold which can be related to the so-called G (3900 ) observed earlier by BABAR and Belle. This scenario can be further scrutinized by measuring the angular distribution in the D*D¯* channel with high luminosity experiments.

  6. Barrier distribution functions for the system 6Li+64Ni and the effect of channel coupling

    NASA Astrophysics Data System (ADS)

    Shaikh, Md. Moin; Roy, Subinit; Rajbanshi, S.; Pradhan, M. K.; Mukherjee, A.; Basu, P.; Pal, S.; Nanal, V.; Pillay, R. G.; Shrivastava, A.

    2015-03-01

    Background: The barrier distribution function is an important observable in low-energy nucleus-nucleus collisions because it carries the distinct signature of the channel-coupling effect that is dominant at low energies. It can be derived from the fusion excitation function as well as from the back-angle quasi-elastic excitation function. The barrier distribution functions derived from the two complimentary measurements, in general, appear to peak at an energy close to the Coulomb barrier for strongly bound systems. But for weakly bound projectiles, like 6Li, a relative shift is observed between the distributions. Purpose: The present work investigates the barrier distribution functions from fusion as well as from the back-angle quasi-elastic excitation function for the 6Li+64Ni system. The purpose is to look for the existence of a shift, if any, between the two measured distribution functions, as reported for 6Li collision with heavy targets. A detailed coupled-channel calculation to probe the behavior of the distribution functions and their relative shift has been attempted. Measurement: A simultaneous measurement of fusion and back-angle quasi-elastic excitation functions for the system 6Li+64Ni was performed. The fusion excitation function was measured for the energy range of 11 to 28 MeV while the quasi-elastic excitation function measurement extended from 11 to 20 MeV. The barrier distribution functions were subsequently extracted from both the excitation functions and compared. Results: A small shift of around 450 keV peak to peak is observed between the barrier distribution functions derived from the complementary measurements. Detailed coupled channel and coupled reaction channel calculations reproduced both the excitation functions and barrier distributions. The shift of about 550 keV resulted from the model predictions corroborate the experimentally observed value for 6Li+64Ni system. Conclusions: The coupling to inelastic channels are found to be

  7. Parallelization strategy for large-scale vibronic coupling calculations.

    PubMed

    Rabidoux, Scott M; Eijkhout, Victor; Stanton, John F

    2014-12-26

    The vibronic coupling model of Köppel, Domcke, and Cederbaum is a powerful means to understand, predict, and analyze electronic spectra of molecules, especially those that exhibit phenomena that involve breakdown of the Born-Oppenheimer approximation. In this work, we describe a new parallel algorithm for carrying out such calculations. The algorithm is conceptually founded upon a "stencil" representation of the required computational steps, which motivates an efficient strategy for coarse-grained parallelization. The equations involved in the direct-CI type diagonalization of the model Hamiltonian are presented, the parallelization strategy is discussed in detail, and the method is illustrated by calculations involving direct-product basis sets with as many as 17 vibrational modes and 130 billion basis functions.

  8. Dissociation of homonuclear diatomic halogens via multireference coupled cluster calculations

    NASA Astrophysics Data System (ADS)

    Chattopadhyay, Sudip; Sinha Mahapatra, Uttam; Chaudhuri, Rajat K.

    2014-10-01

    We have computed the potential energy surfaces (PESs) of F2, Cl2, Br2, and I2 using the size-extensive state specific multireference coupled cluster (SS-MRCC) method. The MR character of the system considered here at large distances and the presence of low-lying intruder states are known to be the major causes of incorrect or inaccurate predictions of the PES. The SS-MRCC theory is tailored to treat degeneracies of varying extent while bypassing the intruder problem. The quality of the computed PES has been gauged by computing spectroscopic constants. The calculated properties show a good agreement with available experimental data and the errors in the calculated molecular properties compare favourably with the most elaborate current-generation calculations of the literature. The accuracy of the computed PES of F2 is such that it has been proved to calculate the vibrational spectrum of the 22 levels with a minimum and maximum absolute deviation of 2 and 57 cm-1, respectively, from the experimental values. The highly satisfactory performance of the SS-MRCC method, vis-a-vis the other sophisticated methods, in describing the vibrational levels is noticeable for one of the more difficult systems such as F2 clearly indicates that the present method is reliable in studying the vibrational energy levels.

  9. Quantum mechanical methods for calculating proton tunneling splittings and proton-coupled electron transfer vibronic couplings

    NASA Astrophysics Data System (ADS)

    Skone, Jonathan H.

    Development of quantum mechanical methods for the calculation of proton tunneling splittings and proton-coupled electron transfer vibronic couplings is presented in this thesis. The fundamental physical principles underlying proton transfer in the electronically adiabatic and nonadiabatic limits are illustrated by applying the quantum mechanical methods we developed to chemical systems exemplary of the electronically adiabatic and nonadiabatic proton-tunneling regimes. Overall, this thesis emphasizes the need for quantum chemical methods that avoid the adiabatic separation of the quantum proton and electron, are computationally tractable, and treat all quantum particles three-dimensionally. The nuclear-electronic orbital nonorthogonal configuration interaction (NEO-NOCI) approach is presented for calculating proton tunneling splittings and vibronic couplings. The NEO approach is a molecular orbital based method that avoids the Born-Oppenheimer separation of the select protons and electrons, thereby making methods developed within this scheme, such as NEO-NOCI, applicable to electronically nonadiabatic proton transfer. In the two-state NEO-NOCI approach, the ground and excited state delocalized nuclear-electronic wavefunctions are expressed as linear combinations of two nonorthogonal localized nuclear-electronic wavefunctions obtained at the NEO-Hartree-Fock level. The advantages of the NEO-NOCI approach are the removal of the adiabatic separation between the electrons and the quantum nuclei, the computational efficiency, the potential for systematic improvement by enhancing the basis sets and number of configurations, and the applicability to a broad range of chemical systems. The tunneling splitting is determined by the energy difference between these two delocalized vibronic states. The proton tunneling splittings calculated with the NEO-NOCI approach for the [He-H-He]+ model system with a range of fixed He-He distances are shown to be in excellent agreement with

  10. Radial Moment Calculations of Coupled Electron-Photon Beams

    SciTech Connect

    FRANKE,BRIAN C.; LARSEN,EDWARD W.

    2000-07-19

    The authors consider the steady-state transport of normally incident pencil beams of radiation in slabs of material. A method has been developed for determining the exact radial moments of 3-D beams of radiation as a function of depth into the slab, by solving systems of 1-D transport equations. They implement these radial moment equations in the ONEBFP discrete ordinates code and simulate energy-dependent, coupled electron-photon beams using CEPXS-generated cross sections. Modified P{sub N} synthetic acceleration is employed to speed up the iterative convergence of the 1-D charged particle calculations. For high-energy photon beams, a hybrid Monte Carlo/discrete ordinates method is examined. They demonstrate the efficiency of the calculations and make comparisons with 3-D Monte Carlo calculations. Thus, by solving 1-D transport equations, they obtain realistic multidimensional information concerning the broadening of electron-photon beams. This information is relevant to fields such as industrial radiography, medical imaging, radiation oncology, particle accelerators, and lasers.

  11. Strongly coupled turbulent gas-particle flows in vertical channels

    NASA Astrophysics Data System (ADS)

    Fox, Rodney O.; Capecelatro, Jesse; Desjardins, Olivier

    2015-11-01

    Eulerian-Lagrangian (EL) simulations of strongly coupled (high mass loading) gas-particle flows in vertical channels are performed with the purpose of exploring the fundamental physics of fully developed, wall-bounded multiphase turbulence. An adaptive spatial filter is developed that accurately decomposes the total granular energy of the particles into correlated and uncorrelated components at each location in the wall-normal direction of the flow. In this manner, Reynolds- and phase-averaged (PA) two-phase turbulence statistics up to second order are reported for both phases and for three values of the PA mean fluid velocity. As expected due to the high mass loading, in all cases the turbulence production due to mean drag dominates production due to mean shear. A multiphase LRR-IP Reynolds-stress turbulence model is developed to predict the turbulent flow statistics as a function of the wall-normal distance. Using a correlation for the vertical drift velocity developed from the EL data, the turbulence model predictions agree satisfactorily with all of one-point EL statistics for the vertical channel flows, as well as for the homogeneous cluster-induced turbulence (CIT) statistics reported previously. Funded by U.S. National Science Foundation (CBET-1437865).

  12. Transmembrane allosteric coupling of the gates in a potassium channel

    PubMed Central

    Wylie, Benjamin J.; Bhate, Manasi P.; McDermott, Ann E.

    2014-01-01

    It has been hypothesized that transmembrane allostery is the basis for inactivation of the potassium channel KcsA: opening the intracellular gate is spontaneously followed by ion expulsion at the extracellular selectivity filter. This suggests a corollary: following ion expulsion at neutral pH, a spontaneous global conformation change of the transmembrane helices, similar to the motion involved in opening, is expected. Consequently, both the low potassium state and the low pH state of the system could provide useful models for the inactivated state. Unique NMR studies of full-length KcsA in hydrated bilayers provide strong evidence for such a mutual coupling across the bilayer: namely, upon removing ambient potassium ions, changes are seen in the NMR shifts of carboxylates E118 and E120 in the pH gate in the hinges of the inner transmembrane helix (98–103), and in the selectivity filter, all of which resemble changes seen upon acid-induced opening and inhibition and suggest that ion release can trigger channel helix opening. PMID:24344306

  13. Transmembrane allosteric coupling of the gates in a potassium channel.

    PubMed

    Wylie, Benjamin J; Bhate, Manasi P; McDermott, Ann E

    2014-01-07

    It has been hypothesized that transmembrane allostery is the basis for inactivation of the potassium channel KcsA: opening the intracellular gate is spontaneously followed by ion expulsion at the extracellular selectivity filter. This suggests a corollary: following ion expulsion at neutral pH, a spontaneous global conformation change of the transmembrane helices, similar to the motion involved in opening, is expected. Consequently, both the low potassium state and the low pH state of the system could provide useful models for the inactivated state. Unique NMR studies of full-length KcsA in hydrated bilayers provide strong evidence for such a mutual coupling across the bilayer: namely, upon removing ambient potassium ions, changes are seen in the NMR shifts of carboxylates E118 and E120 in the pH gate in the hinges of the inner transmembrane helix (98-103), and in the selectivity filter, all of which resemble changes seen upon acid-induced opening and inhibition and suggest that ion release can trigger channel helix opening.

  14. Methodology for calculating shear stress in a meandering channel

    Treesearch

    Kyung-Seop Sin; Christopher I. Thornton; Amanda L. Cox; Steven R. Abt

    2012-01-01

    Natural channels never stop changing their geomorphic characteristics. Natural alluvial streams are similar to living creatures because they generate water flow, develop point bars, alter bed profile, scour the bed, erode the bank, and cause other phenomena in the stream system. The geomorphic changes in a natural system lead to a wide array of research worldwide,...

  15. Calculating bed load transport in steep boulder bed channels

    NASA Astrophysics Data System (ADS)

    Yager, E. M.; Kirchner, J. W.; Dietrich, W. E.

    2007-07-01

    Steep, rough channels occupy a large fraction of the total channel length in mountainous regions. Most sediment mobilized on hillslopes must pass through these streams before reaching lower-gradient channels. Steep channels have wide grain size distributions that are composed of finer, more mobile sediment and large, rarely mobile grains. The large grains can bear a significant portion of the total shear stress and thereby reduce the stress available to move the finer sediment. Conventional bed load transport equations often overpredict the sediment flux in steep channels by several orders of magnitude. We hypothesize that sediment transport equations overpredict the sediment flux because they do not (1) account for the stress borne by rarely mobile grains, (2) differentiate between highly and rarely mobile sediment, and (3) account for the limited availability of mobile sediment. Here we modify a conventional bed load transport equation to include these three effects. We use measurements of the flow, bed properties, and sediment flux in a small, steep flume to test this equation. We supply gravel at a constant rate through fields of regularly spaced immobile spheres and measure the bed coverage by gravel and sphere protrusion (the percent of the sphere that protrudes above the gravel deposit). For a given sphere spacing, the proportion of the bed covered by gravel increases and the sphere protrusion decreases with greater sediment supply. Thus bed coverage and immobile grain protrusion may serve as proxies for sediment availability in steep, rough streams. Unlike most transport equations that we tested, our modified bed load equation predicts sediment fluxes to within an order of magnitude of the measured values. Our results demonstrate that accurately predicting bed load transport in steep, rough streams may require accounting for the effects of local sediment availability (coverage by mobile sediment) and drag due to rarely mobile particles.

  16. Structural basis for the coupling between activation and inactivation gates in K+ channels

    PubMed Central

    Cuello, Luis G.; Jogini, Vishwanath; Cortes, D. Marien.; Pan, Albert C; Gagnon, Dominique G.; Dalmas, Olivier; Cordero-Morales, Julio F.; Chakrapani, Sudha; Roux, Benoit; Perozo, Eduardo

    2011-01-01

    The coupled interplay between activation and inactivation gating is a functional hallmark of K+ channels1,2. This coupling has been experimentally demonstrated from ion interaction effects3,4, cysteine accessibility1 and is associated with a well-defined boundary of energetically coupled residues2. The structure of KcsA in its fully open conformation, as well as four other partial openings, richly illustrates the structural basis of activation-inactivation gating5. Here, we have identified the mechanistic principles by which movements on the inner bundle gate trigger conformational changes at the selectivity filter, leading to the non-conductive C-type inactivated state. Analysis of a series of KcsA open structures suggests that as a consequence of the hinge bending and rotation of TM2, the aromatic ring of Phe103 tilts towards residues Thr74 and Thr75 in the pore helix as well as Ile100 in the neighboring subunit. This allows the network of hydrogen bonds among residues W67, E71, and D80 to destabilize the selectivity filter6,7, facilitating entry to its non-conductive conformation. Mutations at position 103, affect gating kinetics in a size-dependent way: small side chain substitutions F103A and F103C severely impair inactivation kinetics, while larger side chains (F103W) have more subtle effects. This suggests that the allosteric coupling between the inner helical bundle and the selectivity filter might rely on straightforward mechanical deformation propagated through a network of steric contacts. Average interactions calculated from molecular dynamics simulations show favourable open state interaction-energies between Phe103 and surrounding residues. Similar interactions were probed in the Shaker K-channel where inactivation was impaired in the mutant I470A. We propose that side chain rearrangements at position 103 mechanically couple activation and inactivation in KcsA and a variety of other K channels. PMID:20613845

  17. Combined quadrature amplitude modulation and convolutional codes for cross-coupled multidimensional channels

    NASA Astrophysics Data System (ADS)

    Kavehrad, M.; Sundberg, C.-E.; McLane, P. J.

    The performance of cross-coupled, M-ary Quadrature Amplitude Modulation (QAM) systems is determined when bandwidth efficient trellis codes are used to combat interference. Performance with and without compensation for cross-coupled interference is presented. It is found that simple trellis codes can maintain the error probability at an acceptable level for cross-coupling parameters that render uncoded systems unusable. Up to two dimensional trellis codes are considered for four dimensional QAM signals. The average probability of the most likely error events is calculated by using the method of moments. The results are applicable to any digital communication system using multidimensional quadrature amplitude modulation, e.g., voiceband modems and cross-polarized radio systems. In the paper the analysis is restricted to nondispersive cross-coupling models. In most cases the coding gain is larger than in the absence of cross-coupling interference. Specifically, it is found that simple trellis codes have coding gains of more than 5 dB in cross-coupling interference compared to 3 dB for a Gaussian channel. This is obtained for schemes compared at equal bandwidth.

  18. Relativistic R-Matrix Close-Coupling Calculations for Photoionization of Si-Like Ni XV

    NASA Astrophysics Data System (ADS)

    Singh, Jagjit; Jha, A. K. S.; Mohan, Man

    2010-02-01

    We present relativistic close-coupling photoionization calculations of Ni XV using the Breit-Pauli R-matrix method to obtain photoionization cross section of Ni XV from the ground state 3s 23p 2(3 P 0) and the lowest four 3s 23p 2 (3 P 1,2, 1 D 2, 1 S 0) excited states. A multiconfiguration eigenfunction expansion of the core Ni XVI is employed with configurations 3s 23p, 3s3p 2, 3s 23d, 3p 3, 3s3p3d, 3p 23d, 3s3d 2, 3p3d 2. We have included the lowest 40 target level states of Ni XVI in the photoionization calculations of Ni XV. Cross sections are determined by the Rydberg series of autoionizing resonances converging to several ionic states of Ni XVI. In our calculations, we have taken into account all the important physical effects such as exchange, channel coupling, and short-range correlation. Further, relativistic effects are incorporated by including mass correction, Darwin term, and spin-orbit interaction terms. The present calculations using the lowest 40 target levels of Ni XVI are presented for the first time and can be useful for modeling the ionization balance of Ni XV in laboratory and astrophysical plasmas.

  19. RELATIVISTIC R-MATRIX CLOSE-COUPLING CALCULATIONS FOR PHOTOIONIZATION OF Si-LIKE Ni XV

    SciTech Connect

    Singh, Jagjit; Jha, A. K. S.; Mohan, Man

    2010-02-01

    We present relativistic close-coupling photoionization calculations of Ni XV using the Breit-Pauli R-matrix method to obtain photoionization cross section of Ni XV from the ground state 3s {sup 2}3p {sup 2}({sup 3} P {sub 0}) and the lowest four 3s {sup 2}3p {sup 2} ({sup 3} P {sub 1,2}, {sup 1} D {sub 2}, {sup 1} S {sub 0}) excited states. A multiconfiguration eigenfunction expansion of the core Ni XVI is employed with configurations 3s {sup 2}3p, 3s3p {sup 2}, 3s {sup 2}3d, 3p {sup 3}, 3s3p3d, 3p {sup 2}3d, 3s3d {sup 2}, 3p3d {sup 2}. We have included the lowest 40 target level states of Ni XVI in the photoionization calculations of Ni XV. Cross sections are determined by the Rydberg series of autoionizing resonances converging to several ionic states of Ni XVI. In our calculations, we have taken into account all the important physical effects such as exchange, channel coupling, and short-range correlation. Further, relativistic effects are incorporated by including mass correction, Darwin term, and spin-orbit interaction terms. The present calculations using the lowest 40 target levels of Ni XVI are presented for the first time and can be useful for modeling the ionization balance of Ni XV in laboratory and astrophysical plasmas.

  20. Calculation of nuclear spin-spin couplings. VIII. Vicinal proton-proton coupling constants in ethane

    NASA Astrophysics Data System (ADS)

    Fukui, H.; Inomata, H.; Baba, T.; Miura, K.; Matsuda, H.

    1995-10-01

    Ab initio self-consistent-field (SCF) and electron correlation calculations have been carried out for the dihedral angle dependence of the vicinal proton-proton coupling constants, 3JHH, in ethane molecule. The four contributions to 3JHH, (JFC, JSD, JOP, and JOD) have been computed with the three different basis sets, [5s2p1d/2s1p], [5s3p1d/3s1p], and [7s4p2d/5s2p]. The Fermi contact (FC) contribution was largest and the spin-dipole (SD) contribution was smallest. The FC and orbital paramagnetic (OP) contributions showed large basis set dependence, but the SD and orbital diamagnetic (OD) contributions presented little basis set dependence. The calculated total SCF contribution to 3JHH was higher than the experimental coupling. Using the Møller-Plesset perturbation theory we have introduced electron correlation effects on the FC and OP terms. The correlation effects on the OP term was shown to be negligible. The second-order correlation in the FC term was very large and amounted to half of its SCF value in magnitude with opposite sign. However, the third-order correlation in the FC contribution was small. Unfortunately, the calculated 3JHH value including correlation corrections through third order was too small compared to the experimental one. The poor agreement between calculation and experiment is claimed to be due to higher than third-order correlations in the FC term.

  1. Quench Protection for the MICE Cooling Channel CouplingMagnet

    SciTech Connect

    Green, M.A.; Wang, L.; Guo, X.L.

    2007-11-20

    The MICE coupling coil is fabricated from Nb-Ti, which hashigh quench propagation velocities within the coil in all directionscompared to coils fabricated with other superconductors such as niobiumtin. The time for the MICE coupling coil to become fully normal throughnormal region propagation in the coil is shorter than the time needed fora safe quench (as defined by a hot-spot temperature that is less than 300K). A MICE coupling coil quench was simulated using a code written at theInstitute of Cryogenics and Superconductive Technology (ICST) at theHarbin Institute of Technology (HIT). This code simulates quench backfrom the mandrel as well as normal region propagation within the coil.The simulations included sub-division of the coil. Each sub-division hasa back to back diodes and resistor across the coil. Current flows in theresistor when there is enough voltage across the coil to cause current toflow through the diodes in the forward direction. The effects of thenumber of coil sub-divisions and the value of the resistor across thesub-division on the quench were calculated with and without quench back.Sub-division of the coupling coil reduces the peak voltage to ground, thelayer-to-layer voltage and the magnet hot-spot temperature. Quench backreduces the magnet hot-spot temperature, but the peak voltage to groundand layer-to-layer voltage are increased, because the magnet quenchesfaster. The resistance across the coil sub-division affects both thehot-spot temperature and the peak voltage to ground.

  2. A multi-channel, optically coupled spark gap monitor system

    SciTech Connect

    Gribble, R.; Barnes, G.A.

    1987-10-01

    A spark gap monitor system has been installed on FRX-C Large Source Modification, a theta pinch experiment which forms field-reversed configuration (FRC) compact toroids. The field reversing theta pinch produces a vacuum magnetic field of 10kG inside the single turn, 2-m-long straight 0.7-id coil by discharging in series two 50kV, 200..mu..F capacitor banks with a total of 140 2.8..mu..F capacitors each with a start spark-gap switch and a ''piggy-back'' crowbar spark-gap switch. Efficient operation of the bank requires information on the timing and function of each capacitor-spark gap unit. Diagnosing the capacitor-spark-gap unit load cable current (approximately 3kA per cable) is complicated by the fact that the ground return for the capacitor is of a relatively high impedance. Units that are allowed to prefire or postfire not only degrade the performance of the bank but will self destruct or destroy their neighbors. To provide this information without introducing high voltage transients into the data acquisition and control system as optically coupled, 140 channel gap monitor system has been installed. Simplicity and reliability were key requirements in the design of the system. A resistor made of thin wall stainless steel tubing replaces a short section of the braid on one load cable on each capacitor. The voltage developed across the resistor provides the current source to drive an LED. The relatively linear output from the LED is transmitted through approximately 30m of fiber optic cable to the FRX-C control room. The signal is received by a photo diode and simple amplifier circuit that feeds the signal into a 12 channel charge integrating ADC CAMAC module for processing by the computer. The information provided by this system informs the operator as to when and how each gap fired. 2 refs., 8 figs.

  3. Depth oscillations of electronuclear reaction yield initiated by relativistic planar channeled electrons: quantum versus classical calculations

    NASA Astrophysics Data System (ADS)

    Eikhorn, Yu. L.; Korotchenko, K. B.; Pivovarov, Yu. L.; Tukhfatullin, T. A.

    2017-07-01

    The first experiment on electronuclear reaction initated by axially channeled 700 MeV electrons in a Si crystal [1] revealed remarkable depth oscillations of reaction yield. The effect was satisfactory explained [2] by computer simulations using binary collisions model. In this work the oscillations effect is investigated for planar channeled electrons in a Si crystal using the new computer code BCM-1.0 which allows both classical and quantum calculations of channeled electrons flux density.

  4. Calculation of exchange interaction for modified Gaussian coupled quantum dots

    NASA Astrophysics Data System (ADS)

    Khordad, R.

    2017-08-01

    A system of two laterally coupled quantum dots with modified Gaussian potential has been considered. Each quantum dot has an electron under electric and magnetic field. The quantum dots have been considered as hydrogen-like atoms. The physical picture has translated into the Heisenberg spin Hamiltonian. The Schrödinger equation using finite element method has been numerically solved. The exchange energy factor has been calculated as a functions of electric field, magnetic field, and the separation distance between the centers of the dots ( d). According to the results, it is found that there is the transition from anti-ferromagnetic to ferromagnetic for constant electric field. Also, the transition occurs from ferromagnetic to anti-ferromagnetic for constant magnetic field (B>1 T). With decreasing the distance between the centers of the dots and increasing magnetic field, the transition occurs from anti-ferromagnetic to ferromagnetic. It is found that a switching of exchange energy factor is presented without canceling the interactions of the electric and magnetic fields on the system.

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

    PubMed

    Botschwina, Peter; Oswald, Rainer

    2010-09-16

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

  6. Calculation of exchange interaction for modified Gaussian coupled quantum dots

    NASA Astrophysics Data System (ADS)

    Khordad, R.

    2017-03-01

    A system of two laterally coupled quantum dots with modified Gaussian potential has been considered. Each quantum dot has an electron under electric and magnetic field. The quantum dots have been considered as hydrogen-like atoms. The physical picture has translated into the Heisenberg spin Hamiltonian. The Schrödinger equation using finite element method has been numerically solved. The exchange energy factor has been calculated as a functions of electric field, magnetic field, and the separation distance between the centers of the dots (d). According to the results, it is found that there is the transition from anti-ferromagnetic to ferromagnetic for constant electric field. Also, the transition occurs from ferromagnetic to anti-ferromagnetic for constant magnetic field (B>1 T). With decreasing the distance between the centers of the dots and increasing magnetic field, the transition occurs from anti-ferromagnetic to ferromagnetic. It is found that a switching of exchange energy factor is presented without canceling the interactions of the electric and magnetic fields on the system.

  7. Quantum Monte Carlo calculations of magnetic couplings in cuprates

    NASA Astrophysics Data System (ADS)

    Foyevtsova, Kateryna; Krogel, Jaron; Kim, Jeongnim; Reboredo, Fernando

    2014-03-01

    Spin excitations are generally believed to play a fundamental role in the mechanism of high temperature superconductivity in cuprates. However, accurate description of the cuprates' magnetic properties and, in particular, calculation of spin exchange couplings have been a long-standing challenge to the electronic structure theory. While the quantum-mechanically more rigorous cluster methods suffer from finite-size effects, the density functional theory approach, on the other hand, is ambiguous due to a rich variety of approximations to the exchange-correlation functional available which often give very different numbers for the spin exchange constants. For example, in some cuprates the theoretically predicted values of the nearest-neighbor superexchange range from 1 eV (local density approximation) to 0.05 eV (periodic unrestricted Hartree Fock) [C. de Graaf et al, PRB 63 014404 (2000)]. We compute spin exchange constants with the fixed-node diffusion Monte Carlo method (FN-DMC). In one-dimensional cuprates, we find that the FN-DMC computed nearest-neighbor spin superexchange is in an excellent agreement with experiment. This both demonstrates that FN-DMC is capable of describing properly the magnetism of strongly correlated oxides as well as positions this technique as the method of choice for theoretical parameterization of spin models. Research supported by the U.S. Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division.

  8. Coupled-cluster based basis sets for valence correlation calculations

    NASA Astrophysics Data System (ADS)

    Claudino, Daniel; Gargano, Ricardo; Bartlett, Rodney J.

    2016-03-01

    Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These new sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via (-3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within "chemical accuracy" of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.

  9. 2 π production in the Giessen coupled-channels model

    NASA Astrophysics Data System (ADS)

    Shklyar, V.; Lenske, H.; Mosel, U.

    2016-04-01

    The coupled-channels Lagrangian approach underlying the Giessen model (GiM) is extended to describe the π N →π N ,2 π N scattering in the resonance energy region. As a feasibility study we investigate single- and double-pion production up to the second resonance region. The 2 π N production has been significantly improved by using the isobar approximation with σ N and π Δ (1232 ) in the intermediate state. The three-body unitarity is maintained up to an interference pattern between the isobar subchannels. The scattering amplitudes are obtained as a solution of the Bethe-Salpeter equation in the K -matrix approximation. As a first application we perform a partial-wave analysis of the π N →π N ,π0π0N reactions in the Roper resonance region. We obtain Rσ N(1440 ) =27-9+4% and Rπ Δ(1440 ) =12-3+5% for the σ N and π Δ (1232 ) decay branching ratios of N*(1440 ) , respectively. The extracted π N inelasticities and reaction amplitudes are consistent with the results from other groups.

  10. Coupling coefficient calculation for GaSb-based quantum well distributed feedback lasers with laterally coupled gratings

    NASA Astrophysics Data System (ADS)

    Wang, Y. B.; Xu, Y.; Zhang, Y.; Song, G. F.; Chen, L. H.

    2012-12-01

    We calculated the coupling coefficient of different types of laterally coupled distributed feedback (LC-DFB) structures with coupled-wave theory and the two-dimensional semivectorial finite difference method. Effects neglected in previous studies such as other partial waves, the ohmic contact and metal contact layers are taken into account in this calculation. The LC-DFB structure with metal gratings is especially studied due to its advantage over index-coupled structures. The dependence of coupling coefficient on structure parameters is theoretically calculated such as grating order, ridge width, thickness of the residual cladding layer, grating depth and lateral proximity of gratings to the ridge waveguide. A complex-coupled GaSb-based 2 µm LC-DFB structure is optimized to achieve a high coupling coefficient of 14.5 cm-1.

  11. Quantum mechanical calculations of charge effects on gating the KcsA channel.

    PubMed

    Kariev, Alisher M; Znamenskiy, Vasiliy S; Green, Michael E

    2007-05-01

    A series of ab initio (density functional) calculations were carried out on side chains of a set of amino acids, plus water, from the (intracellular) gating region of the KcsA K(+) channel. Their atomic coordinates, except hydrogen, are known from X-ray structures [D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, R. MacKinnon, The structure of the potassium channel: molecular basis of K(+) conduction and selectivity, Science 280 (1998) 69-77; R. MacKinnon, S.L. Cohen, A. Kuo, A. Lee, B.T. Chait, Structural conservation in prokaryotic and eukaryotic potassium channels, Science 280 (1998) 106-109; Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, R. MacKinnon, The open pore conformation of potassium channels. Nature 417 (2001) 523-526], as are the coordinates of some water oxygen atoms. The 1k4c structure is used for the starting coordinates. Quantum mechanical optimization, in spite of the starting configuration, places the atoms in positions much closer to the 1j95, more tightly closed, configuration. This state shows four water molecules forming a "basket" under the Q119 side chains, blocking the channel. When a hydrated K(+) approaches this "basket", the optimized system shows a strong set of hydrogen bonds with the K(+) at defined positions, preventing further approach of the K(+) to the basket. This optimized structure with hydrated K(+) added shows an ice-like 12 molecule nanocrystal of water. If the water molecules exchange, unless they do it as a group, the channel will remain blocked. The "basket" itself appears to be very stable, although it is possible that the K(+) with its hydrating water molecules may be more mobile, capable of withdrawing from the gate. It is also not surprising that water essentially freezes, or forms a kind of glue, in a nanometer space; this agrees with experimental results on a rather different, but similarly sized (nm dimensions) system [K.B. Jinesh, J.W.M. Frenken, Capillary condensation in

  12. Static and dynamic polarizabilities of Na{sup -} within a variationally stable coupled-channel hyperspherical method

    SciTech Connect

    Masili, Mauro; Groote, J.J. de

    2004-11-01

    Using a model potential representation combined with a variationally stable method, we present a precise calculation of the electric dipole polarizabilities of the sodium negative ion (Na{sup -}). The effective two-electron eigensolutions for Na{sup -} are obtained from a hyperspherical coupled-channel calculation. This approach allows efficient error control and insight into the system's properties through one-dimensional potential curves. Our result of 1018.3 a.u. for the static dipole polarizability is in agreement with previous calculations and supports our results for the dynamic polarizability, which has scarcely been investigated hitherto.

  13. Exact and truncated Coriolis coupling calculations for the S(1D)+HD reaction employing the ground adiabatic electronic state.

    PubMed

    Yang, Huan; Han, Keli; Schatz, George C; Smith, Sean C; Hankel, Marlies

    2010-10-21

    We present exact quantum differential cross sections and exact and estimated integral cross sections and branching ratios for the title reaction. We employ a time-dependent wavepacket method as implemented in the DIFFREALWAVE code including all Coriolis couplings and also an adapted DIFFREALWAVE code where the helicity quantum number and with this the Coriolis couplings have been truncated. Our exact differential cross sections at 0.453 eV total energy, one of the experimental energies, show good agreement with the experimental results for one of the product channels. While the truncated calculation present a significant reduction in the computational effort needed they overestimate the exact integral cross sections.

  14. Fully Coupled Channel Approach to Doubly Strange s-Shell Hypernuclei

    SciTech Connect

    Nemura, H.; Shinmura, S.; Akaishi, Y.; Myint, Khin Swe

    2005-05-27

    We describe ab initio calculations of doubly strange, S=-2, s-shell hypernuclei ({sub {lambda}}{sub {lambda}}{sup 4}H, {sub {lambda}}{sub {lambda}}{sup 5}H, {sub {lambda}}{sub {lambda}}{sup 5}He, and {sub {lambda}}{sub {lambda}}{sup 6}He) as a first attempt to explore the few-body problem of the full-coupled channel scheme for these systems. The wave function includes {lambda}{lambda}, {lambda}{sigma}, N{xi}, and {sigma}{sigma} channels. Minnesota NN, D2{sup '} YN, and simulated YY potentials based on the Nijmegen hard-core model are used. Bound-state solutions of these systems are obtained. We find that a set of phenomenological B{sub 8}B{sub 8} interactions among the octet baryons in S=0,-1, and -2 sectors, which is consistent with all of the available experimental binding energies of S=0,-1, and -2 s-shell (hyper)nuclei, can predict a particle stable bound state of {sub {lambda}}{sub {lambda}}{sup 4}H. For {sub {lambda}}{sub {lambda}}{sup 5}H and {sub {lambda}}{sub {lambda}}{sup 5}He, {lambda}N-{sigma}N and {xi}N-{lambda}{sigma} potentials significantly affect the net {lambda}{lambda}-N{xi} coupling, and a large {xi} probability is obtained even for a weaker {lambda}{lambda}-N{xi} potential.

  15. Very low-energy nucleon-16O coupled-channel scattering: Results with a phenomenological vibrational model

    NASA Astrophysics Data System (ADS)

    Svenne, J. P.; Canton, L.; Amos, K.; Fraser, P. R.; Karataglidis, S.; Pisent, G.; van der Knijff, D.

    2017-03-01

    We employ a collective vibration coupled-channel model to describe the nucleon-16O cluster systems, obtaining low-excitation spectra for 17O and 17F. Bound and resonance states of the compound systems have been deduced, showing good agreement with experimental spectra. Low-energy scattering cross sections of neutrons and protons from 16O also have been calculated and the results compare well with available experimental data.

  16. TRPV1 channels are functionally coupled with BK(mSlo1) channels in rat dorsal root ganglion (DRG) neurons.

    PubMed

    Wu, Ying; Liu, Yongfeng; Hou, Panpan; Yan, Zonghe; Kong, Wenjuan; Liu, Beiying; Li, Xia; Yao, Jing; Zhang, Yuexuan; Qin, Feng; Ding, Jiuping

    2013-01-01

    The transient receptor potential vanilloid receptor 1 (TRPV1) channel is a nonselective cation channel activated by a variety of exogenous and endogenous physical and chemical stimuli, such as temperature (≥42 °C), capsaicin, a pungent compound in hot chili peppers, and allyl isothiocyanate. Large-conductance calcium- and voltage-activated potassium (BK) channels regulate the electric activities and neurotransmitter releases in excitable cells, responding to changes in membrane potentials and elevation of cytosolic calcium ions (Ca(2+)). However, it is unknown whether the TRPV1 channels are coupled with the BK channels. Using patch-clamp recording combined with an infrared laser device, we found that BK channels could be activated at 0 mV by a Ca(2+) influx through TRPV1 channels not the intracellular calcium stores in submilliseconds. The local calcium concentration around BK is estimated over 10 μM. The crosstalk could be affected by 10 mM BAPTA, whereas 5 mM EGTA was ineffectual. Fluorescence and co-immunoprecipitation experiments also showed that BK and TRPV1 were able to form a TRPV1-BK complex. Furthermore, we demonstrated that the TRPV1-BK coupling also occurs in dosal root ganglion (DRG) cells, which plays a critical physiological role in regulating the "pain" signal transduction pathway in the peripheral nervous system.

  17. TRPV1 Channels Are Functionally Coupled with BK(mSlo1) Channels in Rat Dorsal Root Ganglion (DRG) Neurons

    PubMed Central

    Yan, Zonghe; Kong, Wenjuan; Liu, Beiying; Li, Xia; Yao, Jing; Zhang, Yuexuan; Qin, Feng; Ding, Jiuping

    2013-01-01

    The transient receptor potential vanilloid receptor 1 (TRPV1) channel is a nonselective cation channel activated by a variety of exogenous and endogenous physical and chemical stimuli, such as temperature (≥42 °C), capsaicin, a pungent compound in hot chili peppers, and allyl isothiocyanate. Large-conductance calcium- and voltage-activated potassium (BK) channels regulate the electric activities and neurotransmitter releases in excitable cells, responding to changes in membrane potentials and elevation of cytosolic calcium ions (Ca2+). However, it is unknown whether the TRPV1 channels are coupled with the BK channels. Using patch-clamp recording combined with an infrared laser device, we found that BK channels could be activated at 0 mV by a Ca2+ influx through TRPV1 channels not the intracellular calcium stores in submilliseconds. The local calcium concentration around BK is estimated over 10 μM. The crosstalk could be affected by 10 mM BAPTA, whereas 5 mM EGTA was ineffectual. Fluorescence and co-immunoprecipitation experiments also showed that BK and TRPV1 were able to form a TRPV1-BK complex. Furthermore, we demonstrated that the TRPV1-BK coupling also occurs in dosal root ganglion (DRG) cells, which plays a critical physiological role in regulating the “pain” signal transduction pathway in the peripheral nervous system. PMID:24147119

  18. Loose coupling between Ca2+ channels and release sensors at a plastic hippocampal synapse.

    PubMed

    Vyleta, Nicholas P; Jonas, Peter

    2014-02-07

    The distance between Ca(2+) channels and release sensors determines the speed and efficacy of synaptic transmission. Tight "nanodomain" channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose "microdomain" coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca(2+) chelator BAPTA [1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca(2+) channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca(2+) buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity.

  19. Measurements and coupled reaction channels analysis of one- and two-proton transfer reactions for the 28Si + 90,94Zr systems

    NASA Astrophysics Data System (ADS)

    Kalkal, Sunil; Mandal, S.; Jhingan, A.; Gehlot, J.; Sugathan, P.; Golda, K. S.; Madhavan, N.; Garg, Ritika; Goyal, Savi; Mohanto, Gayatri; Sandal, Rohit; Chakraborty, Santosh; Verma, Shashi; Behera, Bivash; Eleonora, G.; Wollersheim, H. J.; Singh, R.

    2012-03-01

    Measurements of angular distributions for one- and two-proton stripping reactions for 28Si + 90,94Zr systems were performed at 120 MeV. The experiment was carried out with the 28Si beam at Inter University Accelerator Center, New Delhi. The theoretical calculations were performed using the quantum mechanical coupled reaction channels code fresco. The distorted wave Born approximation calculations reproduced the experimental angular distributions for the one-proton transfer channel for both the systems reasonably well but failed for the two-proton transfer channel. Coupled channels calculations including various intermediate states (involving target and projectile inelastic excitations before and/or after transfer) along with the sequential transfer were able to reproduce the two-proton transfer angular distributions for both the systems reasonably well. It seems that at an energy above the Coulomb barrier, there is significant contribution of the indirect multistep and sequential transfer to the two-proton stripping reaction.

  20. Charge movement in gating-locked HCN channels reveals weak coupling of voltage sensors and gate.

    PubMed

    Ryu, Sujung; Yellen, Gary

    2012-11-01

    HCN (hyperpolarization-activated cyclic nucleotide gated) pacemaker channels have an architecture similar to that of voltage-gated K(+) channels, but they open with the opposite voltage dependence. HCN channels use essentially the same positively charged voltage sensors and intracellular activation gates as K(+) channels, but apparently these two components are coupled differently. In this study, we examine the energetics of coupling between the voltage sensor and the pore by using cysteine mutant channels for which low concentrations of Cd(2+) ions freeze the open-closed gating machinery but still allow the sensors to move. We were able to lock mutant channels either into open or into closed states by the application of Cd(2+) and measure the effect on voltage sensor movement. Cd(2+) did not immobilize the gating charge, as expected for strict coupling, but rather it produced shifts in the voltage dependence of voltage sensor charge movement, consistent with its effect of confining transitions to either closed or open states. From the magnitude of the Cd(2+)-induced shifts, we estimate that each voltage sensor produces a roughly three- to sevenfold effect on the open-closed equilibrium, corresponding to a coupling energy of ∼1.3-2 kT per sensor. Such coupling is not only opposite in sign to the coupling in K(+) channels, but also much weaker.

  1. Study of X(5568) in a unitary coupled-channel approximation of BK¯ and Bs π

    NASA Astrophysics Data System (ADS)

    Sun, Bao-Xi; Dong, Fang-Yong; Pang, Jing-Long

    2017-07-01

    The potential of the B meson and the pseudoscalar meson is constructed up to the next-to-leading order Lagrangian, and then the BK¯ and Bs π interaction is studied in the unitary coupled-channel approximation. A resonant state with a mass about 5568 MeV and JP =0+ is generated dynamically, which can be associated with the X(5568) state announced by the D0 Collaboration recently. The mass and the decay width of this resonant state depend on the regularization scale in the dimensional regularization scheme, or the maximum momentum in the momentum cutoff regularization scheme. The scattering amplitude of the vector B meson and the pseudoscalar meson is calculated, and an axial-vector state with a mass near 5620 MeV and JP =1+ is produced. Their partners in the charm sector are also discussed.

  2. Proton-Nucleus Total Cross Sections in Coupled-Channel Approach

    NASA Technical Reports Server (NTRS)

    Tripathi, R. K.; Wilson, John W.; Cucinotta, Francis A.

    2000-01-01

    Recently, nucleon-nucleon (N-N) cross sections in the medium have been extracted directly from experiment. The in-medium N-N cross sections form the basic ingredients of several heavy-ion scattering approaches including the coupled-channel approach developed at the Langley Research Center. In the present study the ratio of the real to the imaginary part of the two-body scattering amplitude in the medium was investigated. These ratios are used in combination with the in-medium N-N cross sections to calculate total proton-nucleus cross sections. The agreement is excellent with the available experimental data. These cross sections are needed for the radiation risk assessment of space missions.

  3. Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets.

    PubMed

    Liu, Fei; Heiner, Monika

    2013-08-01

    Stochastic modelling of coupled Ca2+ channels is a challenge, especially when the coupling of the channels, as determined by their spatial arrangement relative to each other, has to be considered at multiple spatial scales. In this study, the authors address this problem using coloured stochastic Petri nets (SPNc) as high-level description to generate continuous-time Markov chains. The authors develop several models with increasing complexity. They first apply SPNc to model single clusters of coupled Ca2+ channels arranged in a regular or irregular lattice, where they describe how to represent the geometrical arrangement of Ca2+ channels relative to each other using colours. They then apply this modelling idea to construct more complex models by modelling spatially arranged clusters of channels. The authors' models can be easily reproduced and adapted to different scenarios.

  4. Resonant coupling of Rayleigh waves through a narrow fluid channel causing extraordinary low acoustic transmission.

    PubMed

    Garcia-Chocano, Victor M; Nagaraj; Lòpez-Rios, Tomàs; Gumen, Lyudmila; Sànchez-Dehesa, Josè; Krokhin, Arkadii

    2012-10-01

    Coupling of Rayleigh waves propagating along two metal surfaces separated by a narrow fluid channel is predicted and experimentally observed. Although the coupling through a fluid (water) is weak, a strong synchronization in propagation of Rayleigh waves even for the metals with sufficiently high elastic contrast (brass and aluminum) is observed. Dispersion equation for two polarizations of the coupled Rayleigh waves is derived and experimentally confirmed. Excitation of coupled Rayleigh waves in a channel of finite length leads to anomalously low transmission of acoustic energy at discrete set of resonant frequencies. This effect may find useful applications in the design of acoustic metamaterial screens and reflectors.

  5. Estimating total fusion cross sections by using a coupled-channel method

    NASA Astrophysics Data System (ADS)

    Choi, Ki-Seok; Cheoun, Myung-Ki; Kim, K. S.; Kim, T. H.; So, W. Y.

    2017-01-01

    We calculate the total fusion cross sections for the 6He + 209Bi, 6Li + 209Bi,9Be + 208Pb, 10Be + 209Bi, and 11Li + 208Pb systems by using a coupled-channel (CC) method and compare the results with the experimental data. In the CC approach for the total fusion cross sections, we exploit a globally determined Wood-Saxon potential with Akyüz-Winther parameters and couplings of the ground state to the low-lying excited states in the projectile and the target nuclei. The total fusion cross sections obtained with the CC are compared with those obtained without the CC couplings. The latter approach is tantamount to a one-dimensional barrier penetration model. Finally, our approach is applied to understand new data for the 11Li+208Pb system. Possible ambiguities inherent in those approaches are discussed in detail for further applications to the fusion system of halo and/or neutron-rich nuclei.

  6. Dynamical coupled-channels study of meson production reactions from EBAC@Jlab

    SciTech Connect

    Hiroyuki Kamano

    2011-10-01

    We present the current status of a combined and simultaneous analysis of meson production reactions based on a dynamical coupled-channels (DCC) model, which is conducted at Excited Baryon Analysis Center (EBAC) of Jefferson Lab.

  7. Dynamical coupled-channels study of meson production reactions from EBACatJLab

    SciTech Connect

    Kamano, Hiroyuki

    2011-10-24

    We present the current status of a combined and simultaneous analysis of meson production reactions based on a dynamical coupled-channels (DCC) model, which is conducted at Excited Baryon Analysis Center (EBAC) of Jefferson Lab.

  8. Solving non-Markovian open quantum systems with multi-channel reservoir coupling

    NASA Astrophysics Data System (ADS)

    Broadbent, Curtis J.; Jing, Jun; Yu, Ting; Eberly, Joseph H.

    2012-08-01

    We extend the non-Markovian quantum state diffusion (QSD) equation to open quantum systems which exhibit multi-channel coupling to a harmonic oscillator reservoir. Open quantum systems which have multi-channel reservoir coupling are those in which canonical transformation of reservoir modes cannot reduce the number of reservoir operators appearing in the interaction Hamiltonian to one. We show that the non-Markovian QSD equation for multi-channel reservoir coupling can, in some cases, lead to an exact master equation which we derive. We then derive the exact master equation for the three-level system in a vee-type configuration which has multi-channel reservoir coupling and give the analytical solution. Finally, we examine the evolution of the three-level vee-type system with generalized Ornstein-Uhlenbeck reservoir correlations numerically.

  9. G-protein-coupled inward rectifier potassium channels involved in corticostriatal presynaptic modulation.

    PubMed

    Meneses, David; Mateos, Verónica; Islas, Gustavo; Barral, Jaime

    2015-09-01

    Presynaptic modulation has been associated mainly with calcium channels but recent data suggests that inward rectifier potassium channels (K(IR)) also play a role. In this work we set to characterize the role of presynaptic K(IR) channels in corticostriatal synaptic transmission. We elicited synaptic potentials in striatum by stimulating cortical areas and then determined the synaptic responses of corticostriatal synapsis by using paired pulse ratio (PPR) in the presence and absence of several potassium channel blockers. Unspecific potassium channels blockers Ba(2+) and Cs(+) reduced the PPR, suggesting that these channels are presynaptically located. Further pharmacological characterization showed that application of tertiapin-Q, a specific K(IR)3 channel family blocker, also induced a reduction of PPR, suggesting that K(IR)3 channels are present at corticostriatal terminals. In contrast, exposure to Lq2, a specific K(IR)1.1 inward rectifier potassium channel, did not induce any change in PPR suggesting the absence of these channels in the presynaptic corticostriatal terminals. Our results indicate that K(IR)3 channels are functionally expressed at the corticostriatal synapses, since blockage of these channels result in PPR decrease. Our results also help to explain how synaptic activity may become sensitive to extracellular signals mediated by G-protein coupled receptors. A vast repertoire of receptors may influence neurotransmitter release in an indirect manner through regulation of K(IR)3 channels.

  10. Coupled-Channel Computation of Direct Neutron Capture on Non-Spherical Nuclei

    NASA Astrophysics Data System (ADS)

    Arbanas, Goran; Thompson, Ian; Escher, Jutta; Nunes, Filomena; Elster, Charlotte; Zhang, Shi-Sheng

    2014-09-01

    Models of direct neutron capture of neutrons have so far accounted for the effects of non-spherical nuclei either in the incoming wave functions (via non-spherical optical model potentials), or in the final bound states (via non-spherical real potential wells), but not in both. Since it is known that spherical optical potentials do not give a good reproduction of low energy neutron-scattering observables of deformed nuclei, we have performed calculations in which the initial and final states are both treated in a self-consistent, non-spherical-nucleus picture. We have done this in the coupled-channels model of nuclear reactions implemented in the FRESCO code by using the same deformation-length for the couplings to the rotational-band states in the incoming and the final state configurations. We compute direct capture using this method for even-mass calcium isotopes 40 , 42 , 44 , 46 , 48Ca to study the effect across the two closed neutron shells, for neutron-rich even-mass tin isotopes relevant to models of astrophysical nucleosynthesis, and for 56Fe that is an important structural material used in nuclear applications. Models of direct neutron capture of neutrons have so far accounted for the effects of non-spherical nuclei either in the incoming wave functions (via non-spherical optical model potentials), or in the final bound states (via non-spherical real potential wells), but not in both. Since it is known that spherical optical potentials do not give a good reproduction of low energy neutron-scattering observables of deformed nuclei, we have performed calculations in which the initial and final states are both treated in a self-consistent, non-spherical-nucleus picture. We have done this in the coupled-channels model of nuclear reactions implemented in the FRESCO code by using the same deformation-length for the couplings to the rotational-band states in the incoming and the final state configurations. We compute direct capture using this method for even

  11. Partitioning modes and rates of sediment flux derived from terrace-channel coupling

    NASA Astrophysics Data System (ADS)

    Higson, J. L.; Singer, M. B.

    2012-12-01

    Sediment supply to channels from failed banks/terraces is a geomorphic problem that has received scant treatment in the literature, especially with respect to the partitioning of such laterally eroded sediment into bedload v. suspended load and the resultant channel grain size distribution. Such coupling between terraces/banks and channels is an important component for understanding the exhaustion of the legacy sediments in disturbed watersheds, especially where terraces are contaminated by past mining activities. More than 4x106 kg of mercury (Hg) was lost during the 19th Century hydraulic mining process in the Sierra Nevada foothills of California and documented levels of total Hg concentration in legacy terraces all along the Yuba River are up to 3 orders of magnitude higher than background values. Thus, the ongoing erosion of legacy terraces from the mining period poses important risks to sensitive and ecologically productive lowlands downstream. The problem of bank/terrace erosion in river corridors is generally treated either using a channel centerline (toe cutting) approach or by infinite slope stability at a cross section, but the interaction of failed sediment with the channel is an important and missing component for fully assessing downstream risks of failing contaminated terraces. We have developed a new physically based model that can be used to quantify the extent and caliber of episodic erosion of legacy terrace sediments. The model combines analysis of bank/terrace failure in response to variable fluvial hydrology with a representation of local cross section evolution of grain size distribution and sediment routing. Terrace stability is calculated through an infinite slope stability model, driven by a Dupuit-Forchheimer groundwater model to assess soil moisture contributing to failure. The grain size distribution (GSD) in the channel bed is evolved based on calculation of sediment transport, which also yields net flux of fine material that is known

  12. Resonant excitation of coupled Rayleigh waves in a short and narrow fluid channel clad between two identical metal plates

    SciTech Connect

    García-Chocano, Victor M.; López-Rios, Tomás; Krokhin, Arkadii; Sanchez-Dehesa, Jose

    2011-12-23

    Transmission of ultrasonic waves through a slit between two water immersed brass plates is studied for sub-wavelength plate thicknesses and slit apertures. Extraordinary high absorption is observed at discrete frequencies corresponding to resonant excitation of Rayleigh waves on the both sides of the channel. The coupling of the Rayleigh waves occurs through the fluid and the corresponding contribution to the dispersion has been theoretically derived and also experimentally confirmed. Symmetric and anti-symmetric modes are predicted but only the symmetric mode resonances have been observed. It follows from the dispersion equation that the coupled Rayleigh waves cannot be excited in a channel with apertures less than the critical one. The calculated critical aperture is in a good agreement with the measured acoustic spectra. These findings could be applied to design a broadband absorptive metamaterial.

  13. Resonant excitation of coupled Rayleigh waves in a short and narrow fluid channel clad between two identical metal plates

    DOE PAGES

    García-Chocano, Victor M.; López-Rios, Tomás; Krokhin, Arkadii; ...

    2011-12-23

    Transmission of ultrasonic waves through a slit between two water immersed brass plates is studied for sub-wavelength plate thicknesses and slit apertures. Extraordinary high absorption is observed at discrete frequencies corresponding to resonant excitation of Rayleigh waves on the both sides of the channel. The coupling of the Rayleigh waves occurs through the fluid and the corresponding contribution to the dispersion has been theoretically derived and also experimentally confirmed. Symmetric and anti-symmetric modes are predicted but only the symmetric mode resonances have been observed. It follows from the dispersion equation that the coupled Rayleigh waves cannot be excited in amore » channel with apertures less than the critical one. The calculated critical aperture is in a good agreement with the measured acoustic spectra. These findings could be applied to design a broadband absorptive metamaterial.« less

  14. Coupled-channel analysis of KΣ production on the nucleon up to 2.0 GeV

    NASA Astrophysics Data System (ADS)

    Cao, Xu; Shklyar, V.; Lenske, H.

    2013-11-01

    A coupled-channel effective Lagrangian model respecting unitary and gauge invariance is applied to the combined analysis of (π,γ)N→KΣ reactions for center-of-mass energies up to 2 GeV. The recent photoproduction data obtained by the CLAS, CBELSA, LEPS, and GRAAL groups are included into our calculations with the aim to extract the resonance couplings to the KΣ state. Both resonances and background contributions are found to be important to reproduce correct shapes of the angular distributions and polarization observables. Our description of the data is of good quality. The extracted properties of isospin I=3/2 resonances are discussed in detail while the I=1/2 resonances are largely determined by the nonstrangeness channels.

  15. Enhanced Polarimetric Radar Imaging Using Cross-Channel Coupling Constraints

    DTIC Science & Technology

    2014-06-19

    classification. Overall, the jointly enhanced image channels displayed significantly better polarimet- ric preservation compared to the corresponding...Potter, E. Ertin, J. T. Parker , and M. Cetin, “Sparsity and compressed sensing in radar imaging,” Proceedings of the IEEE, vol. 98, no. 6, pp. 1006

  16. Coupled hydro-neutronic calculations for fast burst reactor accidents

    SciTech Connect

    Paternoster, R.; Kimpland, R.; Jaegers, P.; McGhee, J.

    1994-01-01

    Methods are described for determining the fully coupled neutronic/hydrodynamic response of fast burst reactors (FBR) under disruptive accident conditions. Two code systems, PAD (1 -D Lagrangian) and NIKE-PAGOSA (3-D Eulerian) were used to accomplish this. This is in contrast to the typical methodology that computes these responses by either single point kinetics or in a decoupled manner. This methodology is enabled by the use of modem supercomputers (CM-200). Two examples of this capability are presented: an unreflected metal fast burst assembly, and a reflected fast burst assembly typical of the Skua or SPR-III class of fast burst reactor.

  17. The Effect of Extending the Length of the Coupling Coils in a Muon Ionization Cooling Channel

    NASA Astrophysics Data System (ADS)

    Green, Michael A.

    2008-02-01

    RF cavities are used to re-accelerate muons that have been cooled by absorbers that are in low beta regions of a muon ionization cooling channel. A superconducting coupling magnet (or magnets) are around or among the RF cavities of a muon ionization-cooling channel. The field from the magnet guides the muons so that they are kept within the iris of the RF cavities that are used to accelerate the muons. This report compares the use of a single short coupling magnet with an extended coupling magnet that has one or more superconducting coils as part of a muon-cooling channel of the same design as the muon ionization cooling experiment (MICE). Whether the superconducting magnet is short and thick or long and this affects the magnet stored energy and the peak field in the winding. The magnetic field distribution also affects is the muon beam optics in the cooling cell of a muon cooling channel.

  18. Principal pathway coupling agonist binding to channel gating in nicotinic receptors

    NASA Astrophysics Data System (ADS)

    Lee, Won Yong; Sine, Steven M.

    2005-11-01

    Synaptic receptors respond to neurotransmitters by opening an intrinsic ion channel in the final step in synaptic transmission. How binding of the neurotransmitter is conveyed over the long distance to the channel remains a central question in neurobiology. Here we delineate a principal pathway that links neurotransmitter binding to channel gating by using a structural model of the Torpedo acetylcholine receptor at 4-Å resolution, recordings of currents through single receptor channels and determinations of energetic coupling between pairs of residues. We show that a pair of invariant arginine and glutamate residues in each receptor α-subunit electrostatically links peripheral and inner β-sheets from the binding domain and positions them to engage with the channel. The key glutamate and flanking valine residues energetically couple to conserved proline and serine residues emerging from the top of the channel-forming α-helix, suggesting that this is the point at which the binding domain triggers opening of the channel. The series of interresidue couplings identified here constitutes a primary allosteric pathway that links neurotransmitter binding to channel gating.

  19. Radially excited axial mesons and the enigmatic Zc and Zb in a coupled-channel model

    NASA Astrophysics Data System (ADS)

    Coito, Susana

    2016-07-01

    The enigmatic charged states Zc(3900 ), Zc(4020 ), Zc(4050 ), Zb(10610 ), and Zb(10650 ) are studied within a coupled-channel Schrödinger model, where radially excited quark-antiquark pairs, with the same angular momenta and isospin as the a1(1260 ) and b1(1235 ), are strongly coupled to their Okubo-Zweig-Iizuka-allowed decay channels D D¯*+D ¯D* and D*D¯*, or B B¯*+B ¯B* and B*B¯*, in S and D waves. Poles, matching the experimental mass and width of the above states, are found by varying only two free parameters. From the wave-function analysis of each resonance, the probability of each of the components contributing to the coupled system is estimated, and predictions can be made for the relative decay fractions among the coupled open-charm or open-bottom decay channels.

  20. Coupled cluster calculations of neutron-rich nuclei

    NASA Astrophysics Data System (ADS)

    Hagen, Gaute

    2016-09-01

    In this talk I will present recent highlights from ab initio computations of atomic nuclei using coupled-cluster methods with state-of-the-art interactions from chiral effective field theory (EFT). The recent progress in computing nuclei from scratch is based on new optimizations of interactions from chiral EFT, and ab initio methods with a polynomial computational cost together with available super computing resources. The physics advancements I will discuss include: (i) accurate nuclear binding energies and radii of light and medium-mass nuclei, (ii) the neutron distribution and electric dipole polarizability of the nucleus 48Ca, (iii) and the structure of the rare nucleus 78Ni from first principles. All these quantities are currently targeted by precision measurements worldwide.

  1. Unitary coupled-channels model for three-mesons decays of heavy mesons

    SciTech Connect

    Hiroyuki Kamano; Nakamura, Satoshi X.; Lee, Tsung-Shung H.; Sato, Toru

    2011-12-16

    In this study, a unitary coupled-channels model is presented for investigating the decays of heavy mesons and excited meson states into three light pseudoscalar mesons. The model accounts for the three-mesons final state interactions in the decay processes, as required by both the three-body and two-body unitarity conditions. In the absence of the Z-diagram mechanisms that are necessary consequences of the three-body unitarity, our decay amplitudes are reduced to a form similar to those used in the so-called isobar-model analysis. We apply our coupled-channels model to the three-pions decays of α1(1260), π2(1670), π2(2100), and D0 mesons, and show that the Z-diagram mechanisms can contribute to the calculated Dalitz plot distributions by as much as 30% in magnitudes in the regions where f0(600), ρ(770), and f2(1270) dominate the distributions. Also, by fitting to the same Dalitz plot distributions, we demonstrate that the decay amplitudes obtained with the unitary model and the isobar model can be rather different, particularly in the phase that plays a crucial role in extracting the CKM CP-violating phase from the data of B meson decays. Our results indicate that the commonly used isobar model analysis must be extended to account for the final state interactions required by the three-body unitarity to reanalyze the three-mesons decays of heavy mesons, thereby exploring hybrid or exotic mesons, and signatures of physics beyond the standard model.

  2. Unitary coupled-channels model for three-mesons decays of heavy mesons

    DOE PAGES

    Hiroyuki Kamano; Nakamura, Satoshi X.; Lee, Tsung-Shung H.; ...

    2011-12-16

    In this study, a unitary coupled-channels model is presented for investigating the decays of heavy mesons and excited meson states into three light pseudoscalar mesons. The model accounts for the three-mesons final state interactions in the decay processes, as required by both the three-body and two-body unitarity conditions. In the absence of the Z-diagram mechanisms that are necessary consequences of the three-body unitarity, our decay amplitudes are reduced to a form similar to those used in the so-called isobar-model analysis. We apply our coupled-channels model to the three-pions decays of α1(1260), π2(1670), π2(2100), and D0 mesons, and show that themore » Z-diagram mechanisms can contribute to the calculated Dalitz plot distributions by as much as 30% in magnitudes in the regions where f0(600), ρ(770), and f2(1270) dominate the distributions. Also, by fitting to the same Dalitz plot distributions, we demonstrate that the decay amplitudes obtained with the unitary model and the isobar model can be rather different, particularly in the phase that plays a crucial role in extracting the CKM CP-violating phase from the data of B meson decays. Our results indicate that the commonly used isobar model analysis must be extended to account for the final state interactions required by the three-body unitarity to reanalyze the three-mesons decays of heavy mesons, thereby exploring hybrid or exotic mesons, and signatures of physics beyond the standard model.« less

  3. TRPV4 and K(Ca) ion channels functionally couple as osmosensors in the paraventricular nucleus.

    PubMed

    Feetham, C H; Nunn, N; Lewis, R; Dart, C; Barrett-Jolley, R

    2015-04-01

    Transient receptor potential vanilloid type 4 (TRPV4) and calcium-activated potassium channels (KCa ) mediate osmosensing in many tissues. Both TRPV4 and KCa channels are found in the paraventricular nucleus (PVN) of the hypothalamus, an area critical for sympathetic control of cardiovascular and renal function. Here, we have investigated whether TRPV4 channels functionally couple to KCa channels to mediate osmosensing in PVN parvocellular neurones and have characterized, pharmacologically, the subtype of KCa channel involved. We investigated osmosensing roles for TRPV4 and KCa channels in parvocellular PVN neurones using cell-attached and whole-cell electrophysiology in mouse brain slices and rat isolated PVN neurons. Intracellular Ca(2+) was recorded using Fura-2AM. The system was modelled in the NEURON simulation environment. Hypotonic saline reduced action current frequency in hypothalamic slices; a response mimicked by TRPV4 channel agonists 4αPDD (1 μM) and GSK1016790A (100 nM), and blocked by inhibitors of either TRPV4 channels (RN1734 (5 μM) and HC067047 (300 nM) or the low-conductance calcium-activated potassium (SK) channel (UCL-1684 30 nM); iberiotoxin and TRAM-34 had no effect. Our model was compatible with coupling between TRPV4 and KCa channels, predicting the presence of positive and negative feedback loops. These predictions were verified using isolated PVN neurons. Both hypotonic challenge and 4αPDD increased intracellular Ca(2+) and UCL-1684 reduced the action of hypotonic challenge. There was functional coupling between TRPV4 and SK channels in parvocellular neurones. This mechanism contributes to osmosensing in the PVN and may provide a novel pharmacological target for the cardiovascular or renal systems. © 2014 The Authors. British Journal of Pharmacology published by John Wiley & Sons Ltd on behalf of The British Pharmacological Society.

  4. Quantum calculation of disordered length in fcc single crystals using channelling techniques

    NASA Astrophysics Data System (ADS)

    Abu-Assy, M. K.

    2006-04-01

    Lattices of face-centred cubic crystals (fcc), due to irradiation processes, may become disordered in stable configurations like the dumb-bell configuration (DBC) or body-centred interstitial (BCI). In this work, a quantum mechanical treatment for the calculation of transmission coefficients of channelled positrons from their bound states in the normal lattice regions into the allowed bound states in the disordered regions is given as a function of the length of the disordered regions. In order to obtain more reliable results, higher anharmonic terms in the planar channelling potential are considered in the calculations by using first-order perturbation theory where new bound states have been found. The calculations were executed in the energy range 10 200 MeV of the incident positron on a copper single crystal in the planar direction (100).

  5. Coupling of activation and inactivation gate in a K+-channel: potassium and ligand sensitivity.

    PubMed

    Ader, Christian; Schneider, Robert; Hornig, Sönke; Velisetty, Phanindra; Vardanyan, Vitya; Giller, Karin; Ohmert, Iris; Becker, Stefan; Pongs, Olaf; Baldus, Marc

    2009-09-16

    Potassium (K(+))-channel gating is choreographed by a complex interplay between external stimuli, K(+) concentration and lipidic environment. We combined solid-state NMR and electrophysiological experiments on a chimeric KcsA-Kv1.3 channel to delineate K(+), pH and blocker effects on channel structure and function in a membrane setting. Our data show that pH-induced activation is correlated with protonation of glutamate residues at or near the activation gate. Moreover, K(+) and channel blockers distinctly affect the open probability of both the inactivation gate comprising the selectivity filter of the channel and the activation gate. The results indicate that the two gates are coupled and that effects of the permeant K(+) ion on the inactivation gate modulate activation-gate opening. Our data suggest a mechanism for controlling coordinated and sequential opening and closing of activation and inactivation gates in the K(+)-channel pore.

  6. Role of protein dynamics in ion selectivity and allosteric coupling in the NaK channel

    PubMed Central

    Brettmann, Joshua B.; Urusova, Darya; Tonelli, Marco; Silva, Jonathan R.; Henzler-Wildman, Katherine A.

    2015-01-01

    Flux-dependent inactivation that arises from functional coupling between the inner gate and the selectivity filter is widespread in ion channels. The structural basis of this coupling has only been well characterized in KcsA. Here we present NMR data demonstrating structural and dynamic coupling between the selectivity filter and intracellular constriction point in the bacterial nonselective cation channel, NaK. This transmembrane allosteric communication must be structurally different from KcsA because the NaK selectivity filter does not collapse under low-cation conditions. Comparison of NMR spectra of the nonselective NaK and potassium-selective NaK2K indicates that the number of ion binding sites in the selectivity filter shifts the equilibrium distribution of structural states throughout the channel. This finding was unexpected given the nearly identical crystal structure of NaK and NaK2K outside the immediate vicinity of the selectivity filter. Our results highlight the tight structural and dynamic coupling between the selectivity filter and the channel scaffold, which has significant implications for channel function. NaK offers a distinct model to study the physiologically essential connection between ion conduction and channel gating. PMID:26621745

  7. Role of protein dynamics in ion selectivity and allosteric coupling in the NaK channel.

    PubMed

    Brettmann, Joshua B; Urusova, Darya; Tonelli, Marco; Silva, Jonathan R; Henzler-Wildman, Katherine A

    2015-12-15

    Flux-dependent inactivation that arises from functional coupling between the inner gate and the selectivity filter is widespread in ion channels. The structural basis of this coupling has only been well characterized in KcsA. Here we present NMR data demonstrating structural and dynamic coupling between the selectivity filter and intracellular constriction point in the bacterial nonselective cation channel, NaK. This transmembrane allosteric communication must be structurally different from KcsA because the NaK selectivity filter does not collapse under low-cation conditions. Comparison of NMR spectra of the nonselective NaK and potassium-selective NaK2K indicates that the number of ion binding sites in the selectivity filter shifts the equilibrium distribution of structural states throughout the channel. This finding was unexpected given the nearly identical crystal structure of NaK and NaK2K outside the immediate vicinity of the selectivity filter. Our results highlight the tight structural and dynamic coupling between the selectivity filter and the channel scaffold, which has significant implications for channel function. NaK offers a distinct model to study the physiologically essential connection between ion conduction and channel gating.

  8. Dynamical coupled-channels study of {pi}N {right arrow} {pi pi}N reactions.

    SciTech Connect

    Kamano, H.; Julia-Diaz, B.; Lee, T.-S. H.; Matsuyama, A.; Sato, T.; Physics; Jefferson Lab.; Univ. of Barcelona; Shizuoka Univ.; Osaka Univ.

    2009-02-24

    As a step toward performing a complete coupled-channels analysis of the world data of {pi}N,{gamma}*N {yields} {pi}N,{eta}N,{pi}{pi}N reactions, the {pi}N {yields} {pi}{pi}N reactions are investigated starting with the dynamical coupled-channels model developed in Phys. Rev. C 76, 065201 (2007). The channels included are {pi}N,{eta}N, and {pi}{pi}N which has {pi}{Delta},{rho}N, and {sigma}N resonant components. The nonresonant amplitudes are generated from solving a set of coupled-channels equations with the meson-baryon potentials defined by effective Lagrangians. The resonant amplitudes are generated from 16 bare excited nucleon (N*) states that are dressed by the nonresonant interactions as constrained by the unitarity condition. The data of total cross sections and {pi}N and {pi}{pi} invariant mass distributions of {pi} + p {yields} {pi} + {pi} + n, {pi} + {pi}0p and {pi} - p {yields} {pi} + {pi} - n, {pi} - {pi}0p,{pi}0{pi}0n reactions from threshold to the invariant mass W = 2 GeV can be described to a very large extent. We show the importance of the coupled-channels effects and the strong interference among the contributions from the {pi}{Delta},{sigma}N, and {rho}N channels. The large interference between the resonant and nonresonant amplitudes is also demonstrated. Possible future developments are discussed.

  9. Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance.

    PubMed

    Wilson, Michael A; Nguyen, Thuy Hien; Pohorille, Andrew

    2014-12-14

    Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation.

  10. Functional Coupling of Ca2+ Channels and Ryanodine Receptors in Cardiac Myocytes

    NASA Astrophysics Data System (ADS)

    Sham, James S. K.; Cleemann, Lars; Morad, Martin

    1995-01-01

    In skeletal muscle, dihydropyridine receptors are functionally coupled to ryanodine receptors of the sarcoplasmic reticulum in triadic or diadic junctional complexes. In cardiac muscle direct physical or functional couplings have not been demonstrated. We have tested the hypothesis of functional coupling of L-type Ca2+ channels and ryanodine receptors in rat cardiac myocytes by comparing the efficacies of Ca2+ in triggering Ca2+ release when the ion enters the cell via the Ca2+ channels or the Na^+/Ca2+ exchanger. Ca2+ transported through the Ca2+ channels was 20-160 times more effective than Ca2+ influx via the Na^+/Ca2+ exchanger in gating Ca2+ release from the sarcoplasmic reticulum, suggesting privileged communication between Ca2+ channels and ryanodine receptors. In support of this hypothesis we found that Ca2+ channels were inactivated by Ca2+ release from the sarcoplasmic reticulum, even though the myoplasmic Ca2+ concentrations were buffered with 10 mM EGTA. The data thus suggest privileged cross signaling between the dihydropyridine and ryanodine receptors such that Ca2+ flux through either the Ca2+ channel or the ryanodine receptor alters the gating kinetics of the other channel.

  11. Probing the Structure of {sup 74}Ge Nucleus with Coupled-channels Analysis of {sup 74}Ge+{sup 74}Ge Fusion Reaction

    SciTech Connect

    Zamrun F, Muhammad; Kasim, Hasan Abu

    2010-12-23

    We study the fusion reaction of the {sup 74}Ge+{sup 74}Ge system in term of the full order coupled-channels formalism. We especially calculated the fusion cross section as well as the fusion barrier distribution of this reaction using transition matrix suggested by recent Coulomb excitation experiment. We compare the results with the one obtained by coupling matrix based on pure vibrational and rotational models. The present coupled-channels calculations for the barrier distributions obtained using experiment coupling matrix is in good agreement with the one obtained with vibrational model, in contrast to the rotational model. This is indicates that {sup 74}Ge nucleus favor a spherical shape than a deformed shape in its ground state. Our results will resolve the debates concerning the structure of this nucleus.

  12. Leptonic widths of high ψ -resonances in a unitary coupled-channel model

    NASA Astrophysics Data System (ADS)

    Badalian, A. M.; Bakker, B. L. G.

    2017-07-01

    The leptonic widths of high ψ -resonances are calculated in a coupled-channel model with unitary inelasticity, where analytical expressions for the mixing angles between (n +1 )3S1 and n 3D1 states and probabilities Zi of the c c ¯ component are derived. These factors depend on energy (mass) and can be different for ψ (4040 ) and ψ (4160 ). However, our calculations give a small difference between the mixing angles, θ (ψ (4040 ))=(2 8-2+1)° and θ (ψ (4160 ))=(2 9-3+2)°, and ˜10 % difference between the probabilities Z1(ψ (4040 ))=0.8 5-0.02+0.05 and Z2(ψ (4160 ))=0.79 ±0.01 . It provides the leptonic widths Γe e(ψ (4040 ))=(1.0 ±0.1 ) keV and Γe e(ψ (4160 ))=(0.62 ±0.0.07 ) keV in agreement with experiment; for ψ (4415 ) the value Γe e(ψ (4415 ))=(0.66 ±0.06 ) keV is obtained, while for the missing resonance ψ (4510 ), we predict its mass, M (ψ (4500 ))=(4512 ±2 ) MeV , and Γe e(ψ (4510 ))=(0.68 ±0.14 ) keV .

  13. The effects of dual-channel coupling on the transition from amplitude death to oscillation death

    NASA Astrophysics Data System (ADS)

    Chen, Jiangnan; Liu, Weiqing; Zhu, Yun; Xiao, Jinghua

    2016-07-01

    Oscillation quenching including amplitude death (AD) and oscillation death (OD) in addition to the transition processes between them have been hot topics in aspect of chaos control, physical and biological applications. The effects of dual-channel coupling on the AD and OD dynamics regimes, and their transition processes in coupled nonidentical oscillators are explored numerically and theoretically. Our results indicate that an additional repulsive coupling tends to shrink the AD domain while it enlarges the OD domain, however, an additional attractive coupling acts inversely. As a result, the transitions from AD to OD are replaced by transitions from oscillation state (OS) to AD or from OS to OD in the dual-channel coupled oscillators with different frequency mismatches. Our results are helpful to better understand the control of AD and OD and their transition processes.

  14. Macro-channel cooled high power fiber coupled diode lasers exceeding 1.2kW of output power

    NASA Astrophysics Data System (ADS)

    Koenning, Tobias; Alegria, Kim; Wang, Zuolan; Segref, Armin; Stapleton, Dean; Faßbender, Wilhelm; Flament, Marco; Rotter, Karsten; Noeske, Axel; Biesenbach, Jens

    2011-03-01

    We report on a new series of fiber coupled diode laser modules exceeding 1.2kW of single wavelength optical power from a 400um / 0.2NA fiber. The units are constructed from passively cooled laser bars as opposed to other comparably powered, commercially available modules that use micro-channel heat-sinks. Micro-channel heat sinks require cooling water to meet demanding specifications and are therefore prone to failures due to contamination and increase the overall cost to operate and maintain the laser. Dilas' new series of high power fiber coupled diode lasers are designed to eliminate micro channel coolers and their associated failure mechanisms. Low-smile soldering processes were developed to maximize the brightness available from each diode laser bar. The diode laser brightness is optimally conserved using Dilas' recently developed propriety laser bar stacking geometry and optics. A total of 24 bars are coupled into a single fiber core using a polarization multiplexing scheme. The modular design permits further power scaling through wavelength multiplexing. Other customer critical features such as industrial grade fibers, pilot beams, fiber interlocks and power monitoring are standard features on these modules. The optical design and the beam parameter calculations will be presented to explain the inherit design trade offs. Results for single and dual wavelengths modules will be presented.

  15. Deletion of cytosolic gating ring decreases gate and voltage sensor coupling in BK channels.

    PubMed

    Zhang, Guohui; Geng, Yanyan; Jin, Yakang; Shi, Jingyi; McFarland, Kelli; Magleby, Karl L; Salkoff, Lawrence; Cui, Jianmin

    2017-03-06

    Large conductance Ca(2+)-activated K(+) channels (BK channels) gate open in response to both membrane voltage and intracellular Ca(2+) The channel is formed by a central pore-gate domain (PGD), which spans the membrane, plus transmembrane voltage sensors and a cytoplasmic gating ring that acts as a Ca(2+) sensor. How these voltage and Ca(2+) sensors influence the common activation gate, and interact with each other, is unclear. A previous study showed that a BK channel core lacking the entire cytoplasmic gating ring (Core-MT) was devoid of Ca(2+) activation but retained voltage sensitivity (Budelli et al. 2013. Proc. Natl. Acad. Sci. USA http://dx.doi.org/10.1073/pnas.1313433110). In this study, we measure voltage sensor activation and pore opening in this Core-MT channel over a wide range of voltages. We record gating currents and find that voltage sensor activation in this truncated channel is similar to WT but that the coupling between voltage sensor activation and gating of the pore is reduced. These results suggest that the gating ring, in addition to being the Ca(2+) sensor, enhances the effective coupling between voltage sensors and the PGD. We also find that removal of the gating ring alters modulation of the channels by the BK channel's β1 and β2 subunits.

  16. Evidence for conformational coupling between two calcium channels.

    PubMed

    Paolini, C; Fessenden, James D; Pessah, Isaac N; Franzini-Armstrong, C

    2004-08-24

    Ryanodine receptor 1 (RyR1, the sarcoplasmic reticulum Ca(2+) release channel) and alpha(1S)dihydropyridine receptor (DHPR, the surface membrane voltage sensor) of skeletal muscle belong to separate membrane systems but are functionally and structurally linked. Four alpha(1S)DHPRs associated with the four identical subunits of a RyR form a tetrad. We treated skeletal muscle cell lines with ryanodine, at concentrations that block RyRs, and determined whether this treatment affects the distance between DHPRs in the tetrad. We find a substantial ( approximately 2-nm) shift in the alpha(1S)DHPR positions, indicating that ryanodine induces large conformational changes in the RyR1 cytoplasmic domain and that the alpha(1S)DHPR-RyR complex acts as a unit.

  17. Evidence for conformational coupling between two calcium channels

    PubMed Central

    Paolini, C.; Fessenden, James D.; Pessah, Isaac N.; Franzini-Armstrong, C.

    2004-01-01

    Ryanodine receptor 1 (RyR1, the sarcoplasmic reticulum Ca2+ release channel) and α1Sdihydropyridine receptor (DHPR, the surface membrane voltage sensor) of skeletal muscle belong to separate membrane systems but are functionally and structurally linked. Four α1SDHPRs associated with the four identical subunits of a RyR form a tetrad. We treated skeletal muscle cell lines with ryanodine, at concentrations that block RyRs, and determined whether this treatment affects the distance between DHPRs in the tetrad. We find a substantial (≈2-nm) shift in the α1SDHPR positions, indicating that ryanodine induces large conformational changes in the RyR1 cytoplasmic domain and that the α1SDHPR-RyR complex acts as a unit. PMID:15310845

  18. Nanodomain coupling between Ca2+ channels and sensors of exocytosis at fast mammalian synapses

    PubMed Central

    Eggermann, Emmanuel; Bucurenciu, Iancu; Goswami, Sarit Pati; Jonas, Peter

    2013-01-01

    The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant of the signalling properties of synapses in the nervous system. Recent functional analysis indicates that in some fast central synapses, transmitter release is triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors at the nanometre scale. Molecular analysis suggests that this tight coupling is generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors and various other synaptic proteins. Nanodomain coupling has several functional advantages, as it increases the efficacy, speed and energy efficiency of synaptic transmission. PMID:22183436

  19. Calculation of Dipole Transition Matrix Elements and Expectation Values by Vibrational Coupled Cluster Method.

    PubMed

    Banik, Subrata; Pal, Sourav; Prasad, M Durga

    2010-10-12

    An effective operator approach based on the coupled cluster method is described and applied to calculate vibrational expectation values and absolute transition matrix elements. Coupled cluster linear response theory (CCLRT) is used to calculate excited states. The convergence pattern of these properties with the rank of the excitation operator is studied. The method is applied to a water molecule. Arponen-type double similarity transformation in extended coupled cluster (ECCM) framework is also used to generate an effective operator, and the convergence pattern of these properties is compared to the normal coupled cluster (NCCM) approach. It is found that the coupled cluster method provides an accurate description of these quantities for low lying vibrational excited states. The ECCM provides a significant improvement for the calculation of the transition matrix elements.

  20. Parallelisation of MONK with Coupling to Thermal Hydraulics and Gamma Heating Calculations for Reactor Physics Applications

    NASA Astrophysics Data System (ADS)

    Richards, Simon D.; Davies, Nigel; Armishaw, Malcolm J.; Dobson, Geoff P.; Wright, George A.

    2014-06-01

    Monte Carlo methods are increasingly being used for whole core reactor physics modelling. We describe a number of recent developments to the MONK nuclear criticality and reactor physics code to implement parallel processing, mesh-dependent burn-up and coupling to both thermal hydraulics and gamma transport codes. Results are presented which demonstrate the e_ects of gamma heating in a MONK calculation coupled to the MCBEND Monte Carlo shielding code. Experimental validation of the mesh-dependent tracking and gamma coupling methods is provided by comparison with the results of the NESSUS experiment. The gamma heating calculated by coupled MONK-MCBEND, and the neutron heating calculated by MONK, both compare well against measurement. Finally results are presented from a parallel MONK calculation of a highly detailed PWR benchmark model, which show encouraging speed-up factors on a small development cluster.

  1. Ultrafast relaxation inside proteins: Calculation and measurement of electron-vibration coupling in enzymes

    NASA Astrophysics Data System (ADS)

    Cho, B. M.; Walker, R. C.; Mercer, I. P.; Gould, I. R.; Klug, D. R.

    Electron-vibration coupling in alcohol dehydrogenase and zinc substituted myoglobin was calculated using a quantum mechanics/molecular mechanics method. Good agreement with experimental measurements demonstrates the viability of the method.

  2. Inverse coupling in leak and voltage-activated K+ channel gates underlies distinct roles in electrical signaling.

    PubMed

    Ben-Abu, Yuval; Zhou, Yufeng; Zilberberg, Noam; Yifrach, Ofer

    2009-01-01

    Voltage-activated (Kv) and leak (K(2P)) K(+) channels have key, yet distinct, roles in electrical signaling in the nervous system. Here we examine how differences in the operation of the activation and slow inactivation pore gates of Kv and K(2P) channels underlie their unique roles in electrical signaling. We report that (i) leak K(+) channels possess a lower activation gate, (ii) the activation gate is an important determinant controlling the conformational stability of the K(+) channel pore, (iii) the lower activation and upper slow inactivation gates of leak channels cross-talk and (iv) unlike Kv channels, where the two gates are negatively coupled, these two gates are positively coupled in K(2P) channels. Our results demonstrate how basic thermodynamic properties of the K(+) channel pore, particularly conformational stability and coupling between gates, underlie the specialized roles of Kv and K(2P) channel families in electrical signaling.

  3. COUPLING

    DOEpatents

    Frisch, E.; Johnson, C.G.

    1962-05-15

    A detachable coupling arrangement is described which provides for varying the length of the handle of a tool used in relatively narrow channels. The arrangement consists of mating the key and keyhole formations in the cooperating handle sections. (AEC)

  4. Effects of Na(+) channel and cell coupling abnormalities on vulnerability to reentry: a simulation study.

    PubMed

    Qu, Zhilin; Karagueuzian, Hrayr S; Garfinkel, Alan; Weiss, James N

    2004-04-01

    The role of dynamic instabilities in the initiation of reentry in diseased (remodeled) hearts remains poorly explored. Using computer simulations, we studied the effects of altered Na(+) channel and cell coupling properties on the vulnerable window (VW) for reentry in simulated two-dimensional cardiac tissue with and without dynamic instabilities. We related the VW for reentry to effects on conduction velocity, action potential duration (APD), effective refractory period dispersion and restitution, and concordant and discordant APD alternans. We found the following: 1). reduced Na(+) current density and slowed recovery promoted postrepolarization refractoriness and enhanced concordant and discordant APD alternans, which increased the VW for reentry; 2). uniformly reduced cell coupling had little effect on cellular electrophysiological properties and the VW for reentry. However, randomly reduced cell coupling combined with decoupling promoted APD dispersion and alternans, which also increased the VW for reentry; 3). the combination of decreased Na(+) channel conductance, slowed Na(+) channel recovery, and cellular uncoupling synergistically increased the VW for reentry; and 4) the VW for reentry was greater when APD restitution slope was steep than when it was flat. In summary, altered Na(+) channel and cellular coupling properties increase vulnerability to reentrant arrhythmias. In remodeled hearts with altered Na(+) channel properties and cellular uncoupling, dynamic instabilities arising from electrical restitution exert important influences on the VW for reentry.

  5. Field-aligned currents calculated based on the upgraded Prairie View Magnetosphere- ionosphere Coupling Model

    NASA Astrophysics Data System (ADS)

    Romashets, E.; Huang, T.

    2006-12-01

    Using the experimental magnetic field and the newly defined Eular Potentials, we upgraded Prairie View Magnetosphere-ionosphere Coupling Model that was originally created in the frame of IGRF. The electric fields in the ionosphere and the field-aligned currents in the magnetosphere are calculated with the upgraded magnetosphere-ionosphere coupling model, and a preliminary comparison of the calculations with the measurements from ST5 will be presented.

  6. Calculation of Coupling Efficiencies for Laser-Driven Photonic Bandgap Structures

    SciTech Connect

    England, R. J.; Ng, C.; Noble, R.; Spencer, J. E.

    2010-11-04

    We present a technique for calculating the power coupling efficiency for a laser-driven photonic bandgap structure using electromagnetic finite element simulations, and evaluate the efficiency of several coupling scenarios for the case of a hollow-core photonic bandgap fiber accelerator structure.

  7. Results of Nucleon Resonance Extraction via Dynamical Coupled-Channels Analysis from Collaboration @ EBAC

    SciTech Connect

    Hiroyuki Kamano

    2012-04-01

    We review a global analysis of meson production reactions off the nucleons by a collaboration at Excited Baryon Analysis Center of Jefferson Lab. The analysis is pursued with a dynamical coupled-channels approach, within which the dynamics of multi-channel reaction processes are taken into account in a fully consistent way with the two-body as well as three-body unitarity of the S-matrix. With this approach, new features of nucleon excitations are revealed as resonant particles originating from the non-trivial multi-channel reaction dynamics, which cannot be addressed by static hadron models where the nucleon excitations are treated as stable particles.

  8. Multi channel quantum defect theory calculations of the Rydberg spectra of HCO

    NASA Astrophysics Data System (ADS)

    Douguet, Nicolas; Orel, Ann

    2014-05-01

    We present a first-principles theoretical study of the photoionization spectra of vibrationally autoionizing Rydberg states converging to excited states of HCO+. The clamped-nuclei scattering matrix, quantum defects parameters and transition dipole moments are explicitly calculated using the complex variational Kohn technique. The multi-channel quantum defect theory and vibrational frame transformation are then used to calculate the absorption spectrum. The results are compared with experimental data on double-resonance spectroscopy of the high Rydberg states of formyl radical. This work is supported by the DOE Office of Basic Energy Science and the National Science Foundation, Grant No's PHY-10-68785 and PHY-11-60611.

  9. Random-phase-approximation calculations and residual interactions in the sigmatau channel

    SciTech Connect

    Cohen, J.

    1986-05-01

    We compare numerical results for renormalized spin-isospin matrix elements within the random phase approximation. Extended calculations are carried out for a pionlike excitation in a finite nucleus; the effects of contact versus momentum-dependent residual interactions, and of ..delta..-h configurations, are demonstrated. We point out the implications of our results on nuclear structure calculations, where such effects are sometimes neglected. The role of the finite geometry of the system is crucial in determining the features of the spin-isospin responses. We emphasize that a crucial test of the theory can only be achieved through a direct comparison of the longitudinal and transverse channels.

  10. Coupling between Voltage Sensors and Activation Gate in Voltage-gated K+ Channels

    PubMed Central

    Lu, Zhe; Klem, Angela M.; Ramu, Yajamana

    2002-01-01

    Current through voltage-gated K+ channels underlies the action potential encoding the electrical signal in excitable cells. The four subunits of a voltage-gated K+ channel each have six transmembrane segments (S1–S6), whereas some other K+ channels, such as eukaryotic inward rectifier K+ channels and the prokaryotic KcsA channel, have only two transmembrane segments (M1 and M2). A voltage-gated K+ channel is formed by an ion-pore module (S5–S6, equivalent to M1–M2) and the surrounding voltage-sensing modules. The S4 segments are the primary voltage sensors while the intracellular activation gate is located near the COOH-terminal end of S6, although the coupling mechanism between them remains unknown. In the present study, we found that two short, complementary sequences in voltage-gated K+ channels are essential for coupling the voltage sensors to the intracellular activation gate. One sequence is the so called S4–S5 linker distal to the voltage-sensing S4, while the other is around the COOH-terminal end of S6, a region containing the actual gate-forming residues. PMID:12407078

  11. Janocchio--a Java applet for viewing 3D structures and calculating NMR couplings and NOEs.

    PubMed

    Evans, David A; Bodkin, Michael J; Baker, S Richard; Sharman, Gary J

    2007-07-01

    We present a Java applet, based on the open source Jmol program, which allows the calculation of coupling constants and NOEs from a three-dimensional structure. The program has all the viewing features of Jmol, but adds the capability to calculate both H-H and H-C 3-bond couplings constants. In the case of H--H couplings, the Altona equation is used to perform this. The program also calculates NOEs using the full relaxation matrix approach. All these calculations are driven from a simple point and click interface. The program can calculate values for multi-structure files, and can produce input files for the conformational fitting program NAMFIS.

  12. Temperature and voltage coupling to channel opening in transient receptor potential melastatin 8 (TRPM8).

    PubMed

    Raddatz, Natalia; Castillo, Juan P; Gonzalez, Carlos; Alvarez, Osvaldo; Latorre, Ramon

    2014-12-19

    Expressed in somatosensory neurons of the dorsal root and trigeminal ganglion, the transient receptor potential melastatin 8 (TRPM8) channel is a Ca(2+)-permeable cation channel activated by cold, voltage, phosphatidylinositol 4,5-bisphosphate, and menthol. Although TRPM8 channel gating has been characterized at the single channel and macroscopic current levels, there is currently no consensus regarding the extent to which temperature and voltage sensors couple to the conduction gate. In this study, we extended the range of voltages where TRPM8-induced ionic currents were measured and made careful measurements of the maximum open probability the channel can attain at different temperatures by means of fluctuation analysis. The first direct measurements of TRPM8 channel temperature-driven conformational rearrangements provided here suggest that temperature alone is able to open the channel and that the opening reaction is voltage-independent. Voltage is a partial activator of TRPM8 channels, because absolute open probability values measured with fully activated voltage sensors are less than 1, and they decrease as temperature rises. By unveiling the fast temperature-dependent deactivation process, we show that TRPM8 channel deactivation is well described by a double exponential time course. The fast and slow deactivation processes are temperature-dependent with enthalpy changes of 27.2 and 30.8 kcal mol(-1). The overall Q10 for the closing reaction is about 33. A three-tiered allosteric model containing four voltage sensors and four temperature sensors can account for the complex deactivation kinetics and coupling between voltage and temperature sensor activation and channel opening.

  13. Temperature and Voltage Coupling to Channel Opening in Transient Receptor Potential Melastatin 8 (TRPM8)*♦

    PubMed Central

    Raddatz, Natalia; Castillo, Juan P.; Gonzalez, Carlos; Alvarez, Osvaldo; Latorre, Ramon

    2014-01-01

    Expressed in somatosensory neurons of the dorsal root and trigeminal ganglion, the transient receptor potential melastatin 8 (TRPM8) channel is a Ca2+-permeable cation channel activated by cold, voltage, phosphatidylinositol 4,5-bisphosphate, and menthol. Although TRPM8 channel gating has been characterized at the single channel and macroscopic current levels, there is currently no consensus regarding the extent to which temperature and voltage sensors couple to the conduction gate. In this study, we extended the range of voltages where TRPM8-induced ionic currents were measured and made careful measurements of the maximum open probability the channel can attain at different temperatures by means of fluctuation analysis. The first direct measurements of TRPM8 channel temperature-driven conformational rearrangements provided here suggest that temperature alone is able to open the channel and that the opening reaction is voltage-independent. Voltage is a partial activator of TRPM8 channels, because absolute open probability values measured with fully activated voltage sensors are less than 1, and they decrease as temperature rises. By unveiling the fast temperature-dependent deactivation process, we show that TRPM8 channel deactivation is well described by a double exponential time course. The fast and slow deactivation processes are temperature-dependent with enthalpy changes of 27.2 and 30.8 kcal mol−1. The overall Q10 for the closing reaction is about 33. A three-tiered allosteric model containing four voltage sensors and four temperature sensors can account for the complex deactivation kinetics and coupling between voltage and temperature sensor activation and channel opening. PMID:25352597

  14. Different calcium channels are coupled to potassium channels with distinct physiological roles in vagal neurons.

    PubMed

    Sah, P

    1995-04-22

    Whole-cell and sharp microelectrode recordings were obtained from neurons of rat dorsal motor nucleus of the vagus (DMV) in transverse slices of the rat medulla maintained in vitro. Calcium currents were studied with sodium currents blocked with tetrodotoxin, potassium currents blocked by perfusing the cell with caesium as the main cation and using barium as the charge carrier. From a holding potential of -60 mV, inward currents activated at potentials positive of -50 mV and peaked around 0 mV. Voltage clamping the neuron at more hyperpolarised potentials did not reveal any low-threshold inward current. The inward current was effectively blocked by cadmium (100 microM) and nicked (1 mM), suggesting that it is carried by voltage-dependent calcium channels. The inward current could be separated into three pharmacologically distinct components: 40% of the whole cell current was omega-conotoxin sensitive; 20% of the current was nifedipine sensitive; and the rest was blocked by high concentrations of cadmium and nickel. This remaining current cannot be due to P-type calcium channels as omega-agatoxin had no effect on the inward current. Nifedipine had no significant effect on the action potential. Application of omega-conotoxin reduced the calcium component of the action potential and significantly reduced the potassium current underlying the afterhyperpolarization. Application of charybdotoxin slowed action potential repolarization. When N-type calcium channels were blocked with omega-conotoxin, charybdotoxin was still effective in slowing repolarization. In contrast, charybdotoxin was ineffective ineffective when calcium influx was blocked with the non-specific calcium channel blocker cadmium.(ABSTRACT TRUNCATED AT 250 WORDS)

  15. Influence of hillslope-channel coupling on two mountain headwater streams, Swiss National Park, Switzerland

    NASA Astrophysics Data System (ADS)

    Schoch, Anna; Hoffmann, Thomas; Dikau, Richard

    2014-05-01

    Sediment fluxes in mountain headwater streams are strongly conditioned by sediment supply from hillslopes and thus hillslope-channel coupling, defined as linkages connecting slopes and channels through sediment transport processes. Sediment supply from hillslopes can have major influences on channel characteristics. The main goal of my research is to achieve a better understanding of these influences on mountain headwater streams in two study areas. This is conducted through the investigation of "channel-reach morphology" according to MONTGOMERY AND BUFFINGTON (1997), morphometric and sedimentological characteristics of the channels and analysis of the slope-channel coupling system. The study was conducted in two valleys in the Swiss National Park, i.e. Val dal Botsch (VdB) and Val Mueschauns (VMu). In both headwaters slopes and channel are coupled effectively due to the small spatial vicinity and frequent debris flow processes connecting the two system components. Both catchments were glaciated in the Pleistocene but show contrasting glacial imprints today. While VdB has a V-shaped morphometry that is dominated by unconsolidated sediments (mainly talus and moraine material), VMu is U-shaped in the upper valley segments and the surface is mainly covered with bedrock. Several methods for data collection and analyses were used: (1) Channel-reach morphology classification, (2) DEM-based analysis of long profiles, ksn-values, slope-area plots and measurement of cross sections in the field, (3) investigation of sedimentological characteristics with pebble counts as well as (4) mapping of recent linkages between slopes and channel and determination of connectivity (effectivity of coupling) using a heuristic approach. The results show that sediment input into both headwater streams is dominated by debris flows. The debris flow catchments, as parts of the slope system, have the highest connectivity to the channels. Channel changes are greatest where debris flows cause

  16. Benchmarking density-functional-theory calculations of rotational g tensors and magnetizabilities using accurate coupled-cluster calculations

    NASA Astrophysics Data System (ADS)

    Lutnæs, Ola B.; Teale, Andrew M.; Helgaker, Trygve; Tozer, David J.; Ruud, Kenneth; Gauss, Jürgen

    2009-10-01

    An accurate set of benchmark rotational g tensors and magnetizabilities are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster single-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the results obtained is established for the rotational g tensors by careful comparison with experimental data, taking into account zero-point vibrational corrections. After an analysis of the basis sets employed, extrapolation techniques are used to provide estimates of the basis-set-limit quantities, thereby establishing an accurate benchmark data set. The utility of the data set is demonstrated by examining a wide variety of density functionals for the calculation of these properties. None of the density-functional methods are competitive with the CCSD or CCSD(T) methods. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of density-functional calculations constrained to give the same electronic density. The importance of current dependence in exchange-correlation functionals is discussed in light of this comparison.

  17. Analysing connectivity through landslide-channel geomorphic coupling in a large drainage system of Southern Romania

    NASA Astrophysics Data System (ADS)

    Jurchescu, Marta

    2014-05-01

    Unlike creep, splash erosion and linear erosion which sometimes are called "continuous" slope processes, since they are perceived as causing relatively continuous erosion on slopes and a rather rapid transport towards river channels, mass movement processes, excepting flows, have a discontinuous behavior, manifesting stochastically on time intervals ranging from one year to tens of years, while the displaced material can remain suspended in different parts of the slope forming sediment stores. It is obviously why estimating the sediment delivered to the river network by landslides becomes a difficult task. Landslide control on channel dynamics is just one of the several forms of hillslope-channel coupling. Landslide-channel connectivity is relevant for understanding the way landslides are contributing to the sediment flux within catchments and how their study should be integrated in the estimation of sediment budgets. This paper explores the geomorphic coupling of landslides with river channels based on an extensive landslide inventory. The study area is a large drainage basin (> 2400 km2) in southern Romania encompassing four different geomorphic units (mountains, hills, piedmont and plain). The region is highly affected by a wide range of geomorphic processes which contribute to supplying sediments to the drainage network. The presence of a reservoir at the river outlet emphasizes the importance of estimating sediment budgets, the first stage of which consists in studying sediment sources. High sediment transport is associated to flash floods, a fraction of which is due to the slope failures occurring in response to the undercutting of river channels. Nominal classification systems as well as quantitative measures available in the connectivity literature are adopted here to describe the landslides-channels contact zones. Characteristics of the geomorphic coupling interfaces are further linked to the resulting geomorphic effects of landslides on the drainage

  18. Electronic coupling calculations with transition charges, dipoles, and quadrupoles derived from electrostatic potential fitting

    SciTech Connect

    Fujimoto, Kazuhiro J.

    2014-12-07

    A transition charge, dipole, and quadrupole from electrostatic potential (TrESP-CDQ) method for electronic coupling calculations is proposed. The TrESP method is based on the classical description of electronic Coulomb interaction between transition densities for individual molecules. In the original TrESP method, only the transition charge interactions were considered as the electronic coupling. In the present study, the TrESP method is extended to include the contributions from the transition dipoles and quadrupoles as well as the transition charges. Hence, the self-consistent transition density is employed in the ESP fitting procedure. To check the accuracy of the present approach, several test calculations are performed to a helium dimer, a methane dimer, and an ethylene dimer. As a result, the TrESP-CDQ method gives a much improved description of the electronic coupling, compared with the original TrESP method. The calculated results also show that the self-consistent treatment to the transition densities contributes significantly to the accuracy of the electronic coupling calculations. Based on the successful description of the electronic coupling, the contributions to the electronic coupling are also analyzed. This analysis clearly shows a negligible contribution of the transition charge interaction to the electronic coupling. Hence, the distribution of the transition density is found to strongly influence the magnitudes of the transition charges, dipoles, and quadrupoles. The present approach is useful for analyzing and understanding the mechanism of excitation-energy transfer.

  19. [Magnetic field numerical calculation and analysis for magnetic coupling of centrifugal blood pump for extracorporeal circulation].

    PubMed

    Hu, Zhaoyan; Lu, Lijun; Zhang, Tianyi; Chen, Zhenglong; Zhang, Tao

    2013-12-01

    This paper mainly studies the driving system of centrifugal blood pump for extracorporeal circulation, with the core being disc magnetic coupling. Structure parameters of disc magnetic coupling are related to the ability of transferring magnetic torque. Therefore, it is necessary to carry out disc magnetic coupling permanent magnet pole number (n), air gap length (L(g)), permanent magnet thickness (L(m)), permanent magnet body inside diameter (R(i)) and outside diameter (R(o)), etc. thoroughly. This paper adopts the three-dimensional static magnetic field edge element method of Ansys for numerical calculation, and analyses the relations of magnetic coupling each parameter to transmission magnetic torque. It provides a good theory basis and calculation method for further optimization of the disc magnetic coupling.

  20. Ab initio calculation of the deuterium quadrupole coupling in liquid water

    NASA Astrophysics Data System (ADS)

    Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc

    1992-10-01

    The quadrupole coupling constant and asymmetry parameter for the deuteron in liquid heavy water was determined using purely theoretical methods. Molecular-dynamics simulations with the ab initio potential-energy surface of Lie and Clementi were used to generate snapshots of the liquid. The electric-field gradient at the deuteron was then calculated for these configurations and averaged to obtain the liquid quadrupole coupling constant. At 300 K a quadrupole coupling constant of 256±5 kHz and an asymmetry parameter of 0.164±0.003 were obtained. The temperature dependence of the quadrupole coupling constant was investigated.

  1. Dynamical coupled-channels model for neutrino-induced meson productions in resonance region

    NASA Astrophysics Data System (ADS)

    Nakamura, S. X.; Kamano, H.; Sato, T.

    2015-10-01

    A dynamical coupled-channels (DCC) model for neutrino-nucleon reactions in the resonance region is developed. Starting from the DCC model that we have previously developed through an analysis of π N ,γ N →π N ,η N ,K Λ ,K Σ reaction data for W ≤2.1 GeV , we extend the model of the vector current to Q2≤3.0 (GeV /c )2 by analyzing electron-induced reaction data for both proton and neutron targets. We derive axial-current matrix elements that are related to the π N interactions of the DCC model through the partially conserved axial current (PCAC) relation. Consequently, the interference pattern between resonant and nonresonant amplitudes is uniquely determined. We calculate cross sections for neutrino-induced meson productions, and compare them with available data. Our result for the single-pion production reasonably agrees with the data. We also make a comparison with the double-pion production data. Our model is the first DCC model that can give the double-pion production cross sections in the resonance region. We also make comparison of our result with other existing models to reveal an importance of testing the models in the light of PCAC and electron reaction data. The DCC model developed here will be a useful input for constructing a neutrino-nucleus reaction model and a neutrino event generator for analyses of neutrino experiments.

  2. Convergent close-coupling calculations of positron scattering on metastable helium

    SciTech Connect

    Utamuratov, R.; Kadyrov, A. S.; Fursa, D. V.; Bray, I.; Stelbovics, A. T.

    2010-10-15

    The convergent close-coupling method has been applied to positron scattering on a helium atom in the 2 {sup 3}S metastable state. For this system the positronium (Ps) formation channel is open even at zero scattering energy making the inclusion of the Ps channels especially important. Spin algebra is presented for the general case of arbitrary spins. A proof is given of the often-used assumption about the relationship between the amplitudes for ortho-positronium and para-positronium formation. The cross sections for scattering from 2 {sup 3}S are shown to be significantly larger than those obtained for the ground state.

  3. Higher-order results for the relation between channel conductance and the Coulomb blockade for two tunnel-coupled quantum dots

    NASA Astrophysics Data System (ADS)

    Golden, John M.; Halperin, Bertrand I.

    1996-12-01

    We extend earlier results on the relation between the dimensionless tunneling channel conductance g and the fractional Coulomb-blockade peak splitting f for two electrostatically equivalent dots connected by an arbitrary number Nch of tunneling channels with bandwidths W much larger than the two-dot differential charging energy U2. By calculating f through the second order in g in the limit of weak coupling (g-->0), we illuminate the difference in behavior of the large-Nch and small-Nch regimes and make more plausible extrapolation to the strong-coupling (g-->1) limit. For the special case of Nch=2 and strong coupling, we eliminate an apparent ultraviolet divergence and obtain the next leading term of an expansion in (1-g). We show that the results we calculate are independent of such band structure details as the fraction of occupied fermionic single-particle states in the weak-coupling theory and the nature of the cutoff in the bosonized strong-coupling theory. The results agree with calculations for metallic junctions in the Nch-->∞ limit and improve the previous good agreement with recent two-channel experiments.

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

    PubMed

    Liao, Ke; Grüneis, Andreas

    2016-10-14

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

  5. Regulation of channel function due to physical energetic coupling with a lipid bilayer

    SciTech Connect

    Ashrafuzzaman, Md.; Tseng, C.-Y.; Tuszynski, J.A.

    2014-03-07

    Highlights: • Lipid membrane regulation of membrane protein functions has been addressed. • Energetics behind ion channel-membrane coupling phenomena has been investigated. • Charge based interactions stabilize peptide–lipid complex. • Screened Coulomb interaction model explains the energetics. • Van der Waals and electrostatic forces drive peptides and lipids to close proximity. - Abstract: Regulation of membrane protein functions due to hydrophobic coupling with a lipid bilayer has been investigated. An energy formula describing interactions between lipid bilayer and integral ion channels with different structures, which is based on the screened Coulomb interaction approximation, has been developed. Here the interaction energy is represented as being due to charge-based interactions between channel and lipid bilayer. The hydrophobic bilayer thickness channel length mismatch is found to induce channel destabilization exponentially while negative lipid curvature linearly. Experimental parameters related to channel dynamics are consistent with theoretical predictions. To measure comparable energy parameters directly in the system and to elucidate the mechanism at an atomistic level we performed molecular dynamics (MD) simulations of the ion channel forming peptide–lipid complexes. MD simulations indicate that peptides and lipids experience electrostatic and van der Waals interactions for short period of time when found within each other’s proximity. The energies from these two interactions are found to be similar to the energies derived theoretically using the screened Coulomb and the van der Waals interactions between peptides (in ion channel) and lipids (in lipid bilayer) due to mainly their charge properties. The results of in silico MD studies taken together with experimental observable parameters and theoretical energetic predictions suggest that the peptides induce ion channels inside lipid membranes due to peptide–lipid physical interactions

  6. Influence of RF channels mismatch and mutual coupling phenomenon on performance of a multistatic passive radar

    NASA Astrophysics Data System (ADS)

    Hossa, Robert; Górski, Maksymilian

    2010-09-01

    In the paper we analyze the influence of RF channels mismatch and mutual coupling effect on the performance of the multistatic passive radar with Uniform Circular Array (UCA) configuration. The problem was tested intensively in numerous different scenarios with a reference virtual multistatic passive radar. Finally, exemplary results of the computer software simulations are provided and discussed.

  7. Light-Quark Baryon Spectroscopy from ANL-Osaka Dynamical Coupled-Channels Analysis

    NASA Astrophysics Data System (ADS)

    Kamano, Hiroyuki

    We review our recent efforts for determining resonance parameters associated with light-quark baryons (N*,Δ *,Λ *,Σ *) through comprehensive analyses of various meson production reactions off the nucleon within the ANL-Osaka dynamical coupled-channels approach.

  8. Calculation of indirect nuclear spin-spin coupling constants within the regular approximation for relativistic effects.

    PubMed

    Filatov, Michael; Cremer, Dieter

    2004-06-22

    A new method for calculating the indirect nuclear spin-spin coupling constant within the regular approximation to the exact relativistic Hamiltonian is presented. The method is completely analytic in the sense that it does not employ numeric integration for the evaluation of relativistic corrections to the molecular Hamiltonian. It can be applied at the level of conventional wave function theory or density functional theory. In the latter case, both pure and hybrid density functionals can be used for the calculation of the quasirelativistic spin-spin coupling constants. The new method is used in connection with the infinite-order regular approximation with modified metric (IORAmm) to calculate the spin-spin coupling constants for molecules containing heavy elements. The importance of including exact exchange into the density functional calculations is demonstrated.

  9. Molar conductivity calculation of Li-ion battery electrolyte based on mode coupling theory

    NASA Astrophysics Data System (ADS)

    Pu, Weihua; He, Xiangming; Lu, Jiufang; Jiang, Changyin; Wan, Chunrong

    2005-12-01

    A method is proposed to calculate molar conductivity based on mode coupling theory in which the ion transference number is introduced into the theory. The molar conductivities of LiPF6, LiClO4, LiBF4, LiAsF6 in PC (propylene carbonate) are calculated based on this method. The results fit well to the literature data. This presents a potential way to calculate the conductivities of Li-ion battery electrolytes.

  10. Molar conductivity calculation of Li-ion battery electrolyte based on mode coupling theory.

    PubMed

    Pu, Weihua; He, Xiangming; Lu, Jiufang; Jiang, Changyin; Wan, Chunrong

    2005-12-15

    A method is proposed to calculate molar conductivity based on mode coupling theory in which the ion transference number is introduced into the theory. The molar conductivities of LiPF6, LiClO4, LiBF4, LiAsF6 in PC (propylene carbonate) are calculated based on this method. The results fit well to the literature data. This presents a potential way to calculate the conductivities of Li-ion battery electrolytes.

  11. Onsager's cross coupling effects in gas flows confined to micro-channels

    NASA Astrophysics Data System (ADS)

    Wang, Ruijie; Xu, Xinpeng; Xu, Kun; Qian, Tiezheng

    2016-08-01

    In rarefied gases, mass and heat transport processes interfere with each other, leading to the mechano-caloric effect and thermo-osmotic effect, which are of interest to both theoretical study and practical applications. We employ the unified gas-kinetic scheme to investigate these cross coupling effects in gas flows in micro-channels. Our numerical simulations cover channels of planar surfaces and also channels of ratchet surfaces, with Onsager's reciprocal relation verified for both cases. For channels of planar surfaces, simulations are performed in a wide range of Knudsen number, and our numerical results show good agreement with the literature results. For channels of ratchet surfaces, simulations are performed for both the slip and transition regimes, and our numerical results not only confirm the theoretical prediction [Phys. Rev. Lett. 107, 164502 (2011), 10.1103/PhysRevLett.107.164502] for the Knudsen number in the slip regime but also show that the off-diagonal kinetic coefficients for cross coupling effects are maximized at a Knudsen number in the transition regime. Finally, a preliminary optimization study is carried out for the geometry of Knudsen pump based on channels of ratchet surfaces.

  12. Allosteric coupling of the inner activation gate to the outer pore of a potassium channel.

    PubMed

    Peters, Christian J; Fedida, David; Accili, Eric A

    2013-10-23

    In potassium channels, functional coupling of the inner and outer pore gates may result from energetic interactions between residues and conformational rearrangements that occur along a structural path between them. Here, we show that conservative mutations of a residue near the inner activation gate of the Shaker potassium channel (I470) modify the rate of C-type inactivation at the outer pore, pointing to this residue as part of a pathway that couples inner gate opening to changes in outer pore structure and reduction of ion flow. Because they remain equally sensitive to rises in extracellular potassium, altered inactivation rates of the mutant channels are not secondary to modified binding of potassium to the outer pore. Conservative mutations of I470 also influence the interaction of the Shaker N-terminus with the inner gate, which separately affects the outer pore.

  13. Allosteric coupling of the inner activation gate to the outer pore of a potassium channel

    NASA Astrophysics Data System (ADS)

    Peters, Christian J.; Fedida, David; Accili, Eric A.

    2013-10-01

    In potassium channels, functional coupling of the inner and outer pore gates may result from energetic interactions between residues and conformational rearrangements that occur along a structural path between them. Here, we show that conservative mutations of a residue near the inner activation gate of the Shaker potassium channel (I470) modify the rate of C-type inactivation at the outer pore, pointing to this residue as part of a pathway that couples inner gate opening to changes in outer pore structure and reduction of ion flow. Because they remain equally sensitive to rises in extracellular potassium, altered inactivation rates of the mutant channels are not secondary to modified binding of potassium to the outer pore. Conservative mutations of I470 also influence the interaction of the Shaker N-terminus with the inner gate, which separately affects the outer pore.

  14. Two-channel Kondo physics in a Majorana island coupled to a Josephson junction

    NASA Astrophysics Data System (ADS)

    Landau, L. A.; Sela, E.

    2017-01-01

    We study a Majorana island coupled to a bulk superconductor via a Josephson junction and to multiple external normal leads. In the absence of the Josephson coupling, the system displays a topological Kondo state, which had been largely studied recently. However, we find that this state is unstable even to small Josephson coupling, which instead leads at low temperature T to a new fixed point. Most interesting is the case of three external leads, forming a minimal electronic realization of the long sought two-channel Kondo effect. While the T =0 conductance corresponds to simple resonant Andreev reflection, the leading T dependence forms an experimental fingerprint for non-Fermi-liquid properties.

  15. Electrical coupling between the human serotonin transporter and voltage-gated Ca(2+) channels.

    PubMed

    Ruchala, Iwona; Cabra, Vanessa; Solis, Ernesto; Glennon, Richard A; De Felice, Louis J; Eltit, Jose M

    2014-07-01

    Monoamine transporters have been implicated in dopamine or serotonin release in response to abused drugs such as methamphetamine or ecstasy (MDMA). In addition, monoamine transporters show substrate-induced inward currents that may modulate excitability and Ca(2+) mobilization, which could also contribute to neurotransmitter release. How monoamine transporters modulate Ca(2+) permeability is currently unknown. We investigate the functional interaction between the human serotonin transporter (hSERT) and voltage-gated Ca(2+) channels (CaV). We introduce an excitable expression system consisting of cultured muscle cells genetically engineered to express hSERT. Both 5HT and S(+)MDMA depolarize these cells and activate the excitation-contraction (EC)-coupling mechanism. However, hSERT substrates fail to activate EC-coupling in CaV1.1-null muscle cells, thus implicating Ca(2+) channels. CaV1.3 and CaV2.2 channels are natively expressed in neurons. When these channels are co-expressed with hSERT in HEK293T cells, only cells expressing the lower-threshold L-type CaV1.3 channel show Ca(2+) transients evoked by 5HT or S(+)MDMA. In addition, the electrical coupling between hSERT and CaV1.3 takes place at physiological 5HT concentrations. The electrical coupling between monoamine neurotransmitter transporters and Ca(2+) channels such as CaV1.3 is a novel mechanism by which endogenous substrates (neurotransmitters) or exogenous substrates (like ecstasy) could modulate Ca(2+)-driven signals in excitable cells.

  16. Functional coupling of TRPV4 channels and BK channels in regulating spontaneous contractions of the guinea pig urinary bladder.

    PubMed

    Isogai, Ayu; Lee, Ken; Mitsui, Retsu; Hashitani, Hikaru

    2016-09-01

    We investigated the role of TRPV4 channels (TRPV4) in regulating the contractility of detrusor smooth muscle (DSM) and muscularis mucosae (MM) of the urinary bladder. Distribution of TRPV4 in DSM and MM of guinea-pig bladders was examined by fluorescence immunohistochemistry. Changes in the contractility of DSM and MM bundles were measured using isometric tension recording. Intracellular Ca(2+) dynamics were visualized by Cal-520 fluorescent Ca(2+) imaging, while membrane potential changes were recorded using intracellular microelectrode technique. DSM and MM expressed TRPV4 immunoreactivity. GSK1016790A (GSK, 1 nM), a TRPV4 agonist, evoked a sustained contraction in both DSM and MM associated with a cessation of spontaneous phasic contractions in a manner sensitive to HC-067047 (10 μM), a TRPV4 antagonist. Iberiotoxin (100 nM) and paxilline (1 μM), large conductance Ca(2+)-activated K(+) (BK) channel blockers restored the spontaneous contractions in GSK. The sustained contractions in DSM and MM were reduced by nifedipine (10 μM), a blocker of L-type voltage-dependent Ca(2+) channels (LVDCCs) by about 40 % and by nominally Ca(2+)-free solution by some 90 %. GSK (1 nM) abolished spontaneous Ca(2+) transients, increased basal Ca(2+) levels and also prevented spontaneous action potential discharge associated with DSM membrane hyperpolarization. In conclusion, Ca(2+) influx through TRPV4 appears to activate BK channels to suppress spontaneous contractions and thus a functional coupling of TRPV4 with BK channels may act as a self-limiting mechanism for bladder contractility during its storage phase. Despite the membrane hyperpolarization in GSK, Ca(2+) entry mainly through TRPV4 develops the tonic contraction.

  17. The coupling of acetylcholine-induced BK channel and calcium channel in guinea pig saccular type II vestibular hair cells.

    PubMed

    Kong, Wei-Jia; Guo, Chang-Kai; Zhang, Xiao-Wen; Chen, Xiong; Zhang, Song; Li, Guan-Qiao; Li, Zhi-Wang; Van Cauwenberge, Paul

    2007-01-19

    Molecular biological studies and electrophysiological data have demonstrated that acetylcholine (ACh) is the principal cochlear and vestibular efferent neurotransmitter among mammalians. However, the functional roles of ACh in type II vestibular hair cells (VHCs II) among mammalians are still unclear, with the exception of the well-known alpha9-containing nicotinic ACh receptor (alpha9-containing nAChR)-activated small conductance, calcium-dependent potassium current (SK) in cochlear hair cells and frog saccular hair cells. The activation of SK current was necessary for the calcium influx through the alpha9-containing nAChR. Recently, we have demonstrated that ACh-induced big conductance, calcium-dependent potassium current (BK) was present in VHCs II of the vestibular end-organ of guinea pig. In this study, the nature of calcium influx for the activation of ACh-induced BK current in saccular VHCs II of guinea pig was investigated. Following extracellular perfusion of ACh, saccular VHCs II displayed a sustained outward current, which was sensitive to iberiotoxin (IBTX). High concentration of apamin failed to inhibit the current amplitude of ACh-induced outward current. Intracellular application of Cs(+) completely abolished the current evoked by ACh. ACh-induced current was potently inhibited by nifedipine, nimodipine, Cd(2+) and Ni(2+), respectively. The inhibition potency of these four calcium channel antagonists was nimodipine>nifedipine>cadmium>nickel. The L-type Ca(2+) channels agonist, (-)-Bay-K 8644 mimicked the effect of ACh and activated an IBTX-sensitive current. In addition, partial VHCs II displayed a biphasic waveform. In conclusion, the present data showed that in the guinea pig saccular VHCs II, ACh-induced BK channel was coupled with the calcium channel, but not the receptor. The perfusion of ACh will drive the opening of calcium channels; the influx of calcium ions will then activate the BK current.

  18. Calculated coupling efficiency between an elliptical-core optical fiber and an optical waveguide over temperature

    NASA Technical Reports Server (NTRS)

    Tuma, Margaret L.; Weisshaar, Andreas; Li, Jian; Beheim, Glenn

    1995-01-01

    To determine the feasibility of coupling the output of a single-mode optical fiber into a single-mode rib waveguide in a temperature varying environment, a theoretical calculation of the coupling efficiency between the two was investigated. Due to the complex geometry of the rib guide, there is no analytical solution to the wave equation for the guided modes, thus, approximation and/or numerical techniques must be utilized to determine the field patterns of the guide. In this study, three solution methods were used for both the fiber and guide fields; the effective-index method (EIM), Marcatili's approximation, and a Fourier method. These methods were utilized independently to calculate the electric field profile of each component at two temperatures, 20 C and 300 C, representing a nominal and high temperature. Using the electric field profile calculated from each method, the theoretical coupling efficiency between an elliptical-core optical fiber and a rib waveguide was calculated using the overlap integral and the results were compared. It was determined that a high coupling efficiency can be achieved when the two components are aligned. The coupling efficiency was more sensitive to alignment offsets in the y direction than the x, due to the elliptical modal field profile of both components. Changes in the coupling efficiency over temperature were found to be minimal.

  19. Coupling mechanical forces to electrical signaling: molecular motors and the intracellular transport of ion channels.

    PubMed

    Barry, Joshua; Gu, Chen

    2013-04-01

    Proper localization of various ion channels is fundamental to neuronal functions, including postsynaptic potential plasticity, dendritic integration, action potential initiation and propagation, and neurotransmitter release. Microtubule-based forward transport mediated by kinesin motors plays a key role in placing ion channel proteins to correct subcellular compartments. PDZ- and coiled-coil-domain proteins function as adaptor proteins linking ionotropic glutamate and GABA receptors to various kinesin motors, respectively. Recent studies show that several voltage-gated ion channel/transporter proteins directly bind to kinesins during forward transport. Three major regulatory mechanisms underlying intracellular transport of ion channels are also revealed. These studies contribute to understanding how mechanical forces are coupled to electrical signaling and illuminating pathogenic mechanisms in neurodegenerative diseases.

  20. Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values

    NASA Astrophysics Data System (ADS)

    Schober, Christoph; Reuter, Karsten; Oberhofer, Harald

    2016-02-01

    We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or "flavors" of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer), we find that our new scheme gives improved electronic couplings for HAB7 (-6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (-15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.

  1. Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values.

    PubMed

    Schober, Christoph; Reuter, Karsten; Oberhofer, Harald

    2016-02-07

    We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or "flavors" of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer), we find that our new scheme gives improved electronic couplings for HAB7 (-6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (-15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.

  2. Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values

    SciTech Connect

    Schober, Christoph; Reuter, Karsten; Oberhofer, Harald

    2016-02-07

    We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or “flavors” of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer), we find that our new scheme gives improved electronic couplings for HAB7 (−6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (−15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.

  3. Exchange couplings calculation in the Double Perovskite Sr2CrWO6

    NASA Astrophysics Data System (ADS)

    El Rhazouani, O.; Slassi, A.; Ziat, Y.; Benyoussef, A.

    2017-06-01

    In this paper, an approximation method has been used to calculate Super Exchange (SE) and the Double Exchange (DE) couplings in the Double Perovskite (DP) structure of Sr2CrWO6. The method relies on a relation between internal energy per site and magnetization per site and Monte Carlo simulation in the framework of Ising model. A new model parameter has been proposed and varied to find the exchange couplings that verify the experimental Curie temperature measured under an external field h = 0.01 T. SE coupling has been found equal to -7.554 meV and the DE couplings corresponding respectively to Cr and W ions have been found equal to 17.629 and 5.661 meV. Internal energy per site has been calculated.

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

    SciTech Connect

    Egashira, Kazuhiro; Yamada, Yurika; Kita, Yukiumi; Tachikawa, Masanori

    2015-02-07

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

  5. Dynamical coupled-channels study of pi N --> pi pi N reactions

    SciTech Connect

    Kamano, Hiroyuki; Julia Diaz, Bruno; Lee, Tsung-Shung; Matsuyama, Akihiko; Sato, Toru

    2009-01-01

    As a step toward performing a complete coupled-channels analysis of the world data of pi N, gamma^* N --> pi N, eta N, pi pi N reactions, the pi N --> pi pi N reactions are investigated starting with the dynamical coupled-channels model developed in Phys. Rev. C76, 065201 (2007). The channels included are pi N, eta N, and pi pi N which has pi Delta, rho N, and sigma N resonant components. The non-resonant amplitudes are generated from solving a set of coupled-channels equations with the meson-baryon potentials defined by effective Lagrangians. The resonant amplitudes are generated from 16 bare excited nucleon (N^*) states which are dressed by the non-resonant interactions as constrained by the unitarity condition. The available total cross section data of pi^+ p --> pi^+ pi^+ n, pi^+ pi^0 and pi^- p --> pi^+ pi^- n, pi^- pi^0 n, pi^0 pi^0 n can be reproduced to a very large extent both in magnitudes and energy-dependence. Possible improvements of the model are investigated, in p

  6. Accurate collision-induced line-coupling parameters for the fundamental band of CO in He - Close coupling and coupled states scattering calculations

    NASA Technical Reports Server (NTRS)

    Green, Sheldon; Boissoles, J.; Boulet, C.

    1988-01-01

    The first accurate theoretical values for off-diagonal (i.e., line-coupling) pressure-broadening cross sections are presented. Calculations were done for CO perturbed by He at thermal collision energies using an accurate ab initio potential energy surface. Converged close coupling, i.e., numerically exact values, were obtained for coupling to the R(0) and R(2) lines. These were used to test the coupled states (CS) and infinite order sudden (IOS) approximate scattering methods. CS was found to be of quantitative accuracy (a few percent) and has been used to obtain coupling values for lines to R(10). IOS values are less accurate, but, owing to their simplicity, may nonetheless prove useful as has been recently demonstrated.

  7. Calculation of correlation function of a spatially coupled spiking neural network

    NASA Astrophysics Data System (ADS)

    Qiu, Siwei; Chow, Carson

    The dynamics of a large but finite number of coupled spiking neurons is not well understood. We analyze finite size effects in a network of synaptically coupled theta neurons. We show how the system can be characterized by a functional integral from which finite size effects are calculated perturbatively. We discuss the implications of this technique for bump attractors. Thanks to support of the Intramural Research Program of the NIH, NIDDK.

  8. STIM1 dimers undergo unimolecular coupling to activate Orai1 channels

    NASA Astrophysics Data System (ADS)

    Zhou, Yandong; Wang, Xizhuo; Wang, Xianming; Loktionova, Natalia A.; Cai, Xiangyu; Nwokonko, Robert M.; Vrana, Erin; Wang, Youjun; Rothberg, Brad S.; Gill, Donald L.

    2015-09-01

    The endoplasmic reticulum (ER) Ca2+ sensor, STIM1, becomes activated when ER-stored Ca2+ is depleted and translocates into ER-plasma membrane junctions where it tethers and activates Orai1 Ca2+ entry channels. The dimeric STIM1 protein contains a small STIM-Orai-activating region (SOAR)--the minimal sequence sufficient to activate Orai1 channels. Since SOAR itself is a dimer, we constructed SOAR concatemer-dimers and introduced mutations at F394, which is critical for Orai1 coupling and activation. The F394H mutation in both SOAR monomers completely blocks dimer function, but F394H introduced in only one of the dimeric SOAR monomers has no effect on Orai1 binding or activation. This reveals an unexpected unimolecular coupling between STIM1 and Orai1 and argues against recent evidence suggesting dimeric interaction between STIM1 and two adjacent Orai1 channel subunits. The model predicts that STIM1 dimers may be involved in crosslinking between Orai1 channels with implications for the kinetics and localization of Orai1 channel opening.

  9. Coupled channels approach to photo-meson production on the nucleon

    NASA Astrophysics Data System (ADS)

    Lenske, Horst

    2017-01-01

    The coupled channels Lagrangian approach of the Giessen model (GiM) for meson production on the nucleon is discussed and applied to a selected set of meson production channels on the nucleon, ranging from πN → πN and γN → πN, eta-production and associated strangeness production to 2πN channels in the resonance energy region. We present an updated coupled-channel analysis of eta-meson production including all recent photoproduction data on the proton. The dip structure observed in the differential cross sections at c.m. energies W=1.68 GeV is explained by destructive interference between the S11(1535) and S11(1560) states, not confirming the postulated sharp state. Kaon production on the nucleon is investigated in KΛ and KΣ exit channels. The approach to 2πN production has been significantly improved by using the isobar approximation with σN and πΔ1232 intermediate states. Three-body unitarity is maintained up to interference between the isobar subchannels. We obtain RσN(1440)=27+4-9% and RπΔ(1440)=12+5-3% for the for the σN and πΔ1232 decay branching ratios of N*(1440) respectively. The extracted πN inelasticities and reaction amplitudes are consistent with the results of other groups.

  10. Calculation of nuclear spin-spin coupling constants using frozen density embedding

    NASA Astrophysics Data System (ADS)

    Götz, Andreas W.; Autschbach, Jochen; Visscher, Lucas

    2014-03-01

    We present a method for a subsystem-based calculation of indirect nuclear spin-spin coupling tensors within the framework of current-spin-density-functional theory. Our approach is based on the frozen-density embedding scheme within density-functional theory and extends a previously reported subsystem-based approach for the calculation of nuclear magnetic resonance shielding tensors to magnetic fields which couple not only to orbital but also spin degrees of freedom. This leads to a formulation in which the electron density, the induced paramagnetic current, and the induced spin-magnetization density are calculated separately for the individual subsystems. This is particularly useful for the inclusion of environmental effects in the calculation of nuclear spin-spin coupling constants. Neglecting the induced paramagnetic current and spin-magnetization density in the environment due to the magnetic moments of the coupled nuclei leads to a very efficient method in which the computationally expensive response calculation has to be performed only for the subsystem of interest. We show that this approach leads to very good results for the calculation of solvent-induced shifts of nuclear spin-spin coupling constants in hydrogen-bonded systems. Also for systems with stronger interactions, frozen-density embedding performs remarkably well, given the approximate nature of currently available functionals for the non-additive kinetic energy. As an example we show results for methylmercury halides which exhibit an exceptionally large shift of the one-bond coupling constants between 199Hg and 13C upon coordination of dimethylsulfoxide solvent molecules.

  11. Calculation of nuclear spin-spin coupling constants using frozen density embedding.

    PubMed

    Götz, Andreas W; Autschbach, Jochen; Visscher, Lucas

    2014-03-14

    We present a method for a subsystem-based calculation of indirect nuclear spin-spin coupling tensors within the framework of current-spin-density-functional theory. Our approach is based on the frozen-density embedding scheme within density-functional theory and extends a previously reported subsystem-based approach for the calculation of nuclear magnetic resonance shielding tensors to magnetic fields which couple not only to orbital but also spin degrees of freedom. This leads to a formulation in which the electron density, the induced paramagnetic current, and the induced spin-magnetization density are calculated separately for the individual subsystems. This is particularly useful for the inclusion of environmental effects in the calculation of nuclear spin-spin coupling constants. Neglecting the induced paramagnetic current and spin-magnetization density in the environment due to the magnetic moments of the coupled nuclei leads to a very efficient method in which the computationally expensive response calculation has to be performed only for the subsystem of interest. We show that this approach leads to very good results for the calculation of solvent-induced shifts of nuclear spin-spin coupling constants in hydrogen-bonded systems. Also for systems with stronger interactions, frozen-density embedding performs remarkably well, given the approximate nature of currently available functionals for the non-additive kinetic energy. As an example we show results for methylmercury halides which exhibit an exceptionally large shift of the one-bond coupling constants between (199)Hg and (13)C upon coordination of dimethylsulfoxide solvent molecules.

  12. Calculation of nuclear spin-spin coupling constants using frozen density embedding

    SciTech Connect

    Götz, Andreas W.; Autschbach, Jochen; Visscher, Lucas

    2014-03-14

    We present a method for a subsystem-based calculation of indirect nuclear spin-spin coupling tensors within the framework of current-spin-density-functional theory. Our approach is based on the frozen-density embedding scheme within density-functional theory and extends a previously reported subsystem-based approach for the calculation of nuclear magnetic resonance shielding tensors to magnetic fields which couple not only to orbital but also spin degrees of freedom. This leads to a formulation in which the electron density, the induced paramagnetic current, and the induced spin-magnetization density are calculated separately for the individual subsystems. This is particularly useful for the inclusion of environmental effects in the calculation of nuclear spin-spin coupling constants. Neglecting the induced paramagnetic current and spin-magnetization density in the environment due to the magnetic moments of the coupled nuclei leads to a very efficient method in which the computationally expensive response calculation has to be performed only for the subsystem of interest. We show that this approach leads to very good results for the calculation of solvent-induced shifts of nuclear spin-spin coupling constants in hydrogen-bonded systems. Also for systems with stronger interactions, frozen-density embedding performs remarkably well, given the approximate nature of currently available functionals for the non-additive kinetic energy. As an example we show results for methylmercury halides which exhibit an exceptionally large shift of the one-bond coupling constants between {sup 199}Hg and {sup 13}C upon coordination of dimethylsulfoxide solvent molecules.

  13. Electro-osmotic flow of couple stress fluids in a micro-channel propagated by peristalsis

    NASA Astrophysics Data System (ADS)

    Tripathi, Dharmendra; Yadav, Ashu; Anwar Bég, O.

    2017-04-01

    A mathematical model is developed for electro-osmotic peristaltic pumping of a non-Newtonian liquid in a deformable micro-channel. Stokes' couple stress fluid model is employed to represent realistic working liquids. The Poisson-Boltzmann equation for electric potential distribution is implemented owing to the presence of an electrical double layer (EDL) in the micro-channel. Using long wavelength, lubrication theory and Debye-Huckel approximations, the linearized transformed dimensionless boundary value problem is solved analytically. The influence of electro-osmotic parameter (inversely proportional to Debye length), maximum electro-osmotic velocity (a function of external applied electrical field) and couple stress parameter on axial velocity, volumetric flow rate, pressure gradient, local wall shear stress and stream function distributions is evaluated in detail with the aid of graphs. The Newtonian fluid case is retrieved as a special case with vanishing couple stress effects. With increasing the couple stress parameter there is a significant increase in the axial pressure gradient whereas the core axial velocity is reduced. An increase in the electro-osmotic parameter both induces flow acceleration in the core region (around the channel centreline) and it also enhances the axial pressure gradient substantially. The study is relevant in the simulation of novel smart bio-inspired space pumps, chromatography and medical micro-scale devices.

  14. SLO BK Potassium Channels Couple Gap Junctions to Inhibition of Calcium Signaling in Olfactory Neuron Diversification

    PubMed Central

    Schumacher, Jennifer A.; Wang, Xiaohong; Merrill, Sean A.; Millington, Grethel; Bayne, Brittany; Jorgensen, Erik M.; Chuang, Chiou-Fen

    2016-01-01

    The C. elegans AWC olfactory neuron pair communicates to specify asymmetric subtypes AWCOFF and AWCON in a stochastic manner. Intercellular communication between AWC and other neurons in a transient NSY-5 gap junction network antagonizes voltage-activated calcium channels, UNC-2 (CaV2) and EGL-19 (CaV1), in the AWCON cell, but how calcium signaling is downregulated by NSY-5 is only partly understood. Here, we show that voltage- and calcium-activated SLO BK potassium channels mediate gap junction signaling to inhibit calcium pathways for asymmetric AWC differentiation. Activation of vertebrate SLO-1 channels causes transient membrane hyperpolarization, which makes it an important negative feedback system for calcium entry through voltage-activated calcium channels. Consistent with the physiological roles of SLO-1, our genetic results suggest that slo-1 BK channels act downstream of NSY-5 gap junctions to inhibit calcium channel-mediated signaling in the specification of AWCON. We also show for the first time that slo-2 BK channels are important for AWC asymmetry and act redundantly with slo-1 to inhibit calcium signaling. In addition, nsy-5-dependent asymmetric expression of slo-1 and slo-2 in the AWCON neuron is necessary and sufficient for AWC asymmetry. SLO-1 and SLO-2 localize close to UNC-2 and EGL-19 in AWC, suggesting a role of possible functional coupling between SLO BK channels and voltage-activated calcium channels in AWC asymmetry. Furthermore, slo-1 and slo-2 regulate the localization of synaptic markers, UNC-2 and RAB-3, in AWC neurons to control AWC asymmetry. We also identify the requirement of bkip-1, which encodes a previously identified auxiliary subunit of SLO-1, for slo-1 and slo-2 function in AWC asymmetry. Together, these results provide an unprecedented molecular link between gap junctions and calcium pathways for terminal differentiation of olfactory neurons. PMID:26771544

  15. A method for calculating turbulent boundary layers and losses in the flow channels of turbomachines

    NASA Technical Reports Server (NTRS)

    Schumann, Lawrence F.

    1987-01-01

    An interactive inviscid core flow-boundary layer method is presented for the calculation of turbomachine channel flows. For this method, a one-dimensional inviscid core flow is assumed. The end-wall and blade surface boundary layers are calculated using an integral entrainment method. The boundary layers are assumed to be collateral and thus are two-dimensional. The boundary layer equations are written in a streamline coordinate system. The streamwise velocity profiles are approximated by power law profiles. Compressibility is accounted for in the streamwise direction but not in the normal direction. Equations are derived for the special cases of conical and two-dimensional rectangular diffusers. For these cases, the assumptions of a one-dimensional core flow and collateral boundary layers are valid. Results using the method are compared with experiment and good quantitative agreement is obtained.

  16. Ab initio calculations of spectroscopic properties of Cr5+ using coupled-cluster theory

    NASA Astrophysics Data System (ADS)

    Dutta, N. N.; Majumder, S.

    2016-04-01

    In this paper, we present ionization potentials, excitation energies, fine-structure splittings, and allowed and forbidden transition amplitudes of five-times-ionized chromium ion as calculated using the relativistic coupled-cluster theory. The wave functions of different single-valence electron configurations are generated using the Dirac-Coulomb-Gaunt Hamiltonian. Effects of electron correlation and Gaunt interaction in the calculations of these properties are studied explicitly. Contributions from different correlation terms associated with the coupled-cluster theory are reported in the calculations of the transition amplitudes. Using these amplitudes and the experimental wavelengths, we calculate astrophysically important transition parameters of several transition lines. Lifetime of the metastable state 3d^2D_{5/2} is found to be 111.66 s.

  17. Grain size indicators of sedimentary coupling between hillslopes and channels in a dryland basin

    NASA Astrophysics Data System (ADS)

    Hollings, Rory; Michealides, Katerina; Bliss Singer, Michael

    2017-04-01

    In dryland landscapes, heterogeneous and short-lived rainstorms generate runoff on slopes and streamflow in channels, which drive sediment movement from hillslope surfaces to channels and the transport of bed material sediment within channels. Long-term topographic evolution of drainage basins is partly determined by the relative balance of hillslope sediment supply to channels and the evacuation of channel sediment. However, it is not clear whether supply or evacuation is dominant over longer timescales (>>100 y) within dryland basins. One important indicator of local cumulative sediment transport is grain size (GS). On dryland hillslopes, grain size is governed over long timescales by weathering, but on short time scales (events to decades), is controlled by event-driven transport of the debris mantle. In the channel, GS reflects the input of hillslope sediment and the selective transport of particles along the bed. It is currently unknown how these two processes are expressed systematically within GS distributions on slopes and in channels within drylands, but this information could be useful to explain the history of the relative balance between hillslope sediment supply to channels and net sediment transport in the channel. We investigate this problem by combining field measurements of surface sediment grain size distributions in channels and on hillslopes with 1m LiDAR topography, >60 years of rainfall and channel discharge data from the Walnut Gulch Experimental Watershed (WGEW) in Arizona, and simple calculations of grain-sized based local stress distributions for various rainfall and discharge events. Hydrological scenarios of overland flow on hillslopes and channel flow conditions were derived from distributions of historic data at WGEW and were selected to reflect the wide range of storm intensities and durations, and channel discharges. 1) We used three quartiles of the entire distribution of measured discharge values for 80 locations throughout the

  18. Quantum Mechanical Calculations of Charge Effects on gating the KcsA channel

    SciTech Connect

    Kariev, Alisher M.; Znamenskiy, Vasiliy S.; Green, Michael E.

    2007-02-06

    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. A series of ab initio (density functional) calculations were carried out on side chains of a set of amino acids, plus water, from the (intracellular) gating region of the KcsA K+ channel. Their atomic coordinates, except hydrogen, are known from X-ray structures [D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, R. MacKinnon, The structure of the potassium channel: molecular basis of K+ conduction and selectivity, Science 280 (1998) 69–77; R. MacKinnon, S.L. Cohen, A. Kuo, A. Lee, B.T. Chait, Structural conservation in prokaryotic and eukaryotic potassium channels, Science 280 (1998) 106–109; Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, R. MacKinnon, The open pore conformation of potassium channels. Nature 417 (2001) 523–526], as are the coordinates of some water oxygen atoms. The 1k4c structure is used for the starting coordinates. Quantum mechanical optimization, in spite of the starting configuration, places the atoms in positions much closer to the 1j95, more tightly closed, configuration. This state shows four water molecules forming a “basket” under the Q119 side chains, blocking the channel. When a hydrated K+ approaches this “basket”, the optimized system shows a strong set of hydrogen bonds with the K+ at defined positions, preventing further approach of the K+ to the basket. This optimized structure with hydrated K+ added shows an ice-like 12 molecule nanocrystal of water. If the water molecules exchange, unless they do it as a group, the channel will remain blocked. The “basket” itself appears to be very stable, although it is possible that the K+ with its hydrating water molecules may be more mobile, capable

  19. Regulation of Ca(V)2 calcium channels by G protein coupled receptors.

    PubMed

    Zamponi, Gerald W; Currie, Kevin P M

    2013-07-01

    Voltage gated calcium channels (Ca²⁺ channels) are key mediators of depolarization induced calcium influx into excitable cells, and thereby play pivotal roles in a wide array of physiological responses. This review focuses on the inhibition of Ca(V)2 (N- and P/Q-type) Ca²⁺-channels by G protein coupled receptors (GPCRs), which exerts important autocrine/paracrine control over synaptic transmission and neuroendocrine secretion. Voltage-dependent inhibition is the most widespread mechanism, and involves direct binding of the G protein βγ dimer (Gβγ) to the α1 subunit of Ca(V)2 channels. GPCRs can also recruit several other distinct mechanisms including phosphorylation, lipid signaling pathways, and channel trafficking that result in voltage-independent inhibition. Current knowledge of Gβγ-mediated inhibition is reviewed, including the molecular interactions involved, determinants of voltage-dependence, and crosstalk with other cell signaling pathways. A summary of recent developments in understanding the voltage-independent mechanisms prominent in sympathetic and sensory neurons is also included. This article is part of a Special Issue entitled: Calcium channels.

  20. Green's function calculation of through-bond electronic coupling in donor bridge acceptor model systems

    NASA Astrophysics Data System (ADS)

    de Santana, O. L.; da Gama, A. A. S.

    1999-12-01

    The Green's function formalism is applied for the calculation of the effective through-bond donor-acceptor coupling in model molecular systems. The calculation is performed at a Hartree-Fock (self-consistent) level, by using semiempirical AM1 and CNDO/S, and ab initio STO-3G methods. The results are compared with that obtained from the splitting of the appropriate levels, by using the Koopmans' theorem, within each one of the selected quantum chemical methods.

  1. TORT/MCNP coupling method for the calculation of neutron flux around a core of BWR.

    PubMed

    Kurosawa, Masahiko

    2005-01-01

    For the analysis of BWR neutronics performance, accurate data are required for neutron flux distribution over the In-Reactor Pressure Vessel equipments taking into account the detailed geometrical arrangement. The TORT code can calculate neutron flux around a core of BWR in a three-dimensional geometry model, but has difficulties in fine geometrical modelling and lacks huge computer resource. On the other hand, the MCNP code enables the calculation of the neutron flux with a detailed geometry model, but requires very long sampling time to give enough number of particles. Therefore, a TORT/MCNP coupling method has been developed to eliminate the two problems mentioned above in each code. In this method, the TORT code calculates angular flux distribution on the core surface and the MCNP code calculates neutron spectrum at the points of interest using the flux distribution. The coupling method will be used as the DOT-DOMINO-MORSE code system. This TORT/MCNP coupling method was applied to calculate the neutron flux at points where induced radioactivity data were measured for 54Mn and 60Co and the radioactivity calculations based on the neutron flux obtained from the above method were compared with the measured data.

  2. A Theoretical Model for Calculating Voltage Sensitivity of Ion Channels and the Application on Kv1.2 Potassium Channel

    PubMed Central

    Yang, Huaiyu; Gao, Zhaobing; Li, Ping; Yu, Kunqian; Yu, Ye; Xu, Tian-Le; Li, Min; Jiang, Hualiang

    2012-01-01

    Voltage sensing confers conversion of a change in membrane potential to signaling activities underlying the physiological processes. For an ion channel, voltage sensitivity is usually experimentally measured by fitting electrophysiological data to Boltzmann distributions. In our study, a two-state model of the ion channel and equilibrium statistical mechanics principle were used to test the hypothesis of empirically calculating the overall voltage sensitivity of an ion channel on the basis of its closed and open conformations, and determine the contribution of individual residues to the voltage sensing. We examined the theoretical paradigm by performing experimental measurements with Kv1.2 channel and a series of mutants. The correlation between the calculated values and the experimental values is at respective level, R2 = 0.73. Our report therefore provides in silico prediction of key conformations and has identified additional residues critical for voltage sensing. PMID:22768937

  3. Double and single pion photoproduction within a dynamical coupled-channels model

    SciTech Connect

    Hiroyuki Kamano; Julia-Diaz, Bruno; Lee, T. -S. H.; Matsuyama, Akihiko; Sato, Toru

    2009-12-16

    Within a dynamical coupled-channels model which has already been fixed from analyzing the data of the πN → πN and γN → πN reactions, we present the predicted double pion photoproduction cross sections up to the second resonance region, W < 1.7 GeV. The roles played by the different mechanisms within our model in determining both the single and double pion photoproduction reactions are analyzed, focusing on the effects due to the direct γN → ππN mechanism, the interplay between the resonant and non-resonant amplitudes, and the coupled-channels effects. As a result, the model parameters which can be determined most effectively in the combined studies of both the single and double pion photoproduction data are identified for future studies.

  4. Double and single pion photoproduction within a dynamical coupled-channels model

    DOE PAGES

    Hiroyuki Kamano; Julia-Diaz, Bruno; Lee, T. -S. H.; ...

    2009-12-16

    Within a dynamical coupled-channels model which has already been fixed from analyzing the data of the πN → πN and γN → πN reactions, we present the predicted double pion photoproduction cross sections up to the second resonance region, W < 1.7 GeV. The roles played by the different mechanisms within our model in determining both the single and double pion photoproduction reactions are analyzed, focusing on the effects due to the direct γN → ππN mechanism, the interplay between the resonant and non-resonant amplitudes, and the coupled-channels effects. As a result, the model parameters which can be determined mostmore » effectively in the combined studies of both the single and double pion photoproduction data are identified for future studies.« less

  5. Multi-scale lattice Boltzmann and mode-coupling theory calculations of the flow of a glass-forming liquid.

    PubMed

    Papenkort, S; Voigtmann, Th

    2015-11-28

    We present a hybrid-lattice Boltzmann (LB) algorithm for calculating the flow of glass-forming fluids that are governed by integral constitutive equations with pronounced nonlinear, non-Markovian dependence of the stresses on the flow history. The LB simulation for the macroscopic flow fields is combined with the mode-coupling theory (MCT) of the glass transition as a microscopic theory, in the framework of the integration-through transients formalism. Using the combined LB-MCT algorithm, pressure-driven planar channel flow is studied for a schematic MCT model neglecting spatial correlations in the microscopic dynamics. The cessation dynamics after removal of the driving pressure gradient shows strong signatures of oscillatory flow both in the macroscopic fields and the microscopic correlation functions.

  6. Coupling of alpha channeling to parallel wavenumber upshift in lower hybrid current drive

    NASA Astrophysics Data System (ADS)

    Ochs, I. E.; Bertelli, N.; Fisch, N. J.

    2015-08-01

    Although lower hybrid (LH) waves have been shown to be effective in driving plasma current in present-day tokamaks, they are predicted to strongly interact with the energetic α particles born from fusion reactions in eventual tokamak reactors. However, in the presence of the expected steep α particle birth gradient, this interaction can produce wave amplification rather than wave damping. Here, we identify the flexibilities and constraints in achieving this amplification effect through a consideration of symmetries in the channeling interaction, in the wave propagation, and in the tokamak field configuration. Interestingly, for standard LH current drive that supports the poloidal magnetic field, we find that wave amplification through α channeling is fundamentally coupled to the poorly understood | k ∥ | upshift. In so doing, we show that wave launch from the tokamak high-field side is favorable both for α-channeling and for achieving the | k ∥ | upshift.

  7. Effect of coupled channels on the energy dependence of phenomenological optical potential parameters

    NASA Astrophysics Data System (ADS)

    Al-Rayashi, W. S.; Jaghoub, M. I.

    2016-06-01

    The phenomenological optical potential parameters are known to vary with incident energy due to sources of nonlocalities in the nucleon-nucleus elastic scattering process. Here we investigate the effect of one source, which is coupling the ground-state elastic channel to collective inelastic excitations on the energy dependence of the optical potential parameters. For incident energies in the range 10-70 MeV, we considered elastic and inelastic nucleon scattering from light, medium, and heavy nuclei ranging from 6Li to 208Pb. The potential parameters were first determined by fitting the elastic angular distributions only. Then we included coupling to collective excitation channels and determined the potential parameters that reproduced the elastic and inelastic angular distribution data simultaneously. Our results show that coupling to inelastic excitations reduces the energy variations of the potential parameters compared to that of the elastic scattering case. In particular, the our best fit values for the real part of the spin-orbit term are highly stable as a function of energy. The values of the surface imaginary term are not only more stable but are also reduced compared to the elastic case. The reduction is a direct consequence of the channel coupling accounting explicitly for part of the flux removed from the elastic channel. In the fitting process we also searched for the best fit values of the deformation parameters. Our values compare well with the corresponding ones obtained in previous works. Finally, we used our best fit values for the potential and deformation parameters to theoretically predict the total elastic, total cross section, and polarization data. The predicted values are in very good agreement with the experimental data.

  8. High-power compact laser with segmented longitudinal pumping of coupled laser channels

    SciTech Connect

    Mamonov, D N; Il'ichev, N N; Sirotkin, A A; Pivovarov, P A; Derzhavin, S I; Klimentov, S M; Rebrov, S G

    2015-06-30

    The characteristics of a compact Nd:YAG/Cr:YAG laser with segmented end pumping using a bundle of seven optical fibres are presented. In the regime of optical coupling of thus formed seven laser channels, 3-ns pulses with an energy up to 20 mJ, as well as their trains, are obtained. The used method makes it possible to scale the energy and power of lasers of this type with controlled spatial beam profile. (lasers)

  9. Dynamical Coupled-Channel Model of Meson Production Reactions in the Nucleon Resonance Region

    SciTech Connect

    T.-S. H. Lee; A. Matsuyama; T. Sato

    2006-11-15

    A dynamical coupled-channel model is presented for investigating the nucleon resonances (N*) in the meson production reactions induced by pions and photons. Our objective is to extract the N* parameters and to investigate the meson production reaction mechanisms for mapping out the quark-gluon substructure of N* from the data. The model is based on an energy-independent Hamiltonian which is derived from a set of Lagrangians by using a unitary transformation method.

  10. Light-Quark Baryon Spectroscopy within ANL-Osaka Dynamical Coupled-Channels Approach

    NASA Astrophysics Data System (ADS)

    Kamano, Hiroyuki

    2016-10-01

    Recent results on the study of light-quark baryons with the ANL-Osaka dynamical coupled-channels (DCC) approach are presented, which contain the N^* and Δ ^* spectroscopy via the analysis of π N and γ N reactions and the Λ ^* and Σ ^* spectroscopy via the analysis of K^- p reactions. A recent application of our DCC approach to neutrino-nucleon reactions in the resonance region is also presented.

  11. Technical Note for 8D Likelihood Effective Higgs Couplings Extraction Framework in the Golden Channel

    SciTech Connect

    Chen, Yi; Di Marco, Emanuele; Lykken, Joe; Spiropulu, Maria; Vega-Morales, Roberto; Xie, Si

    2014-10-17

    In this technical note we present technical details on various aspects of the framework introduced in arXiv:1401.2077 aimed at extracting effective Higgs couplings in the $h\\to 4\\ell$ `golden channel'. Since it is the primary feature of the framework, we focus in particular on the convolution integral which takes us from `truth' level to `detector' level and the numerical and analytic techniques used to obtain it. We also briefly discuss other aspects of the framework.

  12. Dynamical coupled-channels model of meson photo- and electroproduction in the nucleon resonance region

    NASA Astrophysics Data System (ADS)

    Sato, T.

    2007-12-01

    A dynamical approach of the meson production reaction for extracting nucleon resonance parameters has been developed. We report on the γ N Δ form factors extracted from the recent pion electroproduction data and the coupled-channels model of π N scattering up to W ≤ 2 GeV. An analysis of the resonance poles extracted using the speed-plot and time-delay methods is briefly discussed.

  13. Measurement and analysis of channel attenuation characteristics for an implantable galvanic coupling human-body communication.

    PubMed

    Zhang, Shuang; Pun, Sio Hang; Mak, Peng Un; Qin, Yu-Ping; Liu, Yi-He; Vai, Mang I

    2016-11-14

    In this study, an experiment was designed to verify the low power consumption of galvanic coupling human-body communication. A silver electrode (silver content: 99%) is placed in a pig leg and a sine wave signal with the power of 0 dBm is input. Compared with radio frequency communication and antenna transmission communication, attenuation is reduced by approximately 10 to 15 dB, so channel characteristics are highly improved.

  14. A QCDSR calculation for the {phi}D{sub s}D{sub s} coupling constant

    SciTech Connect

    Rodrigues, B. O.; Chiapparini, M.; Bracco, M. E.

    2013-03-25

    In this work, we use the QCD Sum Rules (QCDSR) technique to obtain informations about the strong coupling constant of the three meson vertex {phi}D{sub s}D{sub s}. The calculation is done for the case where the {phi} meson is considered off-shell.

  15. Electronic Couplings for Resonance Energy Transfer from CCSD Calculations: From Isolated to Solvated Systems.

    PubMed

    Caricato, Marco; Curutchet, Carles; Mennucci, Benedetta; Scalmani, Giovanni

    2015-11-10

    Quantum mechanical (QM) calculations of electronic couplings provide great insights for the study of resonance energy transfer (RET). However, most of these calculations rely on approximate QM methods due to the computational limitations imposed by the size of typical donor-acceptor systems. In this work, we present a novel implementation that allows computing electronic couplings at the coupled cluster singles and doubles (CCSD) level of theory. Solvent effects are also taken into account through the polarizable continuum model (PCM). As a test case, we use a dimer of indole, a common model system for tryptophan, which is routinely used as an intrinsic fluorophore in Förster resonance energy transfer studies. We consider two bright π → π* states, one of which has charge transfer character. Lastly, the results are compared with those obtained by applying TD-DFT in combination with one of the most popular density functionals, B3LYP.

  16. Coupling between the voltage-sensing and pore domains in a voltage-gated potassium channel.

    PubMed

    Schow, Eric V; Freites, J Alfredo; Nizkorodov, Alex; White, Stephen H; Tobias, Douglas J

    2012-07-01

    Voltage-dependent potassium (Kv), sodium (Nav), and calcium channels open and close in response to changes in transmembrane (TM) potential, thus regulating cell excitability by controlling ion flow across the membrane. An outstanding question concerning voltage gating is how voltage-induced conformational changes of the channel voltage-sensing domains (VSDs) are coupled through the S4-S5 interfacial linking helices to the opening and closing of the pore domain (PD). To investigate the coupling between the VSDs and the PD, we generated a closed Kv channel configuration from Aeropyrum pernix (KvAP) using atomistic simulations with experiment-based restraints on the VSDs. Full closure of the channel required, in addition to the experimentally determined TM displacement, that the VSDs be displaced both inwardly and laterally around the PD. This twisting motion generates a tight hydrophobic interface between the S4-S5 linkers and the C-terminal ends of the pore domain S6 helices in agreement with available experimental evidence.

  17. Coupled-Channels Predictions of the Fine Structure in the α Decay of Neutron-Deficient Ds, Cn, and 114 Isotopes

    NASA Astrophysics Data System (ADS)

    Ni, Dongdong; Ren, Zhongzhou

    2013-11-01

    The fine structure in the α decay of neutron-deficient Ds, Cn, and 114 isotopes have been systematically predicted using the multi-channel cluster model (MCCM). The theoretical α-decay energy Qα is deduced from the local formula of Qα values for heavy and superheavy nuclei. The ground-state rotational states in a daughter nucleus are established based on the macroscopic- microscopic model with some improved ingredients. Exact five-channels microscopic calculations are performed, and the branching ratios to various daughter states and total α-decay half-lives are evaluated. Any adjustable parameter is not introduced in our calculations. It is expected that the present coupled- channel predictions would provide a reference for future structure researches of superheavy nuclei.

  18. Calculations of the exciton coupling elements between the DNA bases using the transition density cube method.

    PubMed

    Czader, Arkadiusz; Bittner, Eric R

    2008-01-21

    Excited states of the double-stranded DNA model (A)12.(T)12 were calculated in the framework of the Frenkel exciton theory. The off-diagonal elements of the exciton matrix were calculated using the transition densities and ideal dipole approximation associated with the lowest energy pipi* excitations of the individual nucleobases as obtained from time-dependent density functional theory calculations. The values of the coupling calculated with the transition density cubes (TDC) and ideal dipole approximation (IDA) methods were found to be significantly different for the small interchromophore distances. It was shown that the IDA overestimates the coupling significantly. The effects of structural fluctuations of the DNA chain on the magnitude of dipolar coupling were also found to be very significant. The difference between the maximum and minimum values was as large as 1000 and 300 cm(-1) for the IDA and TDC methods, respectively. To account for these effects, the properties of the excited states were averaged over a large number of conformations obtained from the molecular dynamics simulations. Our calculations using the TDC method indicate that the absorption of the UV light creates exciton states carrying the majority of the oscillator strength that are delocalized over at least six DNA bases. Upon relaxation, the excitation states localize over at least four contiguous bases.

  19. Regulatory Conformational Coupling between CLC Anion Channel Membrane and Cytoplasmic Domains.

    PubMed

    Yamada, Toshiki; Strange, Kevin

    2016-11-01

    CLC anion channels are homodimeric proteins. Each subunit is comprised of 18 α-helices designated "A-R" and an intracellular carboxy-terminus containing two cystathionine-β-synthase (CBS1 and CBS2) domains. Conformational coupling between membrane and intracellular domains via poorly understood mechanisms is required for CLC regulation. The activity of the C. elegans CLC channel CLH-3b is reduced by phosphorylation of a carboxy-terminus "activation domain," which disrupts its interaction with CBS domains. CBS2 interfaces with a short intracellular loop, the H-I loop, connecting membrane helices H and I. Alanine mutation of a conserved H-I loop tyrosine residue, Y232, prevents regulation demonstrating that the loop functions to couple phosphorylation-dependent CBS domain conformational changes to channel membrane domains. To gain further insight into the mechanisms of this coupling, we mutated conserved amino acid residues in membrane helices H and I. Only mutation of the H-helix valine residue V228 to leucine prevented phosphorylation-dependent channel regulation. Structural and functional studies of other CLC proteins suggest that V228 may interact with Y529, a conserved R-helix tyrosine residue that forms part of the CLC ion conduction pathway. Mutation of Y529 to alanine also prevented CLH-3b regulation. Intracellular application of the sulfhydryl reactive reagent MTSET using CLH-3b channels engineered with single-cysteine residues in CBS2 indicate that V228L, Y529A, and Y232A disrupt putative regulatory intracellular conformational changes. Extracellular Zn(2+) inhibits CLH-3b and alters the effects of intracellular MTSET on channel activity. The effects of Zn(2+) are disrupted by V228L, Y529A, and Y232A. Collectively, our findings indicate that there is conformational coupling between CBS domains and the H and R membrane helices mediated by the H-I loop. We propose a simple model by which conformational changes in H and R helices mediate CLH-3b regulation

  20. Competing superconducting channels in iron pnictides from the strong coupling theory with biquadratic spin interactions

    NASA Astrophysics Data System (ADS)

    Yu, Rong; Nevidomskyy, Andriy H.

    2016-12-01

    We study the symmetry and strength of the superconducting pairing in a two-orbital t-{{J}1}-{{J}2}-K model for iron pnictides using the slave boson strong coupling approach. We show that the nearest-neighbor biquadratic interaction -K{{({{S}i}\\cdot {{S}j})}2} strongly affects the superconducting pairing phase diagram by promoting the {{d}{{x2}-{{y}2}}} B 1g and the {{s}{{x2}+{{y}2}}} A 1g channels. The resulting phase diagram consists of several competing pairing channels, including the isotropic {{s}+/-} A 1g channel, an anisotropic {{d}{{x2}-{{y}2}}} B 1g channel, and two s+\\text{i}d pairing channels. We have investigated the evolution of superconducting states with electron doping, and find that the biquadratic interaction plays a crucial role in stabilizing the s+\\text{i}d and even pure d-wave pairing in the heavily electron- and hole-doped regimes. In addition, we identify a novel orbital-B 1g pairing channel, which has a s-wave form factor but a B 1g symmetry. This channel has a comparable pairing amplitude to the d-wave pairing, and may strongly influence the superconducting gap anisotropy of the system in the overdoped regime. These findings are crucial in understanding the doping evolution of the superconducting gap anisotropy observed by angle resolved photoemission spectroscopy in the iron pnictides and iron chalcogenides, including the heavily K-doped BaFe2As2 and K-doped FeSe films.

  1. Test case specifications for coupled neutronics-thermal hydraulics calculation of Gas-cooled Fast Reactor

    NASA Astrophysics Data System (ADS)

    Osuský, F.; Bahdanovich, R.; Farkas, G.; Haščík, J.; Tikhomirov, G. V.

    2017-01-01

    The paper is focused on development of the coupled neutronics-thermal hydraulics model for the Gas-cooled Fast Reactor. It is necessary to carefully investigate coupled calculations of new concepts to avoid recriticality scenarios, as it is not possible to ensure sub-critical state for a fast reactor core under core disruptive accident conditions. Above mentioned calculations are also very suitable for development of new passive or inherent safety systems that can mitigate the occurrence of the recriticality scenarios. In the paper, the most promising fuel material compositions together with a geometry model are described for the Gas-cooled fast reactor. Seven fuel pin and fuel assembly geometry is proposed as a test case for coupled calculation with three different enrichments of fissile material in the form of Pu-UC. The reflective boundary condition is used in radial directions of the test case and vacuum boundary condition is used in axial directions. During these condition, the nuclear system is in super-critical state and to achieve a stable state (which is numerical representation of operational conditions) it is necessary to decrease the reactivity of the system. The iteration scheme is proposed, where SCALE code system is used for collapsing of a macroscopic cross-section into few group representation as input for coupled code NESTLE.

  2. CFD-CAA Coupled Calculations of a Tandem Cylinder Configuration to Assess Facility Installation Effects

    NASA Technical Reports Server (NTRS)

    Redonnet, Stephane; Lockard, David P.; Khorrami, Mehdi R.; Choudhari, Meelan M.

    2011-01-01

    This paper presents a numerical assessment of acoustic installation effects in the tandem cylinder (TC) experiments conducted in the NASA Langley Quiet Flow Facility (QFF), an open-jet, anechoic wind tunnel. Calculations that couple the Computational Fluid Dynamics (CFD) and Computational Aeroacoustics (CAA) of the TC configuration within the QFF are conducted using the CFD simulation results previously obtained at NASA LaRC. The coupled simulations enable the assessment of installation effects associated with several specific features in the QFF facility that may have impacted the measured acoustic signature during the experiment. The CFD-CAA coupling is based on CFD data along a suitably chosen surface, and employs a technique that was recently improved to account for installed configurations involving acoustic backscatter into the CFD domain. First, a CFD-CAA calculation is conducted for an isolated TC configuration to assess the coupling approach, as well as to generate a reference solution for subsequent assessments of QFF installation effects. Direct comparisons between the CFD-CAA calculations associated with the various installed configurations allow the assessment of the effects of each component (nozzle, collector, etc.) or feature (confined vs. free jet flow, etc.) characterizing the NASA LaRC QFF facility.

  3. A charged residue in S4 regulates coupling among the activation gate, voltage, and Ca2+ sensors in BK channels.

    PubMed

    Zhang, Guohui; Yang, Huanghe; Liang, Hongwu; Yang, Junqiu; Shi, Jingyi; McFarland, Kelli; Chen, Yihan; Cui, Jianmin

    2014-09-10

    Coupling between the activation gate and sensors of physiological stimuli during ion channel activation is an important, but not well-understood, molecular process. One difficulty in studying sensor-gate coupling is to distinguish whether a structural perturbation alters the function of the sensor, the gate, or their coupling. BK channels are activated by membrane voltage and intracellular Ca(2+) via allosteric mechanisms with coupling among the activation gate and sensors quantitatively defined, providing an excellent model system for studying sensor-gate coupling. By studying BK channels expressed in Xenopus oocytes, here we show that mutation E219R in S4 alters channel function by two independent mechanisms: one is to change voltage sensor activation, shifting voltage dependence, and increase valence of gating charge movements; the other is to regulate coupling among the activation gate, voltage sensor, and Ca(2+) binding via electrostatic interactions with E321/E324 located in the cytosolic side of S6 in a neighboring subunit, resulting in a shift of the voltage dependence of channel opening and increased Ca(2+) sensitivity. These results suggest a structural arrangement of the inner pore of BK channels differing from that in other voltage gated channels.

  4. Functional coupling of TRPV4, IK, and SK channels contributes to Ca(2+)-dependent endothelial injury in rodent lung.

    PubMed

    Lin, Mike T; Jian, Ming-Yuan; Taylor, Mark S; Cioffi, Donna L; Yap, Fui C; Liedtke, Wolfgang; Townsley, Mary I

    2015-06-01

    Our previous work has shown that the increased lung endothelial permeability response to 14,15-epoxyeicosatrienoic acid (14,15-EET) in rat lung requires Ca(2+) entry via vanilloid type-4 transient receptor potential (TRPV4) channels. Recent studies suggest that activation of TRPV4 channels in systemic vascular endothelium prolongs agonist-induced hyperpolarization and amplifies Ca(2+) entry by activating Ca(2+)-activated K(+) (KCa) channels, resulting in vessel relaxation. Activation of endothelial KCa channels thus has potential to increase the electrochemical driving force for Ca(2+) influx via TRPV4 channels and to amplify permeability responses to TRPV4 activation in lung. To examine this hypothesis, we used Western blot analysis, electrophysiological recordings, and isolated-lung permeability measurements to document expression of TRPV4 and KCa channels and the potential for functional coupling. The results show that rat pulmonary microvascular endothelial cells express TRPV4 and 3 KCa channels of different conductances: large (BK), intermediate (IK), and small (SK3). However, TRPV4 channel activity modulates the IK and SK3, but not the BK, channel current density. Furthermore, the TRPV4-mediated permeability response to 14,15-EET in mouse lung is significantly attenuated by pharmacologic blockade of IK and SK3, but not BK, channels. Collectively, this functional coupling suggests that endothelial TRPV4 channels in rodent lung likely form signaling microdomains with IK and SK3 channels and that the integrated response dictates the extent of lung endothelial injury caused by 14,15-EET.

  5. The electronic nonadiabatic coupling term: can it be ignored in dynamic calculations?

    PubMed

    Halász, G J; Vibók, A; Suhai, S; Baer, M

    2007-12-28

    Whereas the search for the degeneracy points which are better known as conical intersections (or ci-points) is usually carried out with a lot of devotion, the nonadiabatic coupling terms (NACTs) which together with the adiabatic potential energy surfaces appear in the nuclear Born-Oppenheimer-Schrodinger equation are ignored in most dynamical calculations. In the present article we consider two well known frameworks, namely, the semiclassical surface hopping method and the vibrational coupling model Hamiltonian that avoid the NACTs and examine to what extent, this procedure is justified.

  6. Calculation of electromechanical coupling coefficient of Lamb waves in multilayered plates.

    PubMed

    Fan, Li; Zhang, Shu-Yi; Zheng, Kai; Lin, Wei; Gao, Hui-Dong

    2006-12-22

    Two methods have been always used to calculate the electromechanical coupling coefficient of a Lamb wave in a multilayered plate: one is an approximate method using the acoustic velocity difference under different electric boundary conditions and the other is the Green's function method. The Green's function method is more accurate but more complicated, because an 8N-order matrix is used for calculating the electromechanical coupling coefficient of the Lamb wave in an N-layered plate, which induces great computation loads and some calculation deviations. In this paper, a transfer matrix method is used for calculating the electromechanical coupling coefficient of Lamb waves in a multilayered plate, in which only an 8-order matrix is needed regardless of the number of layers of the plate. The results show that the transfer matrix method can obtain the same accuracy as those by the Green's function method, but the computation load and deviation are greatly decreased by avoiding the use of a high order matrix used in the Green's function method.

  7. On the calculations of the nuclear spin spin coupling constants in small water clusters

    NASA Astrophysics Data System (ADS)

    Cybulski, Hubert; Pecul, Magdalena; Sadlej, Joanna

    2006-08-01

    The calculations of the nuclear spin-spin coupling constants were carried out for small water clusters (H 2O) n, n = 2-6, 12, and 17, using density functional theory (DFT) and second-order polarization propagator method (SOPPA). A wide range of different standard and modified basis sets was tested to enable the choice of the possibly smallest and most flexible basis set. The changes in the oxygen-proton coupling constants upon the cluster formation between the nuclei involved in hydrogen bonding cover a range of ca. 13 Hz. The range of the calculated changes in intramolecular 1JOH couplings shows that the simple model of rigid water clusters seems to be sufficient to reproduce properly the sign and to estimate the magnitude of the gas-to-liquid shift. The sign of the complexation-induced changes in the intramolecular 2JHH coupling constant is different for molecules with a different coordination number. While the sign is positive for the molecules of the single donor-single acceptor (DA) and single donor-double acceptor (DAA) types, it is negative for the double donor-single acceptor (DDA) molecules. In the four-coordinated double donor-double acceptor (DDAA) molecules the sign of Δ 2JHH varies. The hydrogen-bond transmitted intermolecular coupling constants are substantial: 1hJOH spans the range from 2.8 to 8.4 Hz while 2hJOO varies from -0.6 to 7.5 Hz. The average intermolecular 1hJOH coupling constant decays slowly with the H⋯O distance in the cyclic clusters n = 2-6. The average 2hJOO coupling decreases exponentially with the O⋯O separation for the cyclic clusters n = 2-6.

  8. Coupled-channels density-matrix approach to low-energy nuclear collision dynamics: A technique for quantifying quantum decoherence effects on reaction observables

    SciTech Connect

    Diaz-Torres, Alexis

    2010-11-15

    The coupled-channels density-matrix technique for nuclear reaction dynamics, which is based on the Liouville-von Neumann equation with Lindblad dissipative terms, is developed with the inclusion of full angular momentum couplings. It allows a quantitative study of the role and importance of quantum decoherence in nuclear scattering. Formulas of asymptotic observables that can reveal effects of quantum decoherence are given. A method for extracting energy-resolved scattering information from the time-dependent density matrix is introduced. As an example, model calculations are carried out for the low-energy collision of the {sup 16}O projectile on the {sup 154}Sm target.

  9. Opening of Astrocytic Mitochondrial ATP-Sensitive Potassium Channels Upregulates Electrical Coupling between Hippocampal Astrocytes in Rat Brain Slices

    PubMed Central

    Wang, Jiangping; Li, Zhongxia; Feng, Mei; Ren, Keming; Shen, Guoxia; Zhao, Congying; Jin, Xiaoming; Jiang, Kewen

    2013-01-01

    Astrocytes form extensive intercellular networks through gap junctions to support both biochemical and electrical coupling between adjacent cells. ATP-sensitive K+ (KATP) channels couple cell metabolic state to membrane excitability and are enriched in glial cells. Activation of astrocytic mitochondrial KATP (mitoKATP) channel regulates certain astrocytic functions. However, less is known about its impact on electrical coupling between directly coupled astrocytes ex vivo. By using dual patch clamp recording, we found that activation of mitoKATP channel increased the electrical coupling ratio in brain slices. The electrical coupling ratio started to increase 3 min after exposure to Diazoxide, a mitoKATP channel activator, peaked at 5 min, and maintained its level with little adaptation until the end of the 10-min treatment. Blocking the mitoKATP channel with 5-hydroxydecanoate, inhibited electrical coupling immediately, and by 10-min, the ratio dropped by 71% of the initial level. Activation of mitoKATP channel also decreased the latency time of the transjunctional currents by 50%. The increase in the coupling ratio resulting from the activation of the mitoKATP channel in a single astrocyte was further potentiated by the concurrent inhibiting of the channel on the recipient astrocyte. Furthermore, Meclofenamic acid, a gap-junction inhibitor which completely blocked the tracer coupling, hardly reversed the impact of mitoKATP channel's activation on electrical coupling (by 7%). The level of mitochondrial Connexin43, a gap junctional subunit, significantly increased by 70% in astrocytes after 10-min Diazoxide treatment. Phospho-ERK signals were detected in Connexin43 immunoprecipitates in the Diazoxide-treated astrocytes, but not untreated control samples. Finally, inhibiting ERK could attenuate the effects of Diazoxide on electrical coupling by 61%. These findings demonstrate that activation of astrocytic mitoKATP channel upregulates electrical coupling between

  10. A generalized spin diffusion equation with four electrochemical potentials for channels with spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Sayed, Shehrin; Hong, Seokmin; Datta, Supriyo

    We will present a general semiclassical theory for an arbitrary channel with spin-orbit coupling (SOC), that uses four electrochemical potential (U + , D + , U - , and D -) depending on the sign of z-component of the spin (up (U) , down (D)) and the sign of the x-component of the group velocity (+ , -) . This can be considered as an extension of the standard spin diffusion equation that uses two electrochemical potentials for up and down spin states, allowing us to take into account the unique coupling between charge and spin degrees of freedom in channels with SOC. We will describe applications of this model to answer a number of interesting questions in this field such as: (1) whether topological insulators can switch magnets, (2) how the charge to spin conversion is influenced by the channel resistivity, and (3) how device structures can be designed to enhance spin injection. This work was supported by FAME, one of six centers of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA.

  11. Coupled-channel Treatment of Isobaric Analog Resonances in (p,p‧) Capture Processes

    NASA Astrophysics Data System (ADS)

    Thompson, I. J.; Arbanas, G.

    2014-04-01

    With the advent of nuclear reactions on unstable isotopes, there has been a renewed interest in using isobaric analogue resonances (IAR) as a tool for probing the nuclear structure. The position and width of isobaric analogue resonances in nucleon-nucleus scattering are accurate and detailed indicators of the positions of resonances and bound states with good single-particle characters. We report on implementation within our coupled-channels code FRESCO of the charge-exchange interaction term that transforms an incident proton into a neutron. Isobaric analog resonances are seen as peaks in γ-ray spectrum when the proton is transformed into a neutron at an energy near a neutron bound state. The Lane coupled-channels formalism was extended to follow the non-orthogonality of this neutron channel with that configuration of an inelastic outgoing proton, and the target being left in a particle-hole excited state. This is tested for 208Pb, for which good (p,p'γ) coincidence data exists.

  12. Coupled-channel treatment of Isobaric Analog Resonances in (p,p') Capture Processes

    SciTech Connect

    Thompson, I J; Arbanas, Goran

    2013-01-01

    With the advent of nuclear reactions on unstable isotopes, there has been a renewed interest in using isobaric analogue resonances (IAR) as a tool for probing the nuclear structure. The position and width of isobaric analogue resonances in nucleon-nucleus scattering are accurate and detailed indicators of the positions of resonances and bound states with good single-particle characters. We report on implementation within our coupled-channels code FRESCO of the charge-exchange interaction term that transforms an incident proton into a neutron. Isobaric analog resonances are seen as peaks in gamma-ray spectrum when the proton is transformed into a neutron at an energy near a neutron bound state. The Lane coupled-channels formalism was extended to follow the nonorthogonality of this neutron channel with that configuration of an inelastic outgoing proton, and the target being left in a particle-hole excited state. This is tested for 208Pb, for which good (p,p g)

  13. Spin Circuit Model for 2D Channels with Spin-Orbit Coupling

    PubMed Central

    Hong, Seokmin; Sayed, Shehrin; Datta, Supriyo

    2016-01-01

    In this paper we present a general theory for an arbitrary 2D channel with “spin momentum locking” due to spin-orbit coupling. It is based on a semiclassical model that classifies all the channel electronic states into four groups based on the sign of the z-component of the spin (up (U), down (D)) and the sign of the x-component of the velocity (+, −). This could be viewed as an extension of the standard spin diffusion model which uses two separate electrochemical potentials for U and D states. Our model uses four: U+, D+, U−, and D−. We use this formulation to develop an equivalent spin circuit that is also benchmarked against a full non-equilibrium Green’s function (NEGF) model. The circuit representation can be used to interpret experiments and estimate important quantities of interest like the charge to spin conversion ratio or the maximum spin current that can be extracted. The model should be applicable to topological insulator surface states with parallel channels as well as to other layered structures with interfacial spin-orbit coupling. PMID:26932563

  14. Spin Circuit Model for 2D Channels with Spin-Orbit Coupling.

    PubMed

    Hong, Seokmin; Sayed, Shehrin; Datta, Supriyo

    2016-03-02

    In this paper we present a general theory for an arbitrary 2D channel with "spin momentum locking" due to spin-orbit coupling. It is based on a semiclassical model that classifies all the channel electronic states into four groups based on the sign of the z-component of the spin (up (U), down (D)) and the sign of the x-component of the velocity (+, -). This could be viewed as an extension of the standard spin diffusion model which uses two separate electrochemical potentials for U and D states. Our model uses four: U+, D+, U-, and D-. We use this formulation to develop an equivalent spin circuit that is also benchmarked against a full non-equilibrium Green's function (NEGF) model. The circuit representation can be used to interpret experiments and estimate important quantities of interest like the charge to spin conversion ratio or the maximum spin current that can be extracted. The model should be applicable to topological insulator surface states with parallel channels as well as to other layered structures with interfacial spin-orbit coupling.

  15. Electromagnetic field distribution calculation in solenoidal inductively coupled plasma using finite difference method

    SciTech Connect

    Li, W. P.; Liu, Y.; Long, Q.; Chen, D. H.; Chen, Y. M.

    2008-10-15

    The electromagnetic field (both E and B fields) is calculated for a solenoidal inductively coupled plasma (ICP) discharge. The model is based on two-dimensional cylindrical coordinates, and the finite difference method is used for solving Maxwell equations in both the radial and axial directions. Through one-turn coil measurements, assuming that the electrical conductivity has a constant value in each cross section of the discharge tube, the calculated E and B fields rise sharply near the tube wall. The nonuniform radial distributions imply that the skin effect plays a significant role in the energy balance of the stable ICP. Damped distributions in the axial direction show that the magnetic flux gradually dissipates into the surrounding space. A finite difference calculation allows prediction of the electrical conductivity and plasma permeability, and the induction coil voltage and plasma current can be calculated, which are verified for correctness.

  16. KANTBP 3.0: New version of a program for computing energy levels, reflection and transmission matrices, and corresponding wave functions in the coupled-channel adiabatic approach

    NASA Astrophysics Data System (ADS)

    Gusev, A. A.; Chuluunbaatar, O.; Vinitsky, S. I.; Abrashkevich, A. G.

    2014-12-01

    A FORTRAN program for calculating energy values, reflection and transmission matrices, and corresponding wave functions in a coupled-channel approximation of the adiabatic approach is presented. In this approach, a multidimensional Schrödinger equation is reduced to a system of the coupled second-order ordinary differential equations on a finite interval with the homogeneous boundary conditions of the third type at the left- and right-boundary points for continuous spectrum problem. The resulting system of these equations containing the potential matrix elements and first-derivative coupling terms is solved using high-order accuracy approximations of the finite element method. As a test desk, the program is applied to the calculation of the reflection and transmission matrices and corresponding wave functions for the two-dimensional problem with different barrier potentials.

  17. Benchmark evaluation of the RELAP code to calculate boiling in narrow channels

    SciTech Connect

    Kunze, J.F.; Loyalka, S.K. ); McKibben, J.C.; Hultsch, R.; Oladiran, O.

    1990-06-01

    The RELAP code has been tested with benchmark experiments (such as the loss-of-fluid test experiments at the Idaho National Engineering Laboratory) at high pressures and temperatures characteristic of those encountered in loss-of-coolant accidents (LOCAs) in commercial light water power reactors. Application of RELAP to the LOCA analysis of a low pressure (< 7 atm) and low temperature (< 100{degree}C), plate-type research reactor, such as the University of Missouri Research Reactor (MURR), the high-flux breeder reactor, high-flux isotope reactor, and Advanced Test Reactor, requires resolution of questions involving overextrapolation to very low pressures and low temperatures, and calculations of the pulsed boiling/reflood conditions in the narrow rectangular cross-section channels (typically 2 mm thick) of the plate fuel elements. The practical concern of this problem is that plate fuel temperatures predicted by RELAP5 (MOD2, version 3) during the pulsed boiling period can reach high enough temperatures to cause plate (clad) weakening, though not melting. Since an experimental benchmark of RELAP under such LOCA conditions is not available and since such conditions present substantial challenges to the code, it is important to verify the code predictions. The comparison of the pulsed boiling experiments with the RELAP calculations involves both visual observations of void fraction versus time and measurements of temperatures near the fuel plate surface.

  18. Adaptive behavior of bacterial mechanosensitive channels is coupled to membrane mechanics.

    PubMed

    Belyy, Vladislav; Kamaraju, Kishore; Akitake, Bradley; Anishkin, Andriy; Sukharev, Sergei

    2010-06-01

    Mechanosensitive channel of small conductance (MscS), a tension-driven osmolyte release valve residing in the inner membrane of Escherichia coli, exhibits a complex adaptive behavior, whereas its functional counterpart, mechanosensitive channel of large conductance (MscL), was generally considered nonadaptive. In this study, we show that both channels exhibit similar adaptation in excised patches, a process that is completely separable from inactivation prominent only in MscS. When a membrane patch is held under constant pressure, adaptation of both channels is manifested as a reversible current decline. Their dose-response curves recorded with 1-10-s ramps of pressure are shifted toward higher tension relative to the curves measured with series of pulses, indicating decreased tension sensitivity. Prolonged exposure of excised patches to subthreshold tensions further shifts activation curves for both MscS and MscL toward higher tension with similar magnitude and time course. Whole spheroplast MscS recordings performed with simultaneous imaging reveal activation curves with a midpoint tension of 7.8 mN/m and the slope corresponding to approximately 15-nm(2) in-plane expansion. Inactivation was retained in whole spheroplast mode, but no adaptation was observed. Similarly, whole spheroplast recordings of MscL (V23T mutant) indicated no adaptation, which was present in excised patches. MscS activities tried in spheroplast-attached mode showed no adaptation when the spheroplasts were intact, but permeabilized spheroplasts showed delayed adaptation, suggesting that the presence of membrane breaks or edges causes adaptation. We interpret this in the framework of the mechanics of the bilayer couple linking adaptation of channels in excised patches to the relaxation of the inner leaflet that is not in contact with the glass pipette. Relaxation of one leaflet results in asymmetric redistribution of tension in the bilayer that is less favorable for channel opening.

  19. Adaptive behavior of bacterial mechanosensitive channels is coupled to membrane mechanics

    PubMed Central

    Belyy, Vladislav; Kamaraju, Kishore; Akitake, Bradley; Anishkin, Andriy

    2010-01-01

    Mechanosensitive channel of small conductance (MscS), a tension-driven osmolyte release valve residing in the inner membrane of Escherichia coli, exhibits a complex adaptive behavior, whereas its functional counterpart, mechanosensitive channel of large conductance (MscL), was generally considered nonadaptive. In this study, we show that both channels exhibit similar adaptation in excised patches, a process that is completely separable from inactivation prominent only in MscS. When a membrane patch is held under constant pressure, adaptation of both channels is manifested as a reversible current decline. Their dose–response curves recorded with 1–10-s ramps of pressure are shifted toward higher tension relative to the curves measured with series of pulses, indicating decreased tension sensitivity. Prolonged exposure of excised patches to subthreshold tensions further shifts activation curves for both MscS and MscL toward higher tension with similar magnitude and time course. Whole spheroplast MscS recordings performed with simultaneous imaging reveal activation curves with a midpoint tension of 7.8 mN/m and the slope corresponding to ∼15-nm2 in-plane expansion. Inactivation was retained in whole spheroplast mode, but no adaptation was observed. Similarly, whole spheroplast recordings of MscL (V23T mutant) indicated no adaptation, which was present in excised patches. MscS activities tried in spheroplast-attached mode showed no adaptation when the spheroplasts were intact, but permeabilized spheroplasts showed delayed adaptation, suggesting that the presence of membrane breaks or edges causes adaptation. We interpret this in the framework of the mechanics of the bilayer couple linking adaptation of channels in excised patches to the relaxation of the inner leaflet that is not in contact with the glass pipette. Relaxation of one leaflet results in asymmetric redistribution of tension in the bilayer that is less favorable for channel opening. PMID:20513760

  20. Vibrational Spectrum of (CO)2 on Cu(100): Quantum Calculations with 18 Coupled Mode

    NASA Technical Reports Server (NTRS)

    Dzegilenko, Fedor; Bowman, Joel M.; Carter, Stuart; Saini, Subhash (Technical Monitor)

    1998-01-01

    We report calculations of the vibrational frequencies of CO dimer on Cu(100) using recently developed vibrational self-consistent field code. Eighteen modes are treated explicitly within three modes coupling representation. Nine symmetry distinct doublets are observed and the corresponding frequencies are computed. The thermally broadened spectrum of the CO-stretch fundamental is calculated at various temperatures. Both the temperature and coverage dependence of both the average CO-stretch frequency and the corresponding line-width are consistent with experimentally observed trends. The document contains no classified information International clearance is needed.

  1. Development of High Precision Tsunami Runup Calculation Method Coupled with Structure Analysis

    NASA Astrophysics Data System (ADS)

    Arikawa, Taro; Seki, Katsumi; Chida, Yu; Takagawa, Tomohiro; Shimosako, Kenichiro

    2017-04-01

    The 2011 Great East Japan Earthquake (GEJE) has shown that tsunami disasters are not limited to inundation damage in a specified region, but may destroy a wide area, causing a major disaster. Evaluating standing land structures and damage to them requires highly precise evaluation of three-dimensional fluid motion - an expensive process. Our research goals were thus to develop a coupling STOC-CADMAS (Arikawa and Tomita, 2016) coupling with the structure analysis (Arikawa et. al., 2009) to efficiently calculate all stages from tsunami source to runup including the deformation of structures and to verify their applicability. We also investigated the stability of breakwaters at Kamaishi Bay. Fig. 1 shows the whole of this calculation system. The STOC-ML simulator approximates pressure by hydrostatic pressure and calculates the wave profiles based on an equation of continuity, thereby lowering calculation cost, primarily calculating from a e epi center to the shallow region. As a simulator, STOC-IC solves pressure based on a Poisson equation to account for a shallower, more complex topography, but reduces computation cost slightly to calculate the area near a port by setting the water surface based on an equation of continuity. CS3D also solves a Navier-Stokes equation and sets the water surface by VOF to deal with the runup area, with its complex surfaces of overflows and bores. STR solves the structure analysis including the geo analysis based on the Biot's formula. By coupling these, it efficiently calculates the tsunami profile from the propagation to the inundation. The numerical results compared with the physical experiments done by Arikawa et. al.,2012. It was good agreement with the experimental ones. Finally, the system applied to the local situation at Kamaishi bay. The almost breakwaters were washed away, whose situation was similar to the damage at Kamaishi bay. REFERENCES T. Arikawa and T. Tomita (2016): "Development of High Precision Tsunami Runup

  2. Multireference coupled-cluster calculation of the dissociation energy profile of triplet ketene

    NASA Astrophysics Data System (ADS)

    Ogihara, Yusuke; Yamamoto, Takeshi; Kato, Shigeki

    2011-07-01

    Triplet ketene exhibits a steplike structure in the experimentally observed photodissociation rates, but its mechanism is still unknown despite many theoretical efforts. Here we revisit this problem by calculating the potential energy profile of triplet ketene with the Adamowicz and Mukherjee multireference coupled-cluster (MRCC) theories. At the MRCCSD level, the imaginary frequency of the dissociation barrier is calculated to be about 300i cm-1, which is slightly smaller than the previous estimates but is still much greater than the expected maximum value for reproducing the observed steps (100i cm-1). This implies that other types of mechanisms (including nonadiabatic ones) may be more plausible for the observed steps.

  3. Scalar Relativistic Equation-Of Coupled Cluster Calculations of Core-Ionized States

    NASA Astrophysics Data System (ADS)

    Cheng, Lan

    2017-06-01

    Scalar relativistic equation-of-motion coupled cluster (EOMCC) calculations of core ionization/excitation energies for a set of benchmark molecules are reported. The Arnoldi algorithm as well as the core-valence-separation (CVS) scheme have been used to expedite the convergence of the wave function for the core-ionized/excited states. Scalar relativistic effects have been accounted for using the spin-free exact two-component theory in its one-electron variant (SFX2C-1e) and their importance are assessed. Preliminary calculations of ligand core excitation spectra of transition-metal containing compounds are also presented.

  4. A coupling model of the radiative transport equation for calculating photon migration in biological tissue

    NASA Astrophysics Data System (ADS)

    Fujii, Hiroyuki; Okawa, Shinpei; Yamada, Yukio; Hoshi, Yoko; Watanabe, Masao

    2015-12-01

    Development of a physically accurate and computationally efficient photon migration model for turbid media is crucial for optical computed tomography such as diffuse optical tomography. For the development, this paper constructs a space-time coupling model of the radiative transport equation with the photon diffusion equation. In the coupling model, a space-time regime of the photon migration is divided into the ballistic and diffusive regimes with the interaction between the both regimes to improve the accuracy of the results and the efficiency of computation. The coupling model provides an accurate description of the photon migration in various turbid media in a wide range of the optical properties, and reduces computational loads when compared with those of full calculation of the RTE.

  5. Coupled-channel Dπ, Dη and {D}_soverline{K} scattering from lattice QCD

    NASA Astrophysics Data System (ADS)

    Moir, Graham; Peardon, Michael; Ryan, Sinéad M.; Thomas, Christopher E.; Wilson, David J.

    2016-10-01

    We present the first lattice QCD study of coupled-channel Dπ, Dη and {D}_soverline{K} scattering in isospin-1/2 in three partial waves. Using distillation, we compute matrices of correlation functions with bases of operators capable of resolving both meson and mesonmeson contributions to the spectrum. These correlation matrices are analysed using a variational approach to extract the finite-volume energy eigenstates. Utilising Lüscher's method and its extensions, we constrain scattering amplitudes in S, P and D-wave as a function of energy. By analytically continuing the scattering amplitudes to complex energies, we investigate the S-matrix singularities. Working at m π ≈ 391 MeV, we find a pole corresponding to a J P = 0+ near-threshold bound state with a large coupling to Dπ. We also find a deeply bound J P = 1- state, and evidence for a J P = 2+ narrow resonance coupled predominantly to Dπ. Elastic Dπ scattering in the isospin-3 /2 channel is studied and we find a weakly repulsive interaction in S-wave.

  6. Spatiotemporal Coupling of cAMP Transporter to CFTR Chloride Channel Function in the Gut Epithelia

    PubMed Central

    Li, Chunying; Krishnamurthy, Partha C.; Penmatsa, Himabindu; Marrs, Kevin L.; Wang, Xue Qing; Zaccolo, Manuela; Jalink, Kees; Li, Min; Nelson, Deborah J.; Schuetz, John D.; Naren, Anjaparavanda P.

    2007-01-01

    SUMMARY Cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-regulated chloride channel localized at apical cell membranes and exists in macromolecular complexes with a variety of signaling and transporter molecules. Here we report that the multidrug resistance protein 4 (MRP4), a cAMP transporter, is functionally and physically associates with CFTR. Adenosine-stimulated CFTR-mediated chloride currents are potentiated by MRP4 inhibition, and this potentiation is directly coupled to attenuated cAMP efflux through the apical cAMP transporter. CFTR single-channel recordings and FRET-based intracellular cAMP dynamics suggest that a compartmentalized coupling of cAMP transporter and CFTR occurs via the PDZ scaffolding protein, PDZK1, forming a macromolecular complex at apical surfaces of gut epithelia. Disrupting this complex abrogates the functional coupling of cAMP transporter activity to CFTR function. MRP4 knockout mice are more prone to CFTR-mediated secretory diarrhea. Our findings have important implications for disorders such as inflammatory bowel disease and secretory diarrhea. PMID:18045536

  7. Spatiotemporal coupling of cAMP transporter to CFTR chloride channel function in the gut epithelia.

    PubMed

    Li, Chunying; Krishnamurthy, Partha C; Penmatsa, Himabindu; Marrs, Kevin L; Wang, Xue Qing; Zaccolo, Manuela; Jalink, Kees; Li, Min; Nelson, Deborah J; Schuetz, John D; Naren, Anjaparavanda P

    2007-11-30

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-regulated chloride channel localized at apical cell membranes and exists in macromolecular complexes with a variety of signaling and transporter molecules. Here, we report that the multidrug resistance protein 4 (MRP4), a cAMP transporter, functionally and physically associates with CFTR. Adenosine-stimulated CFTR-mediated chloride currents are potentiated by MRP4 inhibition, and this potentiation is directly coupled to attenuated cAMP efflux through the apical cAMP transporter. CFTR single-channel recordings and FRET-based intracellular cAMP dynamics suggest that a compartmentalized coupling of cAMP transporter and CFTR occurs via the PDZ scaffolding protein, PDZK1, forming a macromolecular complex at apical surfaces of gut epithelia. Disrupting this complex abrogates the functional coupling of cAMP transporter activity to CFTR function. Mrp4 knockout mice are more prone to CFTR-mediated secretory diarrhea. Our findings have important implications for disorders such as inflammatory bowel disease and secretory diarrhea.

  8. The Coupled-Mode Method for Transmission Loss Calculation in a Range- Dependent Oceanic Environment

    DTIC Science & Technology

    1989-02-27

    theory, with eigenray calculations to estimate the coupling coefficients, to simplify the solution to the propagation in a range-dependent...Then Equation (18) becomes V2p + k2p - V2U (24) which, in an unbounded medium, has a general homogeneous solution consisting of an outgoing and an...transform back using Equation (39) to obtain (r,z). The solution of this inhomogeneous equation can be written as the sum of the homogeneous solution and

  9. Calculations of spin-spin coupling constants in aromatic nitrogen heterocyclics

    NASA Astrophysics Data System (ADS)

    Long, S. A. T.; Memory, J. D.

    HH, CH, NH, CC, and NC spin-spin coupling constants were calculated using the FP-INDO method and the Fermi contact interaction for pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, quinoline, quinoxaline, phthalazine, isoquinoline, cinnoline, quinazoline, acridine, phenazine, benzo[ g]quinoxaline, and benzo[ b]-phenazine. The agreement between theory and experiment was comparable to that for polynuclear aromatic hydrocarbons reported earlier.

  10. Development of a coupling code for PWR reactor cavity radiation streaming calculation

    SciTech Connect

    Zheng, Z.; Wu, H.; Cao, L.; Zheng, Y.; Zhang, H.; Wang, M.

    2012-07-01

    PWR reactor cavity radiation streaming is important for the safe of the personnel and equipment, thus calculation has to be performed to evaluate the neutron flux distribution around the reactor. For this calculation, the deterministic codes have difficulties in fine geometrical modeling and need huge computer resource; and the Monte Carlo codes require very long sampling time to obtain results with acceptable precision. Therefore, a coupling method has been developed to eliminate the two problems mentioned above in each code. In this study, we develop a coupling code named DORT2MCNP to link the Sn code DORT and Monte Carlo code MCNP. DORT2MCNP is used to produce a combined surface source containing top, bottom and side surface simultaneously. Because SDEF card is unsuitable for the combined surface source, we modify the SOURCE subroutine of MCNP and compile MCNP for this application. Numerical results demonstrate the correctness of the coupling code DORT2MCNP and show reasonable agreement between the coupling method and the other two codes (DORT and MCNP). (authors)

  11. Quantum close coupling calculation of transport and relaxation properties for Hg-H2 system

    NASA Astrophysics Data System (ADS)

    Nemati-Kande, Ebrahim; Maghari, Ali

    2016-11-01

    Quantum mechanical close coupling calculation of the state-to-state transport and relaxation cross sections have been done for Hg-H2 molecular system using a high-level ab initio potential energy surface. Rotationally averaged cross sections were also calculated to obtain the energy dependent Senftleben-Beenakker cross sections at the energy range of 0.005-25,000 cm-1. Boltzmann averaging of the energy dependent Senftleben-Beenakker cross sections showed the temperature dependency over a wide temperature range of 50-2500 K. Interaction viscosity and diffusion coefficients were also calculated using close coupling cross sections and full classical Mason-Monchick approximation. The results were compared with each other and with the available experimental data. It was found that Mason-Monchick approximation for viscosity is more reliable than diffusion coefficient. Furthermore, from the comparison of the experimental diffusion coefficients with the result of the close coupling and Mason-Monchick approximation, it was found that the Hg-H2 potential energy surface used in this work can reliably predict diffusion coefficient data.

  12. Using X(3823)→ J/ ψπ + π - to identify coupled-channel effects

    NASA Astrophysics Data System (ADS)

    Wang, Bo; Xu, Hao; Liu, Xiang; Chen, Dian-Yong; Coito, Susana; Eichten, Estia

    2016-06-01

    Very recently, the Belle and BESIII experiments observed a new charmonium-like state X(3823), which is a good candidate for the D-wave charmonium ψ(13 D 2). Because the X(3823) is just near the D bar D* threshold, the decay X(3823)→ J/ ψπ + π - can be a golden channel to test the significance of coupled-channel effects. In this work, this decay is considered including both the hidden-charm dipion and the usual quantum chromodynamics multipole expansion (QCDME) contributions. The partial decay width, the dipion invariant mass spectrum distribution d Γ[ X(3823) → J/ ψπ + π -]/d m π+ π-, and the corresponding d Γ[ X(3823) → J/ ψπ + π -]/dcos θ distribution are computed. Many parameters are determined from existing experimental data, so the results depend mainly only on one unknown phase between the QCDME and hidden-charm dipion amplitudes.

  13. Dispersive coupled-channels optical-model potential with soft-rotator couplings for Cr, Fe, and Ni isotopes

    NASA Astrophysics Data System (ADS)

    Li, Rui; Sun, Weili; Soukhovitskiĩ, E. Sh.; Quesada, J. M.; Capote, R.

    2013-05-01

    An approximate Lane-consistent dispersive coupled-channels optical potential is derived that describes nucleon-induced reactions on even iron isotopes. Realistic saturated couplings for 54,56,58Fe nuclei are built using nuclear wave functions of the soft-rotator model with the Hamiltonian parameters adjusted to reproduce the energy of the low-lying collective levels of these isotopes. E2- and E3-transition probabilities between low-lying collective levels are well reproduced. The comprehensive experimental database used in the fitting process includes all scattering data for neutron and proton scattering up to 200 MeV on iron nuclei. The derived potential is shown to be applicable to Ni and Cr isotopes, assuming the applicability of the soft-rotator model to these nuclei and to the odd 57Fe nucleus within the rigid-rotor model. The approximate Lane consistency of the derived potential is validated by describing the quasielastic (p,n) scattering with excitation of isobaric analog states. Elastic and inelastic analyzing powers for both neutron- and proton-induced reactions are shown to be in good agreement with experimental data, demonstrating the reliability of the derived dispersive spin-orbit potential.

  14. Coupling channel hydro-morphodynamics and fish spawning habitat in a forested montane stream

    NASA Astrophysics Data System (ADS)

    Cienciala, P.; Hassan, M. A.

    2011-12-01

    In this paper we couple a hydrodynamic model with field data to investigate channel dynamics and spawning habitat potential for small-bodied salmonids in coarse-bed streams in British Columbia. We studied four reaches of East Creek, a small montane stream near Vancouver, BC, which display rapid (plane bed) and riffle-pool morphologies and provide habitat for a population of resident coastal cutthroat trout. Repeated channel surveys were conducted to obtain detailed information on channel topography and dynamics; net change in bed elevation between successive surveys was utilized as an index of scour and fill. Extensive bed surface sampling and low altitude vertical imagery were used in order to investigate bed surface texture and structures and to identify suitable spawning substrate patches. A 2-D hydrodynamic model, FaSTMECH (within MultiDimensional Surface Water Modeling System interface), was calibrated using field data and applied to simulate the spatial pattern of bed shear stress during a bankfull flow event. During small-to-intermediate floods significant bed scour, deeper than the estimated egg burial depth, occurred on a small proportion of bed area, in well-defined zones associated with obstacles such as large woody debris. Usually, distinct depositional zones developed just downstream of the scour locations. The spatial distribution of forcing elements and modeled bed shear stress explained well the observed pattern of scour and fill. Suitable spawning gravel was very limited in the study sites, particularly in two upstream reaches, primarily due to the coarse nature of the bed. In summary, scour disturbance risk appears to be relatively low in coarse-bed channels, except during extreme flow events, and shortage of suitable spawning substrate may be more important for small-bodied salmonids. This study demonstrates that coupling of hydro-morphodynamic and ecological data can provide a useful tool in fish habitat assessment and restoration.

  15. Fenamates block gap junction coupling and potentiate BKCa channels in guinea pig arteriolar cells

    PubMed Central

    Li, Xin-Zhi; Ma, Ke-Tao; Guan, Bing-Cai; Li, Li; Zhao, Lei; Zhang, Zhong-Shuang; Si, Jun-Qiang; Jiang, Zhi-Gen

    2013-01-01

    We determined the actions of the fenamates, flufenamic acid (FFA) and niflumic acid (NFA), on gap junction-mediated intercellular coupling between vascular smooth muscle cells (VSMC) in situ of acutely isolated arteriole segments from the three vascular beds: the spiral modiolar artery (SMA), anterior inferior cerebellar artery (AICA) and mesenteric artery (MA), and on non-junctional membrane channels in dispersed VSMCs. Conventional whole-cell recording methods were used. FFA reversibly suppressed the input conductance (Ginput) or increased the input resistance (Rinput) in a concentration dependent manner, with slightly different IC50s for the SMA, AICA and MA segments (26, 33 and 56 μM respectively, P>0.05). Complete electrical isolation of the recorded VSMC was normally reached at ≥300 μM. NFA had a similar effect on gap junction among VSMCs with an IC50 of 40, 48 and 62 μM in SMA, AICA and MA segments, respectively. In dispersed VSMCs, FFA and NFA increased outward rectifier K+-current mediated by the big conductance calcium-activated potassium channel (BKCa) in a concentration-dependent manner, with a similar EC50 of ~300 μM for both FFA and NFA in the three vessels. Iberiotoxin, a selective blocker of the BKCa, suppressed the enhancement of the BKCa by FFA and NFA. The KV blocker 4-AP had no effect on the fenamates-induced K+-current enhancement. We conclude that FFA and NFA blocked the vascular gap junction mediated electrical couplings uniformly in arterioles of the three vascular beds, and complete electrical isolation of the recorded VSMC is obtained at ≧300 μM; FFA and NFA also activate BKCa channels in the arteriolar smooth muscle cells in addition to their known inhibitory effects on chloride channels. PMID:23420003

  16. Series-coupled double-ring resonators with asymmetric radii for use in channelizer

    NASA Astrophysics Data System (ADS)

    Gu, Xiaowen; Zhu, Dan; Zhao, Yongjiu; Pan, Shilong

    2014-10-01

    A series-coupled double-ring resonator with asymmetric radii is analyzed to achieve a filter response with a large free spectral range (FSR), a narrow passband of tens of MHz and a small shape factor simultaneously for use in microwave photonic channelizer. By introducing difference to the two radii, based on the vernier effect, the FSR of the resonator filter can be extended while maintaining the narrow passband and the small shape factor. A filter response with a FSR of 29.444 GHz, a 3-dB bandwidth of 96 MHz and a shape factor of 3.17 is realized by numerical analysis.

  17. c b \\xAF spectrum and decay properties with coupled channel effects

    NASA Astrophysics Data System (ADS)

    Monteiro, Antony Prakash; Bhat, Manjunath; Kumar, K. B. Vijaya

    2017-03-01

    The mass spectrum of c b ¯ states has been obtained using the phenomenological relativistic quark model (RQM) with coupled channel effects. The Hamiltonian used in the investigation has confinement potential and confined one gluon exchange potential (COGEP). In the frame work of the RQM, a study of magnetic dipole and electric dipole transitions and radiative decays of c b ¯ states has been made. The weak decay widths in the spectator quark approximation have been estimated. An overall agreement is obtained with the experimental masses and decay widths.

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

    DOE PAGES

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

    2017-02-22

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

  19. Calculation of exchange coupling constants of transition metal complexes with DFT.

    PubMed

    Comba, Peter; Hausberg, Sascha; Martin, Bodo

    2009-06-18

    A broken-symmetry method for the calculation of exchange coupling constants from DFT calculations, using the Heisenberg-Dirac-van Vleck spin Hamiltonian, has been validated for a dinuclear copper(II) complex. Hybrid functionals in combination with a large basis set on the metal centers and their first coordination sphere, and a smaller basis set on the ligand backbone are shown to be efficient and acceptable with respect to the computational cost and precision in comparison with experimental data. This method was thoroughly tested with a series of oligonuclear transition metal complexes with Cr(III), Cu(II), Fe(III), Mn(II), Mn(III), Mn(IV), Ni(II), and V(IV) as magnetic centers. The computed values of J are within approximately 50 cm(-1) of the experimental values for most of the examples; with combined basis sets, there generally is a similar accuracy to that obtained with a large basis set for the entire spin cluster but with significantly reduced computational expense. When the experimentally observed structural data are refined prior to the calculation of the exchange coupling constants, the computed values of J are in most cases in slightly better agreement with the experimental data than those obtained from single point calculations based on the X-ray data.

  20. Control of Energy Density inside a Disordered Medium by Coupling to Open or Closed Channels

    NASA Astrophysics Data System (ADS)

    Sarma, Raktim; Yamilov, Alexey G.; Petrenko, Sasha; Bromberg, Yaron; Cao, Hui

    2016-08-01

    We demonstrate experimentally the efficient control of light intensity distribution inside a random scattering system. The adaptive wave front shaping technique is applied to a silicon waveguide containing scattering nanostructures, and the on-chip coupling scheme enables access to all input spatial modes. By selectively coupling the incident light to the open or closed channels of the disordered system, we not only vary the total energy stored inside the system by a factor of 7.4, but also change the energy density distribution from an exponential decay to a linear decay and to a profile peaked near the center. This work provides an on-chip platform for controlling light-matter interactions in turbid media.

  1. Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels.

    PubMed

    Allen, Toby W; Andersen, Olaf S; Roux, Benoit

    2006-12-01

    Ion channels catalyze the permeation of charged molecules across cell membranes and are essential for many vital physiological functions, including nerve and muscle activity. To understand better the mechanisms underlying ion conduction and valence selectivity of narrow ion channels, we have employed free energy techniques to calculate the potential of mean force (PMF) for ion movement through the prototypical gramicidin A channel. Employing modern all-atom molecular dynamics (MD) force fields with umbrella sampling methods that incorporate one hundred 1-2 ns trajectories, we find that it is possible to achieve semi-quantitative agreement with experimental binding and conductance measurements. We also examine the sensitivity of the MD-PMF results to the choice of MD force field and compare PMFs for potassium, calcium and chloride ions to explore the basis for the valence selectivity of this narrow and uncharged ion channel. A large central barrier is observed for both anions and divalent ions, consistent with lack of experimental conductance. Neither anion or divalent cation is seen to be stabilized inside the channel relative to the bulk electrolyte and each leads to large disruptions to the protein and membrane structure when held deep inside the channel. Weak binding of calcium ions outside the channel corresponds to a free energy well that is too shallow to demonstrate channel blocking. Our findings emphasize the success of the MD-PMF approach and the sensitivity of ion energetics to the choice of biomolecular force field.

  2. Ionic limiting molar conductivity calculation of Li-ion battery electrolyte based on mode coupling theory.

    PubMed

    He, Xiangming; Pu, Weihua; Han, Jingli; Chen, Jian; Lu, Jiufang; Jiang, Changyin; Wan, Chunrong

    2005-12-15

    A method is proposed based on mode coupling theory in which the ion transference number is introduced into the theory. The ionic limiting molar conductivities of LiPF6, LiClO4, LiBF4, LiCF3SO3, Li(CF3SO3)2N, LiC4F9SO3, and LiAsF6 in PC(propylene carbonate), GBL(gamma-butyrolactone), PC(propylene carbonate)/EMC(ethylmethyl carbonate), and PC(propylene carbonate)/DME(dimethoxyethane) are calculated based on this method, which does not involve any adjustable parameter. The results fit well to the literature data which are calculated by an empirically adjusted formula. This presents a potential way to calculate the conductivities of Li-ion battery electrolytes.

  3. Coherent State Variational Methods for Large N Gauge Theories: Numerical Calculations and Strong Coupling Expansions

    NASA Astrophysics Data System (ADS)

    Brown, Frank R.

    Coherent state techniques have proved a useful formal tool for obtaining the N = infty limit of a variety of quantum mechanical systems, in part because they allow one to explicitly construct the classical Hamiltonian and classical phase space that define the dynamics of the large N system. This construction is sufficiently concrete that it naturally suggests methods for carrying out practical calculations. We discuss two such methods, one numerical and the other a classical strong coupling expansion, for calculating the mass spectrum of pure U (infty) Hamiltonian lattice gauge theory. Both involve calculating coherent state expectation values of the quantum Hamiltonian to obtain a classical Hamiltonian as a function on the space of coherent states, and solving for the coherent state (the point in classical configuration space) that minimizes this classical Hamiltonian. Finally the frequencies of classical small oscillations about this minimum give the large N limit of the quantum mechanical excitation spectrum.

  4. State-selective multireference coupled-cluster theory: In pursuit of property calculation

    SciTech Connect

    Ghose, K.B.; Piecuch, P.; Pal, S.; Adamowicz, L. |

    1996-05-01

    In this work, we examine the efficiency of the recently developed [P. Piecuch {ital et} {ital al}., J. Chem. Phys. {bold 99}, 6732 (1993)] state-selective (SS) multi-reference (MR) coupled-cluster (CC) method for calculation of molecular properties. In our earlier papers, we demonstrated that the SSMRCC method with inclusion of single, double, and internal and semi-internal triple excitations [SSCCSD(T) approach] is capable of providing an accurate description of the ground-state potential energy surfaces. In this paper, we present the dipole moment and polarizability values of the HF molecule at equilibrium and stretched geometries calculated using finite field technique and SSCCSD(T) ansatz. The calculations use double zeta quality basis sets with and without polarization functions. Molecular orbital basis sets include both relaxed and nonrelaxed orbitals. {copyright} {ital 1996 American Institute of Physics.}

  5. Rod image: a new method for the calculation of pump efficiency in reflecting close-coupled cavities

    SciTech Connect

    Docchio, F.

    1985-11-15

    Reflecting close-coupling cavities for solid-state lasers often provide beams of better quality, although with a slightly lower efficiency compared with those of the usual ellipticl cavities. A new method for the calculation efficiency in reflecting close-coupled cavities is proposed. Examples of efficiency calculations are discussed.

  6. CORRIGENDUM: Accurate algebraic coupled-state calculation of positron-hydrogen scattering at low energies

    NASA Astrophysics Data System (ADS)

    Gien, T. T.

    1999-05-01

    Our unexpounded writing in the first paragraph of page L24 of the letter may give a false impression to some about what was really meant. We would like, therefore, to clarify it. We simply intended to stress that the deficiency of the polarizability of H(1s) and of Ps(1s) can be seen more easily at low energies in higher-partial-wave phase shifts of e+-H scattering and in higher-partial-wave elastic cross sections of Ps(1s)-p scattering, and that for the purpose of determining the sequences of S, P, D Feshbach resonances (within the assumption of a degenerate threshold limit at -0.25 Ryd, i.e. when the threshold splitting due to fine-structure and QED corrections is ignored), the use of the E6S coupling scheme is appropriate since this coupling scheme contains the 2s and 2p states of H essential for the degenerate dipole interaction. It is therefore quite obvious that for the calculations in a very narrow range of energy of less than 1 × 10-2 Ryd beneath the degenerate threshold (resonance region), the use of the E6PS coupling scheme may not be able to yield reliable results for S, P, D scattering, since the scheme cannot handle the resonances properly, due to the absence of the 2s and 2p H states essential for the degenerate dipole interaction. This is, however, of little concern, since the range of energies that we have considered for our various accurate calculations (such as E6PS, E8PS, E6S, ME6S, E8S) is further below the degenerate threshold. Rigorously speaking, even if the 2s and 2p H states are included in the coupling scheme, care concerning the nondegeneracy of threshold might still have to be taken for calculations in the closest vicinity of the threshold.

  7. Spin-orbit couplings within the equation-of-motion coupled-cluster framework: Theory, implementation, and benchmark calculations.

    PubMed

    Epifanovsky, Evgeny; Klein, Kerstin; Stopkowicz, Stella; Gauss, Jürgen; Krylov, Anna I

    2015-08-14

    We present a formalism and an implementation for calculating spin-orbit couplings (SOCs) within the EOM-CCSD (equation-of-motion coupled-cluster with single and double substitutions) approach. The following variants of EOM-CCSD are considered: EOM-CCSD for excitation energies (EOM-EE-CCSD), EOM-CCSD with spin-flip (EOM-SF-CCSD), EOM-CCSD for ionization potentials (EOM-IP-CCSD) and electron attachment (EOM-EA-CCSD). We employ a perturbative approach in which the SOCs are computed as matrix elements of the respective part of the Breit-Pauli Hamiltonian using zeroth-order non-relativistic wave functions. We follow the expectation-value approach rather than the response-theory formulation for property calculations. Both the full two-electron treatment and the mean-field approximation (a partial account of the two-electron contributions) have been implemented and benchmarked using several small molecules containing elements up to the fourth row of the periodic table. The benchmark results show the excellent performance of the perturbative treatment and the mean-field approximation. When used with an appropriate basis set, the errors with respect to experiment are below 5% for the considered examples. The findings regarding basis-set requirements are in agreement with previous studies. The impact of different correlation treatment in zeroth-order wave functions is analyzed. Overall, the EOM-IP-CCSD, EOM-EA-CCSD, EOM-EE-CCSD, and EOM-SF-CCSD wave functions yield SOCs that agree well with each other (and with the experimental values when available). Using an EOM-CCSD approach that provides a more balanced description of the target states yields more accurate results.

  8. Spin-orbit couplings within the equation-of-motion coupled-cluster framework: Theory, implementation, and benchmark calculations

    SciTech Connect

    Epifanovsky, Evgeny; Klein, Kerstin; Gauss, Jürgen; Stopkowicz, Stella; Krylov, Anna I.

    2015-08-14

    We present a formalism and an implementation for calculating spin-orbit couplings (SOCs) within the EOM-CCSD (equation-of-motion coupled-cluster with single and double substitutions) approach. The following variants of EOM-CCSD are considered: EOM-CCSD for excitation energies (EOM-EE-CCSD), EOM-CCSD with spin-flip (EOM-SF-CCSD), EOM-CCSD for ionization potentials (EOM-IP-CCSD) and electron attachment (EOM-EA-CCSD). We employ a perturbative approach in which the SOCs are computed as matrix elements of the respective part of the Breit-Pauli Hamiltonian using zeroth-order non-relativistic wave functions. We follow the expectation-value approach rather than the response-theory formulation for property calculations. Both the full two-electron treatment and the mean-field approximation (a partial account of the two-electron contributions) have been implemented and benchmarked using several small molecules containing elements up to the fourth row of the periodic table. The benchmark results show the excellent performance of the perturbative treatment and the mean-field approximation. When used with an appropriate basis set, the errors with respect to experiment are below 5% for the considered examples. The findings regarding basis-set requirements are in agreement with previous studies. The impact of different correlation treatment in zeroth-order wave functions is analyzed. Overall, the EOM-IP-CCSD, EOM-EA-CCSD, EOM-EE-CCSD, and EOM-SF-CCSD wave functions yield SOCs that agree well with each other (and with the experimental values when available). Using an EOM-CCSD approach that provides a more balanced description of the target states yields more accurate results.

  9. Dynamical Coupled-Channel Model of pi-N scattering in te W < 2 GeV Nucleon Resonane Region

    SciTech Connect

    Lee, T S.H.; Julia-diaz, B; Matsuyama, A; Sato, T

    2007-12-01

    As a first step to analyze the electromagnetic meson production reactions in the nucleon resonance region, the parameters of the hadronic interactions of a dynamical coupled-channel model, developed in {\\it Physics Reports 439, 193 (2007)}, are determined by fitting the empirical $\\pi N$ elastic scattering amplitudes of SAID up to 2 GeV. The channels included in the calculations are $\\pi N$, $\\eta N$ and $\\pi\\pi N$ which has $\\pi\\Delta$, $\\rho N$, and $\\sigma N$ resonant components. The non-resonant meson-baryon interactions of the model are derived from a set of Lagrangians by using a unitary transformation method. One or two bare excited nucleon states in each of $S$, $P$, $D$, and $F$ partial waves are included to generate the resonant amplitudes in the fits. The predicted total cross sections of $\\pi N$ reactions and $\\pi N\\rightarrow \\eta N$ reactions are in good agreement with the data. Applications of the constructed model in analyzing the electromagnetic meson production data as well as the future developments are discussed.

  10. Effects on calculated half-widths and shifts from the line coupling for asymmetric-top molecules

    SciTech Connect

    Ma, Q.; Tipping, R. H.

    2014-06-28

    The refinement of the Robert-Bonamy formalism by considering the line coupling for linear molecules developed in our previous studies [Q. Ma, C. Boulet, and R. H. Tipping, J. Chem. Phys. 139, 034305 (2013); 140, 104304 (2014)] have been extended to asymmetric-top molecules. For H{sub 2}O immersed in N{sub 2} bath, the line coupling selection rules applicable for the pure rotational band to determine whether two specified lines are coupled or not are established. Meanwhile, because the coupling strengths are determined by relative importance of off-diagonal matrix elements versus diagonal elements of the operator −iS{sub 1} − S{sub 2}, quantitative tools are developed with which one is able to remove weakly coupled lines from consideration. By applying these tools, we have found that within reasonable tolerances, most of the H{sub 2}O lines in the pure rotational band are not coupled. This reflects the fact that differences of energy levels of the H{sub 2}O states are pretty large. But, there are several dozen strongly coupled lines and they can be categorized into different groups such that the line couplings occur only within the same groups. In practice, to identify those strongly coupled lines and to confine them into sub-linespaces are crucial steps in considering the line coupling. We have calculated half-widths and shifts for some groups, including the line coupling. Based on these calculations, one can conclude that for most of the H{sub 2}O lines, it is unnecessary to consider the line coupling. However, for several dozens of lines, effects on the calculated half-widths from the line coupling are small, but remain noticeable and reductions of calculated half-widths due to including the line coupling could reach to 5%. Meanwhile, effects on the calculated shifts are very significant and variations of calculated shifts could be as large as 25%.

  11. Effects on Calculated Half-Widths and Shifts from the Line Coupling for Asymmetric-Top Molecules

    NASA Technical Reports Server (NTRS)

    Ma, Q.; Boulet, C.; Tipping, R. H.

    2014-01-01

    The refinement of the Robert-Bonamy formalism by considering the line coupling for linear molecules developed in our previous studies [Q. Ma, C. Boulet, and R. H. Tipping, J. Chem. Phys. 139, 034305 (2013); 140, 104304 (2014)] have been extended to asymmetric-top molecules. For H2O immersed in N2 bath, the line coupling selection rules applicable for the pure rotational band to determine whether two specified lines are coupled or not are established. Meanwhile, because the coupling strengths are determined by relative importance of off-diagonal matrix elements versus diagonal elements of the operator -iS1 -S2, quantitative tools are developed with which one is able to remove weakly coupled lines from consideration. By applying these tools, we have found that within reasonable tolerances, most of the H2O lines in the pure rotational band are not coupled. This reflects the fact that differences of energy levels of the H2O states are pretty large. But, there are several dozen strongly coupled lines and they can be categorized into different groups such that the line couplings occur only within the same groups. In practice, to identify those strongly coupled lines and to confine them into sub-linespaces are crucial steps in considering the line coupling. We have calculated half-widths and shifts for some groups, including the line coupling. Based on these calculations, one can conclude that for most of the H2O lines, it is unnecessary to consider the line coupling. However, for several dozens of lines, effects on the calculated half-widths from the line coupling are small, but remain noticeable and reductions of calculated half-widths due to including the line coupling could reach to 5%. Meanwhile, effects on the calculated shifts are very significant and variations of calculated shifts could be as large as 25%.

  12. Development of High Precision Tsunami Runup Calculation Method Coupled with Structure Analysis

    NASA Astrophysics Data System (ADS)

    Arikawa, T.

    2016-12-01

    The 2011 Great East Japan Earthquake (GEJE) has shown that tsunami disasters are not limited to inundation damage in a specified region, but may destroy a wide area, causing a major disaster. Evaluating standing land structures and damage to them requires highly precise evaluation of three-dimensional fluid motion - an expensive process. Our research goals were thus to develop a coupling STOC-CADMAS (Arikawa and Tomita, 2016) coupling with the structure analysis (Arikawa et. al., 2009) to efficiently calculate all stages from tsunami source to runup including the deformation of structures and to verify their applicability. We also investigated the stability of breakwaters at Kamaishi Bay. Fig. 1 shows the whole of this calculation system. The STOC-ML simulator approximates pressure by hydrostatic pressure and calculates the wave profiles based on an equation of continuity, thereby lowering calculation cost, primarily calculating from a e epi center to the shallow region. As a simulator, STOC-IC solves pressure based on a Poisson equation to account for a shallower, more complex topography, but reduces computation cost slightly to calculate the area near a port by setting the water surface based on an equation of continuity. CS3D also solves a Navier-Stokes equation and sets the water surface by VOF to deal with the runup area, with its complex surfaces of overflows and bores. STR solves the structure analysis including the geo analysis based on the Biot's formula. By coupling these, it efficiently calculates the tsunami profile from the propagation to the inundation. The numerical results compared with the physical experiments done by Arikawa et. al.,2012. It was good agreement with the experimental ones. Finally, the system applied to the local situation at Kamaishi bay. The almost breakwaters were washed away, whose situation was similar to the damage at Kamaishi bay. ACKNOWLEDGEMENTSThis work was supported by Council for Science, Technology and Innovation (CSTI

  13. Introducing an R-package for calculating channel width and other basic metrics for irregular river polygons

    NASA Astrophysics Data System (ADS)

    Golly, Antonius; Turowski, Jens

    2017-04-01

    The width of fluvial streams and channel beds is an important metric for a large number of hydraulic, geomorphic and ecologic applications. For example, for a given discharge the local channel width determines the water flow velocity and thus the sediment transport capacity of a reach. Since streams often have irregular shapes with uneven channel banks, the channel width strongly varies along the channel. Although, the geometry of streams or their beds can be measured easily in the field (e.g. with a Total Station or GPS) or from maps or aerial images in a GIS, the width of the stream cannot be identified objectively without further data processing, since the results are more or less irregular polygons with sometimes bended shapes. An objective quantification of the channel width and other metrics requires automated algorithms that are applicable over a range of channel shapes and spatial scales. Here, we present a lightweight software suite with a small number of functions that process 2D or 3D geometrical data of channels or channel beds. The software, written as an R-package, accepts various text data formats and can be configured through five parameters. It creates interactive overview plots (if desired) and produces three basic channel metrics: the centerline, the channel width along the centerline and the slope along the centerline. The centerline is an optimized line that minimizes the distances to both channel banks. This centerline gives also a measure for the real length and slope of the channel. From this centerline perpendicular transects are generated which allow for the calculation of the channel width where they intersect with the channel banks. Briefly, we present an example and demonstrate the importance of these metrics in a use case of a steep stream, the Erlenbach stream in Switzerland. We were motivated to develop and publish the algorithm in an open-source framework, since only proprietary solutions were available at that time. The software is

  14. Clustering and Functional Coupling of Diverse Ion Channels and Signaling Proteins Revealed by Super-resolution STORM Microscopy in Neurons.

    PubMed

    Zhang, Jie; Carver, Chase M; Choveau, Frank S; Shapiro, Mark S

    2016-10-19

    The fidelity of neuronal signaling requires organization of signaling molecules into macromolecular complexes, whose components are in intimate proximity. The intrinsic diffraction limit of light makes visualization of individual signaling complexes using visible light extremely difficult. However, using super-resolution stochastic optical reconstruction microscopy (STORM), we observed intimate association of individual molecules within signaling complexes containing ion channels (M-type K(+), L-type Ca(2+), or TRPV1 channels) and G protein-coupled receptors coupled by the scaffolding protein A-kinase-anchoring protein (AKAP)79/150. Some channels assembled as multi-channel supercomplexes. Surprisingly, we identified novel layers of interplay within macromolecular complexes containing diverse channel types at the single-complex level in sensory neurons, dependent on AKAP79/150. Electrophysiological studies revealed that such ion channels are functionally coupled as well. Our findings illustrate the novel role of AKAP79/150 as a molecular coupler of different channels that conveys crosstalk between channel activities within single microdomains in tuning the physiological response of neurons.

  15. Magnetic torque calculations of magnetoelastic coupling and magnetostriction in ultrathin films.

    NASA Astrophysics Data System (ADS)

    Shick, A. B.; Novikov, D. L.; Freeman, A. J.

    1998-03-01

    The magnetic torque method for magnetic anisotropy energy (MAE) calculations ( X.D. Wang, R. Wu, D.S. Wang, A. J. Freeman, Phys. Rev. B 54), 61 (1996). is combined with a self-consistent relativistic spin-polarized version (A.B. Shick, D.L. Novikov, A.J. Freeman, Phys.Rev. B 56) (1997). of the full potential linearized augmented plane wave (FLAPW) method (E. Wimmer, H. Krakauer, M. Weinert and A.J. Freeman, Phys. Rev. B 24), 864 (1981).. To illustrate the high numerical accuracy obtained, we compare with total energy results for 3d-transition metal monolayers. The layer-by-layer contributions to the magnetoelastic coupling and MAE are then calculated for free and Cu-capped Co overlayers on Cu(001). We find surface magnetoelastic coupling coefficients to be positive for Co-layer and negative for the Cu substrate and the Cu-cap layer. The substantial difference of magnetoelastic coupling coefficients for thin films, as opposed to bulk, is demonstrated. This causes a negative magnetostriction coefficient (λ_001) for free Co-overlayer and a positive λ_001 for Cu-capped Co overlayers on Cu(001).

  16. Long-range correlation energy calculated from coupled atomic response functions

    SciTech Connect

    Ambrosetti, Alberto; Reilly, Anthony M.; Tkatchenko, Alexandre; DiStasio, Robert A.

    2014-05-14

    An accurate determination of the electron correlation energy is an essential prerequisite for describing the structure, stability, and function in a wide variety of systems. Therefore, the development of efficient approaches for the calculation of the correlation energy (and hence the dispersion energy as well) is essential and such methods can be coupled with many density-functional approximations, local methods for the electron correlation energy, and even interatomic force fields. In this work, we build upon the previously developed many-body dispersion (MBD) framework, which is intimately linked to the random-phase approximation for the correlation energy. We separate the correlation energy into short-range contributions that are modeled by semi-local functionals and long-range contributions that are calculated by mapping the complex all-electron problem onto a set of atomic response functions coupled in the dipole approximation. We propose an effective range-separation of the coupling between the atomic response functions that extends the already broad applicability of the MBD method to non-metallic materials with highly anisotropic responses, such as layered nanostructures. Application to a variety of high-quality benchmark datasets illustrates the accuracy and applicability of the improved MBD approach, which offers the prospect of first-principles modeling of large structurally complex systems with an accurate description of the long-range correlation energy.

  17. Multi-channel biodetection via resonant microcavities coupled to a photonic crystal waveguide

    NASA Astrophysics Data System (ADS)

    Guillermain, Elisa; Fauchet, Philippe M.

    2009-02-01

    Photonic crystal (PhC) microcavities present multiple advantages for rapid, accurate, label-free, and sensitive detection. But their principle of operation (observation of a peak in transmission) makes their integration in serial arrays difficult. Here we report on multiple resonant cavities coupled to a single photonic crystal waveguide. The device configuration consists of a PhC waveguide with a defect line along which light is guided. Several resonant microcavities, created by modifying the radius of a hole adjacent to the defect line, are coupled to the waveguide. This PhC device, operating as a multi-channel sensor, maintains the advantages of the PhC microcavities and allows for serial arrays: Light is globally transmitted through the waveguide, except for the wavelengths corresponding to the resonant modes of the microcavities. The transmission spectrum shows as many dips as there are cavities. Simulations show that the sensitivity of such structures allows the detection of single particles -typically a virus. Preliminary results show the fabrication and characterization of a double-channel structure with small defects as a solvent sensor.

  18. Postirradiation behavior of p-channel charge-coupled devices irradiated at 153 K

    NASA Astrophysics Data System (ADS)

    Gow, Jason P. D.; Wood, Daniel; Murray, Neil J.; Burt, David; Hall, David J.; Dryer, Ben; Holland, Andrew D.

    2016-04-01

    The displacement damage hardness that can be achieved using p-channel charge-coupled devices (CCD) was originally demonstrated in 1997, and since then a number of other studies have demonstrated an improved tolerance to radiation-induced charge transfer inefficiency when compared to n-channel CCDs. A number of recent studies have also shown that the temperature history of the device after the irradiation impacts the performance of the detector, linked to the mobility of defects at different temperatures. The initial results from an e2v technologies p-channel CCD204 irradiated at 153 K with 10-MeV equivalent proton fluences of 1.24×109 and 1.24×1011 protons cm-2 is described. The dark current, cosmetic quality, and the number of defects identified using trap pumping immediately were monitored after the irradiation for a period of 150 h with the device held at 153 K and then after different periods of time at room temperature. The device also exhibited a flatband voltage shift of around 30 mV/krad, determined by the reduction in full well capacity.

  19. Measurements and coupled reaction channels analysis of one and two proton transfer reactions for 28Si+90,94Zr systems

    NASA Astrophysics Data System (ADS)

    Kalkal, Sunil; Mandal, S.; Jhingan, A.; Gehlot, J.; Sugathan, P.; Golda, K. S.; Madhavan, N.; Garg, Ritika; Goyal, Savi; Mohanto, Gayatri; Verma, S.; Sandal, Rohit; Behera, Bivash; Eleonora, G.; Wollersheim, H. J.; Singh, R.

    2011-10-01

    Measurements of angular distributions for one and two proton stripping reactions for 28Si+90,94Zr systems were performed at lab energy 120 MeV with 28Si beam at Inter University Accelerator Center, New Delhi. Theoretical calculations performed using the quantum mechanical coupled reaction channels code FRESCO (including various intermediate states involving target and projectile excitations before and/or after transfer along with sequential transfer) were able to reproduce one and two proton transfer angular distributions for both the systems reasonably well. It was found that the DWBA calculations could describe the one proton transfer data well for both the systems but failed to reproduce the angular distributions for two proton transfer channels. The present measurements underline the importance of sequential transfer at energies much above the Coulomb barrier. We had also performed transfer reaction measurements for these systems in the sub- and near barrier region using recoil mass separator.

  20. Current status of a coupled-channel partial wave analysis using data from CLAS at Jefferson Lab

    SciTech Connect

    M. Bellis, Z. Krahn, M. McCracken, C. Meyer and M. Williams

    2009-04-01

    The non-strange baryon spectrum has been mapped out predominantly by studying N π elastic scattering with phase-shift analysis as the tool of choice. While there has been much success with these experimental techniques, the results have fueled debates in the community, most notably regarding the missing baryons problem. Theoretical solutions to this discrepancy appeal to a diquark-system within the baryons or a coupling to states other than N π. The CLAS detector at Jefferson Lab has turned out high-statistics, photoproduction datasets which are optimal for resolving these issues. However, new analytical techniques may be required to deal with this rich physics sector. The baryon resonances are photoproduced off liquid hydrogen and the CLAS detector allows us to measure a variety of final states. We will have access to nπ +, pπ 0, pπ + π −, pω,pη, pη′, ΛK + and ΣK + final states. A robust software package has been developed that allows for the fitting of these states individually and in a coupled-channel mode. We make use of flexible C++ based tools that allow fast and general calculations of amplitudes based on a covariant tensor formalism. New techniques have been applied to background subtraction which brings an added level of consistency to the analysis. Polarization information from other experiments is incorporated at fit time to help distinguish potentially ambiguous physics processes by using information outside of the CLAS datasets. Some of these channels have more mature analysis (pω,ΛK +) and the preliminary measuremen will be shown as well as an overview of the analysis tools.

  1. Dispersion calculation method based on S-transform and coordinate rotation for Love channel waves with two components

    NASA Astrophysics Data System (ADS)

    Feng, Lei; Zhang, Yugui

    2017-08-01

    Dispersion analysis is an important part of in-seam seismic data processing, and the calculation accuracy of the dispersion curve directly influences pickup errors of channel wave travel time. To extract an accurate channel wave dispersion curve from in-seam seismic two-component signals, we proposed a time-frequency analysis method based on single-trace signal processing; in addition, we formulated a dispersion calculation equation, based on S-transform, with a freely adjusted filter window width. To unify the azimuth of seismic wave propagation received by a two-component geophone, the original in-seam seismic data undergoes coordinate rotation. The rotation angle can be calculated based on P-wave characteristics, with high energy in the wave propagation direction and weak energy in the vertical direction. With this angle acquisition, a two-component signal can be converted to horizontal and vertical directions. Because Love channel waves have a particle vibration track perpendicular to the wave propagation direction, the signal in the horizontal and vertical directions is mainly Love channel waves. More accurate dispersion characters of Love channel waves can be extracted after the coordinate rotation of two-component signals.

  2. Ab-initio calculation of electron-phonon coupling for spin relaxation in metals.

    NASA Astrophysics Data System (ADS)

    Pruneda, Miguel; Souza, Ivo

    2007-03-01

    Spin-electronic devices have motivated an important effort in understanding the mechanisms for spin-relaxation, because the operation of such devices requires long spin-diffusion lenghts. Two main factors contribute to spin relaxation: (i) spin-orbit interaction, which mixes the spin-up and spin-down components of the electronic wavefunction, and (ii) electron scattering from defects or phonons. In metals, the phonon-mediated Elliot-Yafet mechanism is believed to be dominant. Realistic calculations are computationally demanding, requiring an accurate description of the electronic states near the Fermi surface and their coupling to the lattice (phonons). Here we use a Density Functional Perturbation Theory implementation to calculate from first-principles the electron-phonon interaction in systems with spin-orbit coupling. Combined with recently-developed Wannier-interpolation methods for sampling efficiently the Brillouin zone, this will allow for a fully ab-initio calculation of the spin relaxation in metals. J. Fabian and S. Das Sarma, Phys. Rev. Lett. 83, 1211 (1999).

  3. Lattice dynamics and electron-phonon coupling calculations using nondiagonal supercells

    NASA Astrophysics Data System (ADS)

    Lloyd-Williams, Jonathan H.; Monserrat, Bartomeu

    2015-11-01

    We study the direct calculation of total energy derivatives for lattice dynamics and electron-phonon coupling calculations using supercell matrices with nonzero off-diagonal elements. We show that it is possible to determine the response of a periodic system to a perturbation characterized by a wave vector with reduced fractional coordinates (m1/n1,m2/n2,m3/n3) using a supercell containing a number of primitive cells equal to the least common multiple of n1,n2, and n3. If only diagonal supercell matrices are used, a supercell containing n1n2n3 primitive cells is required. We demonstrate that the use of nondiagonal supercells significantly reduces the computational cost of obtaining converged zero-point energies and phonon dispersions for diamond and graphite. We also perform electron-phonon coupling calculations using the direct method to sample the vibrational Brillouin zone with grids of unprecedented size, which enables us to investigate the convergence of the zero-point renormalization to the thermal and optical band gaps of diamond.

  4. Optimization of nanoparticle focusing by coupling thermophoresis and engineered vortex in a microfluidic channel

    NASA Astrophysics Data System (ADS)

    Zhao, Chao; Cao, Zhibo; Fraser, John; Oztekin, Alparslan; Cheng, Xuanhong

    2017-01-01

    Enriching nanoparticles in an aqueous solution is commonly practiced for various applications. Despite recent advances in microfluidic technologies, a general method to concentrate nanoparticles in a microfluidic channel in a label free and continuous flow fashion is not yet available, due to strong Brownian motion on the nanoscale. Recent research of thermophoresis indicates that thermophoretic force can overcome the Brownian force to direct nanoparticle movement. Coupling thermophoresis with natural convection on the microscale has been shown to induce significant enrichment of biomolecules in a thermal diffusion column. However, the column operates in a batch process, and the concentrated samples are inconvenient to retrieve. We have recently designed a microfluidic device that combines a helical fluid motion and simple one-dimensional temperature gradient to achieve effective nanoparticle focusing in a continuous flow. The helical convection is introduced by microgrooves patterned on the channel floor, which directly controls the focusing speed and power. Here, COMSOL simulations are conducted to study how the device geometry and flow rate influence transport and subsequent nanoparticle focusing, with a constant temperature gradient. The results demonstrate a complex dependence of nanoparticle accumulation on the microgroove tilting angle, depth, and spacing, as well as channel width and flow rate. Further dimensional analyses reveal that the ratio between particle velocities induced by thermophoretic and fluid inertial forces governs the particle concentration factor, with a maximum concentration at a ratio of approximately one. This simple relationship provides fundamental insights about nanoparticle transport in coupled flow and thermal fields. The study also offers a useful guideline to the design and operation of nanoparticle concentrators based on combining engineered helical fluid motion subject to phoretic fields.

  5. Mixed Quantum-Classical Liouville Approach for Calculating Proton-Coupled Electron-Transfer Rate Constants.

    PubMed

    Shakib, Farnaz; Hanna, Gabriel

    2016-07-12

    In this work, we derive a general mixed quantum-classical formula for calculating thermal proton-coupled electron-transfer (PCET) rate constants, starting from the time integral of the quantum flux-flux correlation function. This formula allows for the direct simulation of PCET reaction dynamics via the mixed quantum-classical Liouville approach. Owing to the general nature of the derivation, this formula does not rely on any prior mechanistic assumptions and can be applied across a wide range of electronic and protonic coupling regimes. To test the validity of this formula, we applied it to a reduced model of a condensed-phase PCET reaction. Good agreement with the numerically exact rate constant is obtained, demonstrating the accuracy of our formalism. We believe that this approach constitutes a solid foundation for future investigations of the rates and mechanisms of a wide range of PCET reactions.

  6. Calculation of Dynamic Characteristics of Coupled Herringbone Journal and Thrust Hydrodynamic Bearings

    NASA Astrophysics Data System (ADS)

    Zang, Yan; Hatch, Michael R.

    We describe a numerical method for the analysis of dynamic characteristics of coupled herringbone-type journal and thrust hydrodynamic bearings. The non-dimensional generalized Reynolds equation is discretized on a non-orthogonal grid which is mapped into a square. The computational domain conforms to the herringbone grooves to improve the accuracy of the solution. The journal and thrust regions are mapped separately and connected through internal flux boundary conditions. The discretized pressure field is solved iteratively using the rapidly convergent ADI method. The stiffness and damping coefficients are obtained by perturbing the equilibrium solution of the Reynolds equation and solving the perturbation equations. The accuracy of the present calculation is confirmed by comparing with previously existing data. Analyses are performed for self-contained coupled hydrodynamic bearing systems which can be used to support the spindle motor of a magnetic hard-disk drive.

  7. Influence of channel base current and varying return stroke speed on the calculated fields of three important return stroke models

    NASA Technical Reports Server (NTRS)

    Thottappillil, Rajeev; Uman, Martin A.; Diendorfer, Gerhard

    1991-01-01

    Compared here are the calculated fields of the Traveling Current Source (TCS), Modified Transmission Line (MTL), and the Diendorfer-Uman (DU) models with a channel base current assumed in Nucci et al. on the one hand and with the channel base current assumed in Diendorfer and Uman on the other hand. The characteristics of the field wave shapes are shown to be very sensitive to the channel base current, especially the field zero crossing at 100 km for the TCS and DU models, and the magnetic hump after the initial peak at close range for the TCS models. Also, the DU model is theoretically extended to include any arbitrarily varying return stroke speed with height. A brief discussion is presented on the effects of an exponentially decreasing speed with height on the calculated fields for the TCS, MTL, and DU models.

  8. Gating mechanism of mechanosensitive channel of large conductance: a coupled continuum mechanical-continuum solvation approach.

    PubMed

    Zhu, Liangliang; Wu, Jiazhong; Liu, Ling; Liu, Yilun; Yan, Yuan; Cui, Qiang; Chen, Xi

    2016-12-01

    Gating transition of the mechanosensitive channel of large conductance (MscL) represents a good example of important biological processes that are difficult to describe using atomistic simulations due to the large (submicron) length scale and long (millisecond) time scale. Here we develop a novel computational framework that tightly couples continuum mechanics with continuum solvation models to study the detailed gating behavior of E. coli-MscL. The components of protein molecules are modeled by continuum elements that properly describe their shape, material properties and physicochemical features (e.g., charge distribution). The lipid membrane is modeled as a three-layer material in which the lipid head group and tail regions are treated separately, taking into account the fact that fluidic lipid bilayers do not bear shear stress. Coupling between mechanical and chemical responses of the channel is realized by an iterative integration of continuum mechanics (CM) modeling and continuum solvation (CS) computation. Compared to previous continuum mechanics studies, the present model is capable of capturing the most essential features of the gating process in a much more realistic fashion: due mainly to the apolar solvation contribution, the membrane tension for full opening of MscL is reduced substantially to the experimental measured range. Moreover, the pore size stabilizes constantly during gating because of the intricate interactions of the multiple components of the system, implying the mechanism for sub-conducting states of MscL gating. A significant fraction ([Formula: see text]2/3) of the gating membrane strain is required to reach the first sub-conducting state of our model, which is featured with a relative conductance of 0.115 to the fully opened state. These trends agree well with experimental observations. We anticipate that the coupled CM/CS modeling framework is uniquely suited for the analysis of many biomolecules and their assemblies under external

  9. Terrestrial LiDAR monitoring of rock slope-channel coupling

    NASA Astrophysics Data System (ADS)

    Bell, R.; Blöthe, J. H.; Meyer, N. K.; Hoffmann, T.; Hoffert, H.; Kreiner, D.; Elverfeldt, K. V.

    2009-04-01

    In steep terrain, various types of landslides (e.g. rock falls, debris flows and slides) are important erosional processes which often have a major impact on fluvial systems. On the one hand, they may divert river channels to opposite slopes or even block entire river channels, leading to the formation of landslide-dammed lakes. On the other hand, rivers prepare or even trigger landslides by undercutting slopes, which again will have an impact on the river channel. Our focus is on two study areas. One of them, the Schlichem Valley, is located in the Swabian Alb (SW-Germany), a lower mountain range consisting of Jurassic sedimentary rocks forming a cuesta landscape. There, the focus is on a larger landslide complex which blocked the river Schlichem three times during the 18th century and which is still active. Recent activity, especially at the location where the landslide enters the fluvial system, is investigated using Terrestrial LiDAR monitoring. The second study area is located in the Gesaeuse National Park in the Austrian Alps. There, various geomorphic environments are investigated by Terrestrial LiDAR including a vertical rock face in Dachstein limestone, which talus slope is directly coupled to the river Enns. The talus slope is built up by rock fall deposits, eroded mainly through smaller debris flow events. Furthermore, the talus slope is undercut by flood events of the river Enns. In this study a concept and first results are presented. They suggest how rock slope processes and their interactions with river channels can be monitored.

  10. Mechanical coupling of the multiple structural elements of the large-conductance mechanosensitive channel during expansion

    PubMed Central

    Li, Jie; Guo, Jianli; Ou, Xiaomin; Zhang, Mingfeng; Li, Yuezhou; Liu, Zhenfeng

    2015-01-01

    The prokaryotic mechanosensitive channel of large conductance (MscL) is a pressure-relief valve protecting the cell from lysing during acute osmotic downshock. When the membrane is stretched, MscL responds to the increase of membrane tension and opens a nonselective pore to about 30 Å wide, exhibiting a large unitary conductance of ∼3 nS. A fundamental step toward understanding the gating mechanism of MscL is to decipher the molecular details of the conformational changes accompanying channel opening. By applying fusion-protein strategy and controlling detergent composition, we have solved the structures of an archaeal MscL homolog from Methanosarcina acetivorans trapped in the closed and expanded intermediate states. The comparative analysis of these two new structures reveals significant conformational rearrangements in the different domains of MscL. The large changes observed in the tilt angles of the two transmembrane helices (TM1 and TM2) fit well with the helix-pivoting model derived from the earlier geometric analyses based on the previous structures. Meanwhile, the periplasmic loop region transforms from a folded structure, containing an ω-shaped loop and a short β-hairpin, to an extended and partly disordered conformation during channel expansion. Moreover, a significant rotating and sliding of the N-terminal helix (N-helix) is coupled to the tilting movements of TM1 and TM2. The dynamic relationships between the N-helix and TM1/TM2 suggest that the N-helix serves as a membrane-anchored stopper that limits the tilts of TM1 and TM2 in the gating process. These results provide direct mechanistic insights into the highly coordinated movement of the different domains of the MscL channel when it expands. PMID:26261325

  11. Mg2+ enhances voltage sensor/gate coupling in BK channels.

    PubMed

    Horrigan, Frank T; Ma, Zhongming

    2008-01-01

    BK (Slo1) potassium channels are activated by millimolar intracellular Mg(2+) as well as micromolar Ca(2+) and membrane depolarization. Mg(2+) and Ca(2+) act in an approximately additive manner at different binding sites to shift the conductance-voltage (G(K)-V) relation, suggesting that these ligands might work through functionally similar but independent mechanisms. However, we find that the mechanism of Mg(2+) action is highly dependent on voltage sensor activation and therefore differs fundamentally from that of Ca(2+). Evidence that Ca(2+) acts independently of voltage sensor activation includes an ability to increase open probability (P(O)) at extreme negative voltages where voltage sensors are in the resting state; 2 microM Ca(2+) increases P(O) more than 15-fold at -120 mV. However 10 mM Mg(2+), which has an effect on the G(K)-V relation similar to 2 microM Ca(2+), has no detectable effect on P(O) when voltage sensors are in the resting state. Gating currents are only slightly altered by Mg(2+) when channels are closed, indicating that Mg(2+) does not act merely to promote voltage sensor activation. Indeed, channel opening is facilitated in a voltage-independent manner by Mg(2+) in a mutant (R210C) whose voltage sensors are constitutively activated. Thus, 10 mM Mg(2+) increases P(O) only when voltage sensors are activated, effectively strengthening the allosteric coupling of voltage sensor activation to channel opening. Increasing Mg(2+) from 10 to 100 mM, to occupy very low affinity binding sites, has additional effects on gating that more closely resemble those of Ca(2+). The effects of Mg(2+) on steady-state activation and I(K) kinetics are discussed in terms of an allosteric gating scheme and the state-dependent interactions between Mg(2+) and voltage sensor that may underlie this mechanism.

  12. CFTR chloride channel in the apical compartments: spatiotemporal coupling to its interacting partners.

    PubMed

    Li, Chunying; Naren, Anjaparavanda P

    2010-04-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-regulated chloride channel located primarily at the apical or luminal surfaces of epithelial cells in the airway, intestine, pancreas, kidney, sweat gland, as well as male reproductive tract, where it plays a crucial role in transepithelial fluid homeostasis. CFTR dysfunction can be detrimental and may result in life-threatening disorders. CFTR hypofunctioning because of genetic defects leads to cystic fibrosis, the most common lethal genetic disease in Caucasians, whereas CFTR hyperfunctioning resulting from various infections evokes secretory diarrhea, the leading cause of mortality in early childhood. Therefore, maintaining a dynamic balance between CFTR up-regulating processes and CFTR down-regulating processes is essential for maintaining fluid and body homeostasis. Accumulating evidence suggests that protein-protein interactions play a critical role in the fine-tuned regulation of CFTR function. A growing number of proteins have been reported to interact directly or indirectly with CFTR chloride channel, suggesting that CFTR might be coupled spatially and temporally to a wide variety of interacting partners including ion channels, receptors, transporters, scaffolding proteins, enzyme molecules, signaling molecules, and effectors. Most interactions occur primarily between the opposing terminal tails (amino or carboxyl) of CFTR protein and its binding partners, either directly or mediated through various PDZ scaffolding proteins. These dynamic interactions impact the channel function, as well as localization and processing of CFTR protein within cells. This article reviews the most recent progress and findings about the interactions between CFTR and its binding partners through PDZ scaffolding proteins, as well as the spatiotemporal regulation of CFTR-containing macromolecular signaling complexes in the apical compartments of polarized cells lining the secretory epithelia.

  13. Calculation of the exchange coupling in Si:P donor systems

    NASA Astrophysics Data System (ADS)

    Starling, Timothy R.; Wellard, Cameron J.; Quiney, Harry M.; Haig, Wayne; Hollenberg, Lloyd C. L.

    2005-02-01

    We examine exchange coupling in the Kate quantum computer, which consists of isolated spin-1/2 31P donors in a pure Si lattice. A calculation is made using full configuration interaction, a reasonably large basis set, and a simple physical model. Basis set convergence was not obtained, and increasing the size of the matrix further appears to be computationally impractical. We therefore consider a Gaussian basis set approach. A brief description of the McMurchie-Davidson algorithm for the expansion of SGTF functions into Hermite polynomials is given. We also give the results of a single-donor computation in this basis.

  14. A modified coupled pair functional approach. [for dipole moment calculation of metal hydride ground states

    NASA Technical Reports Server (NTRS)

    Chong, D. P.; Langhoff, S. R.

    1986-01-01

    A modified coupled pair functional (CPF) method is presented for the configuration interaction problem that dramatically improves properties for cases where the Hartree-Fock reference configuration is not a good zeroth-order wave function description. It is shown that the tendency for CPF to overestimate the effect of higher excitations arises from the choice of the geometric mean for the partial normalization denominator. The modified method is demonstrated for ground state dipole moment calculations of the NiH, CuH, and ZnH transition metal hydrides, and compared to singles-plus-doubles configuration interaction and the Ahlrichs et al. (1984) CPF method.

  15. A conformational study of hydroxyflavones by vibrational spectroscopy coupled to DFT calculations

    NASA Astrophysics Data System (ADS)

    Machado, N. F. L.; Batista de Carvalho, L. A. E.; Otero, J. C.; Marques, M. P. M.

    2013-05-01

    The conformational preferences of a series of hydroxyflavones were studied by Raman and FTIR spectroscopies, coupled to Density Functional Theory calculations. Special attention was paid to the effect of hydroxyl substitution, due to its importance on the biological activity of these compounds. Their conformational preferences were found to be determined mainly by the orientation of the hydroxylic groups at C7 and within the catechol moiety, leading to the occurrence of distinct conformers in the solid state. A complete assignment of the experimental spectra was carried out for these molecules, in the light of their most stable conformers and the corresponding predicted vibrational pattern.

  16. A modified coupled pair functional approach. [for dipole moment calculation of metal hydride ground states

    NASA Technical Reports Server (NTRS)

    Chong, D. P.; Langhoff, S. R.

    1986-01-01

    A modified coupled pair functional (CPF) method is presented for the configuration interaction problem that dramatically improves properties for cases where the Hartree-Fock reference configuration is not a good zeroth-order wave function description. It is shown that the tendency for CPF to overestimate the effect of higher excitations arises from the choice of the geometric mean for the partial normalization denominator. The modified method is demonstrated for ground state dipole moment calculations of the NiH, CuH, and ZnH transition metal hydrides, and compared to singles-plus-doubles configuration interaction and the Ahlrichs et al. (1984) CPF method.

  17. Emergent properties of nuclei from ab initio coupled-cluster calculations

    SciTech Connect

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-05-17

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO${}_{{\\rm{sat}}}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the ${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$ states in ${}^{\\mathrm{17,23,25}}$O, and—contrary to naive shell-model expectations—the level ordering of the ${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$ states in ${}^{\\mathrm{53,55,61}}$Ca.

  18. Emergent properties of nuclei from ab initio coupled-cluster calculations

    SciTech Connect

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-05-17

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO${}_{{\\rm{sat}}}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the ${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$ states in ${}^{\\mathrm{17,23,25}}$O, and—contrary to naive shell-model expectations—the level ordering of the ${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$ states in ${}^{\\mathrm{53,55,61}}$Ca.

  19. Emergent properties of nuclei from ab initio coupled-cluster calculations

    NASA Astrophysics Data System (ADS)

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-06-01

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO{}{{sat}} is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon-nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. The coupling to the continuum impacts the energies of the {J}π =1/{2}-,3/{2}-,7/{2}-,3/{2}+ states in {}{17,23,25}O, and—contrary to naive shell-model expectations—the level ordering of the {J}π =3/{2}+,5/{2}+,9/{2}+ states in {}{53,55,61}Ca. ).

  20. Calculation of excited-state properties using general coupled-cluster and configuration-interaction models.

    PubMed

    Kállay, Mihály; Gauss, Jürgen

    2004-11-15

    Using string-based algorithms excitation energies and analytic first derivatives for excited states have been implemented for general coupled-cluster (CC) models within CC linear-response (LR) theory which is equivalent to the equation-of-motion (EOM) CC approach for these quantities. Transition moments between the ground and excited states are also considered in the framework of linear-response theory. The presented procedures are applicable to both single-reference-type and multireference-type CC wave functions independently of the excitation manifold constituting the cluster operator and the space in which the effective Hamiltonian is diagonalized. The performance of different LR-CC/EOM-CC and configuration-interaction approaches for excited states is compared. The effect of higher excitations on excited-state properties is demonstrated in benchmark calculations for NH(2) and NH(3). As a first application, the stationary points of the S(1) surface of acetylene are characterized by high-accuracy calculations.

  1. Equation-of-motion coupled cluster method for high spin double electron attachment calculations

    SciTech Connect

    Musiał, Monika Lupa, Łukasz; Kucharski, Stanisław A.

    2014-03-21

    The new formulation of the equation-of-motion (EOM) coupled cluster (CC) approach applicable to the calculations of the double electron attachment (DEA) states for the high spin components is proposed. The new EOM equations are derived for the high spin triplet and quintet states. In both cases the new equations are easier to solve but the substantial simplification is observed in the case of quintets. Out of 21 diagrammatic terms contributing to the standard DEA-EOM-CCSDT equations for the R{sub 2} and R{sub 3} amplitudes only four terms survive contributing to the R{sub 3} part. The implemented method has been applied to the calculations of the excited states (singlets, triplets, and quintets) energies of the carbon and silicon atoms and potential energy curves for selected states of the Na{sub 2} (triplets) and B{sub 2} (quintets) molecules.

  2. ATP is a coupling modulator of parallel Na,K-ATPase-K-channel activity in the renal proximal tubule.

    PubMed Central

    Tsuchiya, K; Wang, W; Giebisch, G; Welling, P A

    1992-01-01

    A fundamental and essential property of nearly all salt-transporting epithelia is the tight parallel coupling between the magnitude of the K-conductive pathway at the basolateral membrane and the activity of the Na,K-dependent ATPase (Na,K-ATPase). In the present study, we demonstrate that the coupling response in the renal proximal tubule is governed, at least in part, through the interaction between ATP-sensitive K channels and Na,K-ATPase-mediated changes in intracellular ATP levels. First, we identified a K-selective channel at the basolateral membrane, which is inhibited by the cytosolic addition of ATP. Second, conventional microelectrode analysis in the isolated perfused proximal straight tubule revealed that these channels are the major determinant of the macroscopic K conductance so that ATP-mediated changes in the open probability of the K channel could alter the extent of K recycling. Indeed, the increase in the macroscopic K conductance upon stimulation of transcellular Na transport and pump activity was found to be paralleled by a decrease in intracellular ATP. Finally, a causal link between parallel Na,K-ATPase-K-channel activity and ATP was established by the finding that intracellular ATP loading uncoupled the response. With our recent observations that similar ATP-sensitive K channels are expressed abundantly in other epithelia, we postulate that ATP may act as a universal coupling modulator of parallel Na,K-ATPase-K-channel activity. PMID:1321439

  3. Channels

    NASA Image and Video Library

    2014-04-29

    Two channels are visible in this image from NASA 2001 Mars Odyssey spacecraft . The smaller one near the bottom did not carve as deeply as the larger channel at the top. The channel near the top of the image is near the origin of Mamers Valles.

  4. Functional coupling of TRPV4, IK, and SK channels contributes to Ca2+-dependent endothelial injury in rodent lung

    PubMed Central

    Jian, Ming-Yuan; Taylor, Mark S.; Cioffi, Donna L.; Yap, Fui C.; Liedtke, Wolfgang; Townsley, Mary I.

    2015-01-01

    Abstract Our previous work has shown that the increased lung endothelial permeability response to 14,15-epoxyeicosatrienoic acid (14,15-EET) in rat lung requires Ca2+ entry via vanilloid type-4 transient receptor potential (TRPV4) channels. Recent studies suggest that activation of TRPV4 channels in systemic vascular endothelium prolongs agonist-induced hyperpolarization and amplifies Ca2+ entry by activating Ca2+-activated K+ (KCa) channels, resulting in vessel relaxation. Activation of endothelial KCa channels thus has potential to increase the electrochemical driving force for Ca2+ influx via TRPV4 channels and to amplify permeability responses to TRPV4 activation in lung. To examine this hypothesis, we used Western blot analysis, electrophysiological recordings, and isolated-lung permeability measurements to document expression of TRPV4 and KCa channels and the potential for functional coupling. The results show that rat pulmonary microvascular endothelial cells express TRPV4 and 3 KCa channels of different conductances: large (BK), intermediate (IK), and small (SK3). However, TRPV4 channel activity modulates the IK and SK3, but not the BK, channel current density. Furthermore, the TRPV4-mediated permeability response to 14,15-EET in mouse lung is significantly attenuated by pharmacologic blockade of IK and SK3, but not BK, channels. Collectively, this functional coupling suggests that endothelial TRPV4 channels in rodent lung likely form signaling microdomains with IK and SK3 channels and that the integrated response dictates the extent of lung endothelial injury caused by 14,15-EET. PMID:26064452

  5. Functional coupling between sodium-activated potassium channels and voltage-dependent persistent sodium currents in cricket Kenyon cells.

    PubMed

    Takahashi, Izumi; Yoshino, Masami

    2015-10-01

    In this study, we examined the functional coupling between Na(+)-activated potassium (KNa) channels and Na(+) influx through voltage-dependent Na(+) channels in Kenyon cells isolated from the mushroom body of the cricket Gryllus bimaculatus. Single-channel activity of KNa channels was recorded with the cell-attached patch configuration. The open probability (Po) of KNa channels increased with increasing Na(+) concentration in a bath solution, whereas it decreased by the substitution of Na(+) with an equimolar concentration of Li(+). The Po of KNa channels was also found to be reduced by bath application of a high concentration of TTX (1 μM) and riluzole (100 μM), which inhibits both fast (INaf) and persistent (INaP) Na(+) currents, whereas it was unaffected by a low concentration of TTX (10 nM), which selectively blocks INaf. Bath application of Cd(2+) at a low concentration (50 μM), as an inhibitor of INaP, also decreased the Po of KNa channels. Conversely, bath application of the inorganic Ca(2+)-channel blockers Co(2+) and Ni(2+) at high concentrations (500 μM) had little effect on the Po of KNa channels, although Cd(2+) (500 μM) reduced the Po of KNa channels. Perforated whole cell clamp analysis further indicated the presence of sustained outward currents for which amplitude was dependent on the amount of Na(+) influx. Taken together, these results indicate that KNa channels could be activated by Na(+) influx passing through voltage-dependent persistent Na(+) channels. The functional significance of this coupling mechanism was discussed in relation to the membrane excitability of Kenyon cells and its possible role in the formation of long-term memory. Copyright © 2015 the American Physiological Society.

  6. Nonrelativistic structure calculations of two-electron ions in a strongly coupled plasma environment

    SciTech Connect

    Bhattacharyya, S.; Saha, J. K.; Mukherjee, T. K.

    2015-04-01

    In this work, the controversy between the interpretations of recent measurements on dense aluminum plasma created with the Linac coherent light source (LCLS) x-ray free electron laser (FEL) and the Orion laser has been addressed. In both kinds of experiments, heliumlike and hydrogenlike spectral lines are used for plasma diagnostics. However, there exist no precise theoretical calculations for He-like ions within a dense plasma environment. The strong need for an accurate theoretical estimate for spectral properties of He-like ions in a strongly coupled plasma environment leads us to perform ab initio calculations in the framework of the Rayleigh-Ritz variation principle in Hylleraas coordinates where an ion-sphere potential is used. An approach to resolve the long-drawn problem of numerical instability for evaluating two-electron integrals with an extended basis inside a finite domain is presented here. The present values of electron densities corresponding to the disappearance of different spectral lines obtained within the framework of an ion-sphere potential show excellent agreement with Orion laser experiments in Al plasma and with recent theories. Moreover, this method is extended to predict the critical plasma densities at which the spectral lines of H-like and He-like carbon and argon ions disappear. Incidental degeneracy and level-crossing phenomena are being reported for two-electron ions embedded in strongly coupled plasma. Thermodynamic pressure experienced by the ions in their respective ground states inside the ion spheres is also reported.

  7. Lattice dynamics and electron-phonon coupling calculations using nondiagonal supercells

    NASA Astrophysics Data System (ADS)

    Lloyd-Williams, Jonathan; Monserrat, Bartomeu

    Quantities derived from electron-phonon coupling matrix elements require a fine sampling of the vibrational Brillouin zone. Converged results are typically not obtainable using the direct method, in which a perturbation is frozen into the system and the total energy derivatives are calculated using a finite difference approach, because the size of simulation cell needed is prohibitively large. We show that it is possible to determine the response of a periodic system to a perturbation characterized by a wave vector with reduced fractional coordinates (m1 /n1 ,m2 /n2 ,m3 /n3) using a supercell containing a number of primitive cells equal to the least common multiple of n1, n2, and n3. This is accomplished by utilizing supercell matrices containing nonzero off-diagonal elements. We present the results of electron-phonon coupling calculations using the direct method to sample the vibrational Brillouin zone with grids of unprecedented size for a range of systems, including the canonical example of diamond. We also demonstrate that the use of nondiagonal supercells reduces by over an order of magnitude the computational cost of obtaining converged vibrational densities of states and phonon dispersion curves. J.L.-W. is supported by the Engineering and Physical Sciences Research Council (EPSRC). B.M. is supported by Robinson College, Cambridge, and the Cambridge Philosophical Society. This work was supported by EPSRC Grants EP/J017639/1 and EP/K013564/1.

  8. Calculating Hot Spring/Atmospheric Coupling Using the Coefficient of Convective Heat Transfer

    NASA Astrophysics Data System (ADS)

    Lindsey, C.; Price, A. N.; Fairley, J. P., Jr.; Larson, P. B.

    2015-12-01

    We calculated the correlation between discharge temperature and wind speed for multiple hydrothermal springs, both in the Alvord Basin of southeast Oregon and our primary field location in Yellowstone National Park, using spring temperatures, wind speeds, and air temperatures logged at three minute intervals for multiple days. We find that some hydrothermal springs exhibit strong coupling with wind speed and/or air temperatures. The three springs described in this work display this strong coupling, with correlations between wind speed and spring temperature as high as 70 percent; as a result, we can use the changes in spring temperature as a proxy for changes in the coefficient of convective heat transfer (h) between the springs and the atmosphere. The coefficient of convective heat transfer is a complex parameter to measure, but is a necessary input to many heat and mass flux analyses. The results of this study provide a way to estimate h for springs with strong atmospheric coupling, which is a critical component of a total energy balance for hydrothermal discharge areas.

  9. Vicinal fluorine-proton coupling constants. Ab initio calculations of angular dependence and substituent effects

    NASA Astrophysics Data System (ADS)

    San Fabián, J.; Guilleme, J.

    1996-06-01

    A data set of vicinal fluorine-proton coupling constants has been calculated by means of the SCF ab initio and semiempirical INDO/FPT methods. The angular dependence, the effect of individual substituents, and the effect of interaction between two substituents upon the 3JFH couplings have been studied for the molecules CH 2FCH 3, CHF 2CH 3, CH 2FCH 2F, CF 3CH 3, and CHF 2CH 2F. The four contributions to 3JFH ( JFC, JSD, JOD and JOP) have been computed using the standard basis sets 6-31G, 6-31G ∗, 6-31G ∗∗ and 6-311G ∗∗ and a double zeta basis set [4s2p1d/2s1p] with additional tight s functions on the H and F. The agreement with the experimental data is better for the last basis set but the trends of the angular dependence and substituent effects are also reproduced by the remaining basis sets. The major contribution arises from the FC term and the remaining contributions are much smaller being the OP the most important. The individual effect of an electronegative substituent depends on the carbon to which is bonded, being more important when the substituent is bonded to the carbon with the coupled hydrogen. The effect of interaction between two substituents seems to be not negligible, reaching values up to 6 Hz. The most important calculated interaction effects are the geminal δC012FF, δC034FF and δC134FF as well as the vicinal δC213FF and δC214FF.

  10. The Effect of Extending the Length of the Coupling Coils in a MuonIonization Cooling Channel

    SciTech Connect

    Green, Michael A.

    2007-11-10

    RF cavities are used to re-accelerate muons that have beencooled by absorbers that are in low beta regions of a muon ionizationcooling channel. A superconducting coupling magnet (or magnets) arearound or among the RF cavities of a muon ionization-cooling channel. Thefield from the magnet guides the muons so that they are kept within theiris of the RF cavities that are used to accelerate the muons. Thisreport compares the use of a single short coupling magnet with anextended coupling magnet that has one or more superconducting coils aspart of a muon-cooling channel of the same design as the muon ionizationcooling experiment (MICE). Whether the superconducting magnet is shortand thick or long and this affects the magnet stored energy and the peakfield in the winding. The magnetic field distribution also affects is themuon beam optics in the cooling cell of a muon coolingchannel.

  11. Contribution of electromechanical coupling between KV and CaV1.2 channels to coronary dysfunction in obesity

    PubMed Central

    Berwick, Zachary C.; Dick, Gregory M.; O’Leary, Heather A.; Bender, Shawn B.; Goodwill, Adam G.; Moberly, Steven P.; Owen, Meredith Kohr; Miller, Steven J.; Obukhov, Alexander G.

    2013-01-01

    Previous investigations indicate that diminished functional expression of voltage-dependent K+ (KV) channels impairs control of coronary blood flow in obesity/metabolic syndrome. The goal of this investigation was to test the hypothesis that KV channels are electromechanically coupled to CaV1.2 channels and that coronary microvascular dysfunction in obesity is related to subsequent increases in CaV1.2 channel activity. Initial studies revealed that inhibition of KV channels with 4-aminopyridine (4AP, 0.3 mM) increased intracellular [Ca2+], contracted isolated coronary arterioles and decreased coronary reactive hyperemia. These effects were reversed by blockade of CaV1.2 channels. Further studies in chronically instrumented Ossabaw swine showed that inhibition of CaV1.2 channels with nifedipine (10 μg/kg, iv) had no effect on coronary blood flow at rest or during exercise in lean swine. However, inhibition of CaV1.2 channels significantly increased coronary blood flow, conductance, and the balance between coronary flow and metabolism in obese swine (P < 0.05). These changes were associated with a ~50 % increase in inward CaV1.2 current and elevations in expression of the pore-forming subunit (α1c) of CaV1.2 channels in coronary smooth muscle cells from obese swine. Taken together, these findings indicate that electromechanical coupling between KV and CaV1.2 channels is involved in the regulation of coronary vasomotor tone and that increases in CaV1.2 channel activity contribute to coronary microvascular dysfunction in the setting of obesity. PMID:23856709

  12. Isospin decomposition of γN→N* transitions within a dynamical coupled-channels model

    DOE PAGES

    Kamano, Hiroyuki; Nakamura, S. X.; Lee, T. -S. H.; ...

    2016-07-07

    Here, by extending the dynamical coupled-channels analysis performed in our previous work to include the available data of photoproduction of pi mesons off neutrons, the transition amplitudes for the photoexcitation of the neutron-to-nucleon resonances, γn → N*, at the resonance pole positions are determined. The combined fits to the data for both the proton- and neutron-target reactions also revise our results for the resonance pole positions and the γp → N* transition amplitudes. Our results allow an isospin decomposition of the γN → N* transition amplitudes for the isospin I = 1/2 N* resonances, which is necessary for testing hadronmore » structure models and gives crucial inputs for constructing models of neutrino-induced reactions in the nucleon resonance region.« less

  13. Fabrication of surface-channel charge-coupled devices with ultralow density of interface states

    NASA Astrophysics Data System (ADS)

    Saks, Nelson S.

    1982-10-01

    Surface-channel charge-coupled devices (CCD's) have been fabricated with ultralow density of (fast) interface states in the range 1-3×108/cm2 eV. This low interface state density is achieved by hydrogen implantation into the metal-nitride-oxide-silicon (MNOS) insulator structure of the CCD as the final fabrication step after aluminum interconnect metallization. The CCD's are shown to have excellent operating characteristics including high transfer efficiency (˜0.99995 without bias charge), low dark current (0.25-0.50 nA/cm2 at 20°C), and high signal charge capacity (1.55×1012 e/cm2 for 10-V clock swing).

  14. Coupled-Channel Models of Direct-Semidirect Capture via Giant-Dipole Resonances

    NASA Astrophysics Data System (ADS)

    Thompson, I. J.; Escher, J. E.; Arbanas, G.

    2014-04-01

    Semidirect capture, a two-step process that excites a giant-dipole resonance followed by its radiative de-excitation, is a dominant process near giant-dipole resonances, that is, for incoming neutron energies within 5-20 MeV. At lower energies such processes may affect neutron capture rates that are relevant to astrophysical nucleosynthesis models. We implement a semidirect capture model in the coupled-channel reaction code Fresco and validate it by comparing the cross section for direct-semidirect capture 208Pb(n,γ)209Pb to experimental data. We also investigate the effect of low-energy electric dipole strength in the pygmy resonance. We use a conventional single-particle direct-semidirect capture code Cupido for comparison. Furthermore, we present and discuss our results for direct-semidirect capture reaction 130Sn(n,γ)131Sn, the cross section of which is known to have a significant effect on nucleosynthesis models.

  15. Coupled-Channel Models of Direct-Semidirect Capture via Giant-Dipole Resonances

    SciTech Connect

    Thompson, I J; Escher, Jutta E; Arbanas, Goran

    2013-01-01

    Semidirect capture, a two-step process that excites a giant-dipole resonance followed by its radiative de-excitation, is a dominant process near giant-dipole resonances, that is, for incoming neutron energies within 5 20 MeV. At lower energies such processes may affect neutron capture rates that are relevant to astrophysical nucleosynthesis models. We implement a semidirect capture model in the coupled-channel reaction code Fresco and validate it by comparing the cross section for direct-semidirect capture 208Pb(n,g)209Pb to experimental data. We also investigate the effect of low-energy electric dipole strength in the pygmy resonance. We use a conventional single-particle direct-semidirect capture code Cupido for comparison. Furthermore, we present and discuss our results for direct-semidirect capture reaction 130Sn(n,g)131Sn, the cross section of which is known to have a significant effect on nucleosynthesis models.

  16. Chaos synchronization and communication in unidirectionally coupled VCSELs with fiber channel

    NASA Astrophysics Data System (ADS)

    Li, Lin-Fu; Chen, Jian-Jun

    2012-11-01

    A novel chaotic synchronization configuration is proposed. This system is constructed on the basis of unidirectionally coupled VCSELs and signal transmission in fiber. The transmitter VCSEL is subject to an isotropic optical feedback, the receiver VCSEL is subject to an orthogonal optical injection from the transmitter VCSEL, the chaotic signal transmission in fiber channel is adopted, also message encoding and decoding of the chaotic system have been investigated. The results show that, during to the fiber nonlinear and chromatic dispersion, the amplitude characteristics of chaotic signal are distorted partially and the system synchronization quality will be impaired, but message can be hidden efficiently in the chaotic signal during the fiber transmission with additive chaos modulation (ACM). Better decoding performance is achieved by choosing appropriate matched parameters.

  17. Discovery of functional monoclonal antibodies targeting G-protein-coupled receptors and ion channels.

    PubMed

    Wilkinson, Trevor C I

    2016-06-15

    The development of recombinant antibody therapeutics is a significant area of growth in the pharmaceutical industry with almost 50 approved monoclonal antibodies on the market in the US and Europe. Despite this growth, however, certain classes of important molecular targets have remained intractable to therapeutic antibodies due to complexity of the target molecules. These complex target molecules include G-protein-coupled receptors and ion channels which represent a large potential target class for therapeutic intervention with monoclonal antibodies. Although these targets have typically been addressed by small molecule approaches, the exquisite specificity of antibodies provides a significant opportunity to provide selective modulation of these target proteins. Given this opportunity, substantial effort has been applied to address the technical challenges of targeting these complex membrane proteins with monoclonal antibodies. In this review recent progress made in the strategies for discovery of functional monoclonal antibodies for these challenging membrane protein targets is addressed.

  18. Two Ca(2+)-Binding Sites Cooperatively Couple Together in TMEM16A Channel.

    PubMed

    Han, Yuebin; Zhang, Suhua; Ren, Shuxi; Chen, Yafei; Yuan, Hongbo; Chai, Ran; Yu, Hui; Zhang, Hailin; Zhan, Yong; An, Hailong

    2016-04-01

    TMEM16A is the molecular basis of calcium-activated chloride channels and shows Ca(2+)-dependent gating. It is critical to understand how the Ca(2+) sensors dynamically control the gate of TMEM16A. However, the detailed mechanism by which the calcium ions bind and open the channel is still obscure. In this study, the authors confirmed that there are two Ca(2+) sensors which cooperatively couple together in TMEM16A. Our data show that mutations at both Ca(2+)-sensitive domains, E447Y and E702Q-E705Q, weaken the Ca(2+) affinity for TMEM16A channel. The EC50 for WT, E447Y, and E702Q-E705Q are 0.53 ± 0.11, 14.5 ± 0.3, and 26.5 ± 3.6 μM, respectively. The triple mutation, including both of the Ca(2+) sensors, E447Y-E702Q-E705Q, with EC50 as 55.6 ± 5.1 μM, results in much further right-shifted dose response curve than the single sensor's mutations (E447Y, E702Q-E705Q) do, which indicates that there is a cooperation between the two Ca(2+)-sensitive domains. We also found that the divalent cations, both Ca(2+) and Sr(2+), share common mechanism of gating the TMEM16A.

  19. Synchronization and array-enhanced resonances in delayed coupled neuronal network with channel noise

    NASA Astrophysics Data System (ADS)

    Chen, Jianchun; Ding, Shaojie; Li, Hui; He, Guolong; Zhang, Xuejuan

    2014-09-01

    This paper studies the combined effect of transmission delay and channel fluctuations on population behaviors of an excitatory Erdös-Rényi neuronal network. First, it is found that the network reaches a perfect spatial temporal coherence at a suitable membrane size. Such a coherence resonance is stimulus-free and is array-enhanced. Second, the presence of transmission delay can induce intermittent changes of the population dynamics. Besides, two resonant peaks of the population firing rate are observed as delay changes: one is at τd≈7ms for all membrane areas, which reflects the resonance between the delayed interaction and the intrinsic period of channel kinetics; the other occurs when the transmission delay equals to the mean inter-spike intervals of the population firings in the absence of delay, which reflects the resonance between the delayed interaction and the firing period of the non-delayed system. Third, concerning the impact of network topology and population size, it is found that decreasing the connection probability does not change the range of transmission delay but broadens the range of synaptic coupling that supports population neurons to generate action potentials synchronously and temporally coherently. Furthermore, there exists a critical connection probability that distinguishes the population dynamics into an asynchronous and synchronous state. All the results we obtained are based on networks of size N = 500, which are shown to be robust to further increasing the population size.

  20. Uplink Scheduling and Adjacent-Channel Coupling Loss Analysis for TD-LTE Deployment

    PubMed Central

    Yeo, Woon-Young; Moon, Sung Ho

    2014-01-01

    TD-LTE, one of the two duplexing modes in LTE, operates in unpaired spectrum and has the advantages of TDD-based technologies. It is expected that TD-LTE will be more rapidly deployed in near future and most of WiMax operators will upgrade their networks to TD-LTE gradually. Before completely upgrading to TD-LTE, WiMax may coexist with TD-LTE in an adjacent frequency band. In addition, multiple TD-LTE operators may deploy their networks in adjacent bands. When more than one TDD network operates in adjacent frequency bands, severe interference may happen due to adjacent channel interference (ACI) and unsynchronized operations. In this paper, coexistence issues between TD-LTE and other systems are analyzed and coexistence requirements are provided. This paper has three research objectives. First, frame synchronization between TD-LTE and WiMax is discussed by investigating possible combinations of TD-LTE and WiMax configurations. Second, an uplink scheduling algorithm is proposed to utilize a leakage pattern of ACI in synchronized operations. Third, minimum requirements for coexistence in unsynchronized operations are analyzed by introducing a concept of adjacent-channel coupling loss. From the analysis and simulation results, we can see that coexistence of TD-LTE with other TDD systems is feasible if the two networks are synchronized. For the unsynchronized case, some special cell-site engineering techniques may be required to reduce the ACI. PMID:24707214

  1. Coupled-channels study of the {pi}{sup -}p {right arrow} {eta}n process.

    SciTech Connect

    Durand, J.; Julia-Diaz, B.; Lee, T.-S. H.; Saghai, B.; Sato, T.; Physics; Inst. de Recherche sur les lois Fondamentales de l'Univers; Univ. de Barcelona; Thomas Jefferson National Accelerator Facility; Osaka Univ.

    2008-08-01

    The reaction {pi}{sup -}p {yields} {eta}n is investigated within a dynamical coupled-channels model of meson production reactions in the nucleon resonance region. The meson baryon channels included are {pi}N, {eta}N, {pi}{Delta}, {sigma}N, and {rho}N. The nonresonant meson-baryon interactions of the model are derived from a set of Lagrangians by using a unitary transformation method. One or two excited nucleon states in each of S,P,D, and F partial waves are included to generate the resonant amplitudes. Data of the {pi}{sup -}p {yields} {eta}n reaction from threshold up to a total center-of-mass energy of about 2 GeV are satisfactorily reproduced and the roles played by the following nine nucleon resonances are investigated: S{sub 11}(1535),S{sub 11}(1650),P{sub 11}(1440),P{sub 11}(1710),P{sub 13}(1720),D{sub 13}(1520),D{sub 13}(1700),D{sub 15}(1675), and F{sub 15}(1680). The reaction mechanism and the predicted {eta}N scattering length are discussed.

  2. Using $$X(3823)\\to J/\\psi\\pi^+\\pi^-$$ to Identify Coupled-Channel Effects

    DOE PAGES

    Wang, Bo; Xu, Hao; Liu, Xiang; ...

    2016-03-17

    Very recently, a new charmonium-like state X(3823) was observed by the Belle and BESIII experiments, which is a good candidate of D-wave charmonium ψ(13D2). Since the X(3872) is just below the DD¯ * threshold, the decay X(3823) → J/ψπ+π - can be a golden channel to test the significance of coupled-channel effects. In this work, this decay is considered including both the hidden-charm dipion and the usual QCDME contributions. The partial decay width, the dipion invariant mass spectrum distribution dΓ[X(3823) → J/ψπ+π - ]/dmπ +π- , and the corresponding dΓ[X(3823) → J/ψπ+π- ]/d cos θ distribution are computed. Many parametersmore » are determined from existing experimental data, leaving the results mainly dependent on only one unknown phase between the QCDME and hidden-charm dipion amplitudes.« less

  3. Uplink scheduling and adjacent-channel coupling loss analysis for TD-LTE deployment.

    PubMed

    Yeo, Woon-Young; Moon, Sung Ho; Kim, Jae-Hoon

    2014-01-01

    TD-LTE, one of the two duplexing modes in LTE, operates in unpaired spectrum and has the advantages of TDD-based technologies. It is expected that TD-LTE will be more rapidly deployed in near future and most of WiMax operators will upgrade their networks to TD-LTE gradually. Before completely upgrading to TD-LTE, WiMax may coexist with TD-LTE in an adjacent frequency band. In addition, multiple TD-LTE operators may deploy their networks in adjacent bands. When more than one TDD network operates in adjacent frequency bands, severe interference may happen due to adjacent channel interference (ACI) and unsynchronized operations. In this paper, coexistence issues between TD-LTE and other systems are analyzed and coexistence requirements are provided. This paper has three research objectives. First, frame synchronization between TD-LTE and WiMax is discussed by investigating possible combinations of TD-LTE and WiMax configurations. Second, an uplink scheduling algorithm is proposed to utilize a leakage pattern of ACI in synchronized operations. Third, minimum requirements for coexistence in unsynchronized operations are analyzed by introducing a concept of adjacent-channel coupling loss. From the analysis and simulation results, we can see that coexistence of TD-LTE with other TDD systems is feasible if the two networks are synchronized. For the unsynchronized case, some special cell-site engineering techniques may be required to reduce the ACI.

  4. Using $X(3823)\\to J/\\psi\\pi^+\\pi^-$ to Identify Coupled-Channel Effects

    SciTech Connect

    Wang, Bo; Xu, Hao; Liu, Xiang; Chen, Dian-Yong; Coito, Susana; Eichten, Estia

    2016-03-17

    Very recently, a new charmonium-like state X(3823) was observed by the Belle and BESIII experiments, which is a good candidate of D-wave charmonium ψ(13D2). Since the X(3872) is just below the DD¯ * threshold, the decay X(3823) → J/ψπ+π - can be a golden channel to test the significance of coupled-channel effects. In this work, this decay is considered including both the hidden-charm dipion and the usual QCDME contributions. The partial decay width, the dipion invariant mass spectrum distribution dΓ[X(3823) → J/ψπ+π - ]/dmπ +π- , and the corresponding dΓ[X(3823) → J/ψπ+π- ]/d cos θ distribution are computed. Many parameters are determined from existing experimental data, leaving the results mainly dependent on only one unknown phase between the QCDME and hidden-charm dipion amplitudes.

  5. Entangled state teleportation through a couple of quantum channels composed of XXZ dimers in an Ising- XXZ diamond chain

    NASA Astrophysics Data System (ADS)

    Rojas, M.; de Souza, S. M.; Rojas, Onofre

    2017-02-01

    The quantum teleportation plays an important role in quantum information process, in this sense, the quantum entanglement properties involving an infinite chain structure is quite remarkable because real materials could be well represented by an infinite chain. We study the teleportation of an entangled state through a couple of quantum channels, composed by Heisenberg dimers in an infinite Ising-Heisenberg diamond chain, the couple of chains are considered sufficiently far away from each other to be ignored the any interaction between them. To teleporting a couple of qubits through the quantum channel, we need to find the average density operator for Heisenberg spin dimers, which will be used as quantum channels. Assuming the input state as a pure state, we can apply the concept of fidelity as a useful measurement of teleportation performance of a quantum channel. Using the standard teleportation protocol, we have derived an analytical expression for the output concurrence, fidelity, and average fidelity. We study in detail the effects of coupling parameters, external magnetic field and temperature dependence of quantum teleportation. Finally, we explore the relations between entanglement of the quantum channel, the output entanglement and the average fidelity of the system. Through a kind of phase diagram as a function of Ising-Heisenberg diamond chain model parameters, we illustrate where the quantum teleportation will succeed and a region where the quantum teleportation could fail.

  6. Natural triple excitations in local coupled cluster calculations with pair natural orbitals

    NASA Astrophysics Data System (ADS)

    Riplinger, Christoph; Sandhoefer, Barbara; Hansen, Andreas; Neese, Frank

    2013-10-01

    In this work, the extension of the previously developed domain based local pair-natural orbital (DLPNO) based singles- and doubles coupled cluster (DLPNO-CCSD) method to perturbatively include connected triple excitations is reported. The development is based on the concept of triples-natural orbitals that span the joint space of the three pair natural orbital (PNO) spaces of the three electron pairs that are involved in the calculation of a given triple-excitation contribution. The truncation error is very smooth and can be significantly reduced through extrapolation to the zero threshold. However, the extrapolation procedure does not improve relative energies. The overall computational effort of the method is asymptotically linear with the system size O(N). Actual linear scaling has been confirmed in test calculations on alkane chains. The accuracy of the DLPNO-CCSD(T) approximation relative to semicanonical CCSD(T0) is comparable to the previously developed DLPNO-CCSD method relative to canonical CCSD. Relative energies are predicted with an average error of approximately 0.5 kcal/mol for a challenging test set of medium sized organic molecules. The triples correction typically adds 30%-50% to the overall computation time. Thus, very large systems can be treated on the basis of the current implementation. In addition to the linear C150H302 (452 atoms, >8800 basis functions) we demonstrate the first CCSD(T) level calculation on an entire protein, Crambin with 644 atoms, and more than 6400 basis functions.

  7. Calculation of light delay for coupled microrings by FDTD technique and Padé approximation.

    PubMed

    Huang, Yong-Zhen; Yang, Yue-De

    2009-11-01

    The Padé approximation with Baker's algorithm is compared with the least-squares Prony method and the generalized pencil-of-functions (GPOF) method for calculating mode frequencies and mode Q factors for coupled optical microdisks by FDTD technique. Comparisons of intensity spectra and the corresponding mode frequencies and Q factors show that the Padé approximation can yield more stable results than the Prony and the GPOF methods, especially the intensity spectrum. The results of the Prony method and the GPOF method are greatly influenced by the selected number of resonant modes, which need to be optimized during the data processing, in addition to the length of the time response signal. Furthermore, the Padé approximation is applied to calculate light delay for embedded microring resonators from complex transmission spectra obtained by the Padé approximation from a FDTD output. The Prony and the GPOF methods cannot be applied to calculate the transmission spectra, because the transmission signal obtained by the FDTD simulation cannot be expressed as a sum of damped complex exponentials.

  8. Calculations of the giant-dipole-resonance photoneutrons using a coupled EGS4-morse code

    SciTech Connect

    Liu, J.C.; Nelson, W.R.; Kase, K.R.; Mao, X.S.

    1995-10-01

    The production and transport of the photoneutrons from the giant-dipoleresonance reaction have been implemented in a coupled EGS4-MORSE code. The total neutron yield (including both the direct neutron and evaporation neutron components) is calculated by folding the photoneutron yield cross sections with the photon track length distribution in the target. Empirical algorithms based on the measurements have been developed to estimate the fraction and energy of the direct neutron component for each photon. The statistical theory in the EVAP4 code, incorporated as a MORSE subroutine, is used to determine the energies of the evaporation neutrons. These represent major improvements over other calculations that assumed no direct neutrons, a constant fraction of direct neutrons, monoenergetic direct neutron, or a constant nuclear temperature for the evaporation neutrons. It was also assumed that the slow neutrons (< 2.5 MeV) are emitted isotropically and the fast neutrons are emitted anisotropically in the form of 1+Csin{sup 2}{theta}, which have a peak emission at 900. Comparisons between the calculated and the measured photoneutron results (spectra of the direct, evaporation and total neutrons; nuclear temperatures; direct neutron fractions) for materials of lead, tungsten, tantalum and copper have been made. The results show that the empirical algorithms, albeit simple, can produce reasonable results over the interested photon energy range.

  9. Systematic description of the {sup 6}Li(n,n{sup '}){sup 6}Li{sup *}{yields}d+{alpha} reactions with the microscopic coupled-channels method

    SciTech Connect

    Matsumoto, T.; Ichinkhorloo, D.; Kato, K.; Hirabayashi, Y.; Chiba, S.

    2011-06-15

    We investigate {sup 6}Li(n,n{sup '}){sup 6}Li{sup *}{yields}d+{alpha} reactions by using the continuum-discretized coupled-channels method with the complex Jeukenne-Lejeune-Mahaux effective nucleon-nucleon interaction. In this study, the {sup 6}Li nucleus is described by a d+{alpha} cluster model. The calculated elastic cross sections for incident energies between 7.47 and 24.0 MeV are in good agreement with experimental data. Furthermore, we show that the neutron spectra for {sup 6}Li breakup states measured at selected angular points and incident energies can be also reproduced systematically.

  10. Emergent properties of nuclei from ab initio coupled-cluster calculations

    DOE PAGES

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; ...

    2016-05-17

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLOmore » $${}_{{\\rm{sat}}}$$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the $${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$$ states in $${}^{\\mathrm{17,23,25}}$$O, and—contrary to naive shell-model expectations—the level ordering of the $${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$$ states in $${}^{\\mathrm{53,55,61}}$$Ca.« less

  11. Investigating the relationship between watching satellite channels and intimacy and marital satisfaction of couples in Isfahan, Iran, in 2014

    PubMed Central

    Babaie, Zohre; Keshvari, Mahrokh; Zamani, Ahmadreza

    2016-01-01

    Background: In the age of communication and media that families are rapidly driven towards using satellite channels and other media, considering family health in this regard is essential. A determinant of health is marital satisfaction. The aim of this study was to investigate the relationship between watching satellite channels and intimacy and marital satisfaction in Isfahan, Iran. Materials and Methods: This cross-sectional and correlational study was conducted on one group of 480 couples (n = 960) participating from 8 health-treatment centers in Isfahan. Multi-stage cluster sampling was used in this study. Inclusion criteria included at least 2 years of marriage. After completion of Bagarozzi's Marital Intimacy Questionnaire and ENRICH Marital Inventory, the couples were divided into two groups based on watching satellite networks. Data were analyzed using SPSS 18. Results: There was a significant relationship between intimacy and marital satisfaction in both viewers and non-viewers of satellite channels (P < 0.050). Average duration of couple's interaction in the satellite viewing group was 22.4 minutes and in non-viewers group was 47.95 min. In addition, the duration of interaction had a significant relationship with marital satisfaction and intimacy (P < 0.050). Conclusions: This study showed that watching satellite channels reduced the intimacy and marital satisfaction of the couples, and duration of interaction among the couples. PMID:28194193

  12. Investigating the relationship between watching satellite channels and intimacy and marital satisfaction of couples in Isfahan, Iran, in 2014.

    PubMed

    Babaie, Zohre; Keshvari, Mahrokh; Zamani, Ahmadreza

    2016-01-01

    In the age of communication and media that families are rapidly driven towards using satellite channels and other media, considering family health in this regard is essential. A determinant of health is marital satisfaction. The aim of this study was to investigate the relationship between watching satellite channels and intimacy and marital satisfaction in Isfahan, Iran. This cross-sectional and correlational study was conducted on one group of 480 couples (n = 960) participating from 8 health-treatment centers in Isfahan. Multi-stage cluster sampling was used in this study. Inclusion criteria included at least 2 years of marriage. After completion of Bagarozzi's Marital Intimacy Questionnaire and ENRICH Marital Inventory, the couples were divided into two groups based on watching satellite networks. Data were analyzed using SPSS 18. There was a significant relationship between intimacy and marital satisfaction in both viewers and non-viewers of satellite channels (P < 0.050). Average duration of couple's interaction in the satellite viewing group was 22.4 minutes and in non-viewers group was 47.95 min. In addition, the duration of interaction had a significant relationship with marital satisfaction and intimacy (P < 0.050). This study showed that watching satellite channels reduced the intimacy and marital satisfaction of the couples, and duration of interaction among the couples.

  13. Calculations of steady and transient channel flows with a time-accurate L-U factorization scheme

    NASA Technical Reports Server (NTRS)

    Kim, S.-W.

    1991-01-01

    Calculations of steady and unsteady, transonic, turbulent channel flows with a time accurate, lower-upper (L-U) factorization scheme are presented. The L-U factorization scheme is formally second-order accurate in time and space, and it is an extension of the steady state flow solver (RPLUS) used extensively to solve compressible flows. A time discretization method and the implementation of a consistent boundary condition specific to the L-U factorization scheme are also presented. The turbulence is described by the Baldwin-Lomax algebraic turbulence model. The present L-U scheme yields stable numerical results with the use of much smaller artificial dissipations than those used in the previous steady flow solver for steady and unsteady channel flows. The capability to solve time dependent flows is shown by solving very weakly excited and strongly excited, forced oscillatory, channel flows.

  14. A Mathematica package for calculation of planar channeling radiation spectra of relativistic electrons channeled in a diamond-structure single crystal (quantum approach)

    NASA Astrophysics Data System (ADS)

    Azadegan, B.

    2013-03-01

    The presented Mathematica code is an efficient tool for simulation of planar channeling radiation spectra of relativistic electrons channeled along major crystallographic planes of a diamond-structure single crystal. The program is based on the quantum theory of channeling radiation which has been successfully applied to study planar channeling at electron energies between 10 and 100 MeV. Continuum potentials for different planes of diamond, silicon and germanium single crystals are calculated using the Doyle-Turner approximation to the atomic scattering factor and taking thermal vibrations of the crystal atoms into account. Numerical methods are applied to solve the one-dimensional Schrödinger equation. The code is designed to calculate the electron wave functions, transverse electron states in the planar continuum potential, transition energies, line widths of channeling radiation and depth dependencies of the population of quantum states. Finally the spectral distribution of spontaneously emitted channeling radiation is obtained. The simulation of radiation spectra considerably facilitates the interpretation of experimental data. Catalog identifier: AEOH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOH_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.: 446 No. of bytes in distributed program, including test data, etc.: 209805 Distribution format: tar.gz Programming language: Mathematica. Computer: Platforms on which Mathematica is available. Operating system: Operating systems on which Mathematica is available. RAM: 1 MB Classification: 7.10. Nature of problem: Planar channeling radiation is emitted by relativistic charged particles during traversing a single crystal in direction parallel to a crystallographic plane. Channeling is modeled as the motion

  15. Geomorphic (de-) coupling of hillslope and channel systems within headwater catchments in two subarctic tributary valleys, Nordfjord, Western Norway

    NASA Astrophysics Data System (ADS)

    Laute, Katja; Beylich, Achim A.

    2010-05-01

    Hillslopes occupy large areas of the earth surface. Studying the characteristics, development and interaction of hillslopes as components of the geomorphic hillslope-channel coupling process-response system will improve the understanding of the complex response of mountain landscape formation. The rates of hillslope processes are exceptionally varied and affected by many influences of varying intensity. Hillslope-channel coupling and sediment storage within slopes are important factors that influence sediment delivery through catchments, especially in steep environments. Within sediment transfers from sources to sinks in drainage basins, hillslopes function as a key element concerning sediment storage, both for short term periods as between rainstorms as well as for longer periods in colluvial deposits. This PhD project is part of the NFR funded SedyMONT-Norway project within the ESF TOPO-EUROPE SedyMONT (Timescales of sediment dynamics, climate and topographic change in mountain landscapes) programme. The focus of this study is on geomorphic hillslope-channel coupling or de-coupling and sediment transport within four distinct headwater areas of the Erdalen and Bødalen catchments in the Nordfjord valley-fjord system (inner Nordfjord, Western Norway). Both catchments can be described as steep, U-shaped and glacier-fed, subarctic tributary valleys. Approximately 14% of the 49 km2 large headwater area of Erdalen is occupied by hillslope deposits; in Bødalen hillslope deposits occupy 12% of the 42 km2 large headwater area. The main aims of the study are to present preliminary findings on (i) the identification of possible sediment sources and delivery pathways within the headwater areas of the catchments, (ii) to analyze the development of hillslope-channel coupling / de-coupling from postglacial to contemporary timescales as well as (iii) to investigate the current degree of geomorphic hillslope-channel coupling within the different headwater catchments and (iv) to

  16. Using multi-scale remote sensing techniques to quantify hillslope channel coupling in bedrock landscapes

    NASA Astrophysics Data System (ADS)

    Neely, A. B.; DiBiase, R.

    2016-12-01

    Quantifying the role of rock material properties in controlling landscape-scale erosion rates is a long-standing problem in geomorphology, yet is necessary for accurate interpretation of spatial and temporal patterns of climate and tectonics encoded in Earth's topography. In bedrock landscapes, rockfall from cliffs commonly provides the largest and strongest clasts to stream networks and, until these clasts are eroded or mobilized, can inhibit channel incision into bedrock. Hillslope and channel morphology are thought to be coupled through a connection between bedrock fracture spacing and the resulting grain size distribution of stream sediment, but field quantification of this effect in bedrock landscapes is difficult due to the inaccessibility of steep terrain and challenges characterizing heterogeneity at a range of scales. Here, we use a suite of nested field and remote sensing techniques to characterize bedrock landscape morphology in the San Jacinto and San Gabriel mountain ranges of Southern California. These ranges have similar climate, granitic bedrock, and topographic relief, but exhibit a 5-fold difference in erosion rate that we hypothesize to be a result of a contrast in bedrock fracture spacing and grain size of channel-bed material. Using airborne lidar-derived elevation point clouds, we show that bedrock cliffs in the San Jacinto Mountains are systematically steeper and taller across all spatial scales compared with those in the San Gabriel Mountains. From georeferenced high-resolution photographs taken from along exposed ridgelines, we constructed cm-scale topographic models of 100-m scale cliffs and debris chutes using Structure-from-Motion (SfM) techniques, in order to quantify (1) the extent of bedrock on hillslopes, (2) the spacing and orientation of bedrock fractures on cliffs, and (3) the grain size of rockfall deposits at the base of cliffs and in headwater channels. Our results highlight the utility of nesting SfM surveys with airborne

  17. Thermodynamic coupling between activation and inactivation gating in potassium channels revealed by free energy molecular dynamics simulations

    PubMed Central

    Pan, Albert C.; Cuello, Luis G.; Perozo, Eduardo

    2011-01-01

    The amount of ionic current flowing through K+ channels is determined by the interplay between two separate time-dependent processes: activation and inactivation gating. Activation is concerned with the stimulus-dependent opening of the main intracellular gate, whereas inactivation is a spontaneous conformational transition of the selectivity filter toward a nonconductive state occurring on a variety of timescales. A recent analysis of multiple x-ray structures of open and partially open KcsA channels revealed the mechanism by which movements of the inner activation gate, formed by the inner helices from the four subunits of the pore domain, bias the conformational changes at the selectivity filter toward a nonconductive inactivated state. This analysis highlighted the important role of Phe103, a residue located along the inner helix, near the hinge position associated with the opening of the intracellular gate. In the present study, we use free energy perturbation molecular dynamics simulations (FEP/MD) to quantitatively elucidate the thermodynamic basis for the coupling between the intracellular gate and the selectivity filter. The results of the FEP/MD calculations are in good agreement with experiments, and further analysis of the repulsive, van der Waals dispersive, and electrostatic free energy contributions reveals that the energetic basis underlying the absence of inactivation in the F103A mutation in KcsA is the absence of the unfavorable steric interaction occurring with the large Ile100 side chain in a neighboring subunit when the intracellular gate is open and the selectivity filter is in a conductive conformation. Macroscopic current analysis shows that the I100A mutant indeed relieves inactivation in KcsA, but to a lesser extent than the F103A mutant. PMID:22124115

  18. Calculation of residual dipolar couplings from disordered state ensembles using local alignment.

    PubMed

    Marsh, Joseph A; Baker, Jennifer M R; Tollinger, Martin; Forman-Kay, Julie D

    2008-06-25

    Residual dipolar couplings (RDCs) have been observed in disordered states of several proteins. While their nonuniform values were initially surprising, it has been shown that reasonable approximation of experimental RDCs can be obtained using simple statistical coil models and assuming global alignment of each structure, provided that many thousands of conformers are averaged. Here we show that, by using short local alignment tensors, we can achieve good agreement between experimental and simulated RDCs with far fewer structures than required when using global alignment. This makes the possibility of using RDCs as direct restraints in structural calculations of disordered proteins much more feasible. In addition, it provides insight into the nature of RDCs in disordered states, suggesting that they are primarily reporting on local structure.

  19. [Plasma temperature calculation and coupling mechanism analysis of laser-double wire hybrid welding].

    PubMed

    Zheng, Kai; Li, Huan; Yang, Li-Jun; Gu, Xiao-Yan; Gao, Ying

    2013-04-01

    The plasma radiation of laser-double wire hybrid welding was collected by using fiber spectrometer, the coupling mechanism of arc with laser was studied through high-speed photography during welding process, and the temperature of hybrid plasma was calculated by using the method of Boltzmann plot. The results indicated that with laser hybrid, luminance was enhanced; radiation intensity became stronger; arc was attracted to the laser point; cross section contracted and arc was more stable. The laser power, welding current and arc-arc distance are important factors that have great influence on electron temperature. Increase in the laser power, amplification of welding current and reduction of arc-arc distance can all result in the rise of temperature.

  20. Connected triple excitations in coupled-cluster calculations of hyperpolarizabilities: Neon

    NASA Technical Reports Server (NTRS)

    Rice, Julia E.; Scuseria, Gustavo E.; Lee, Timothy J.; Taylor, Peter R.; Almloef, Jan

    1992-01-01

    We have calculated the second hyperpolarizability gamma of neon using the CCSD(T) method. The accuracy of the CCSD(T) approach has been established by explicit comparison with the single, double and triple excitation coupled-cluster (CCSDT) method using extended basis sets that are known to be adequate for the description of gamma. Our best estimate for gamma(sub 0) of 110 +/- 3 a.u. is in good agreement with other recent theoretical values and with Shelton's recent experimental estimate of 108 +/- 2 a.u. Comparison of the MP2 and CCSD(T) hyperpolarizability values indicates that MP2 gives a very good description of the electron correlation contribution to gamma(sub 0). We have combined MP2 frequency-dependent corrections with the CCSD(T) gamma(sub 0) to yield values of gamma(-2 omega;omega,omega,0) and gamma(exp K)(-omega;omega,0,0).

  1. Relativistic convergent close-coupling calculation of inelastic scattering of electrons from cesium

    NASA Astrophysics Data System (ADS)

    Bostock, Christopher J.; Fursa, Dmitry V.; Bray, Igor

    2014-03-01

    We present fully relativistic convergent close-coupling calculations of differential cross sections, spin-asymmetries, and Stokes parameters for inelastic electron-cesium scattering at intermediate energies. Comparison is made with the differential cross section and spin asymmetry measurements of Baum et al. [Phys. Rev. A 70, 012707 (2004), 10.1103/PhysRevA.70.012707] and the Stokes parameter measurements of Slaughter et al. [Phys. Rev. A 75, 062717 (2007), 10.1103/PhysRevA.75.062717]. Comparison is also made with previous semirelativistic and nonrelativistic theories. With a relatively high atomic number for cesium (Z =55) we find surprisingly excellent agreement between the relativistic, semirelativistic, and nonrelativistic theories for most observables. The overall agreement with the measurements is very good, with isolated discrepancies for some observables.

  2. A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings

    NASA Astrophysics Data System (ADS)

    Borkar, Aditi N.; De Simone, Alfonso; Montalvao, Rinaldo W.; Vendruscolo, Michele

    2013-06-01

    We describe a method of determining the conformational fluctuations of RNA based on the incorporation of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) as replica-averaged structural restraints in molecular dynamics simulations. In this approach, the alignment tensor required to calculate the RDCs corresponding to a given conformation is estimated from its shape, and multiple replicas of the RNA molecule are simulated simultaneously to reproduce in silico the ensemble-averaging procedure performed in the NMR measurements. We provide initial evidence that with this approach it is possible to determine accurately structural ensembles representing the conformational fluctuations of RNA by applying the reference ensemble test to the trans-activation response element of the human immunodeficiency virus type 1.

  3. Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis.

    PubMed Central

    Lancaster, C R; Michel, H; Honig, B; Gunner, M R

    1996-01-01

    Based on new Rhodopseudomonas (Rp.) viridis reaction center (RC) coordinates with a reliable structure of the secondary acceptor quinone (QB) site, a continuum dielectric model and finite difference technique have been used to identify clusters of electrostatically interacting ionizable residues. Twenty-three residues within a distance of 25 A from QB (QB cluster) have been shown to be strongly electrostatically coupled to QB, either directly or indirectly. An analogous cluster of 24 residues is found to interact with QA (QA cluster). Both clusters extend to the cytoplasmic surface in at least two directions. However, the QB cluster differs from the QA cluster in that it has a surplus of acidic residues, more strong electrostatic interactions, is less solvated, and experiences a strong positive electrostatic field arising from the polypeptide backbone. Consequently, upon reduction of QA or QB, it is the QB cluster, and not the QA cluster, which is responsible for substoichiometric proton uptake at neutral pH. The bulk of the changes in the QB cluster are calculated to be due to the protonation of a tightly coupled cluster of the three Glu residues (L212, H177, and M234) within the QB cluster. If the lifetime of the doubly reduced state QB2- is long enough, Asp M43 and Ser L223 are predicted to also become protonated. The calculated complex titration behavior of the strongly interacting residues of the QB cluster and the resulting electrostatic response to electron transfer may be a common feature in proton-transferring membrane protein complexes. Images FIGURE 2 p2482-a FIGURE 6 FIGURE 8 FIGURE 10 PMID:8744288

  4. Calculation of the coupling impedances of holes and slots on the liner using MAFIA and scaling

    SciTech Connect

    Thiagarajan, V.; Barts, T.; Kurennoy, S.; Chou, W.

    1993-11-01

    The location of a liner inside the beam tube is one of the options considered for the Super Colliders. The liner could serve as a synchrotron radiation intercept and also help enhance the vacuum. A definite distribution of holes or slots is required to be located on the liner for pumping out the desorbing gases. There will be wake fields propagating within the liner due to diffraction at discontinuities following the incident beam fields. The effect of these wake fields can be minimized by adopting the least number of pumping holes/slots required and through an optimal choice of hole/slot shape and size. The effect of the wake fields on the beam may be expressed through coupling impedances defined proportional to the corresponding forces integrated through distance per unit charge. It is necessary to compute the impedance of holes and slots and determine the scaling of the impedance with the dimensions of the hole/slot and the liner, in order to optimize the choice of pumping holes/slots. The coupling impedances of slots and holes have been calculated here using the code MAFIA and the scaling assessed. The results compare favorably with existing analytical results.

  5. GW Many-Body Perturbation Theory for Electron-Phonon Coupling Calculations

    NASA Astrophysics Data System (ADS)

    Faber, Carina

    2015-03-01

    Within many-body perturbation theory (MBPT) and the GW approximation, we study the electron-phonon coupling (EPC) in carbon-based systems, taking as paradigmatic examples the fullerene molecule, graphene and diamond. It has been demonstrated by several groups that the strength of the electron-phonon coupling potential is in these cases significantly underestimated at the DFT-LDA level, while GW calculations offer an excellent agreement with experiments. Similar results have been obtained for superconducting bismuthates and transition-metal chloronitrides. However, the related computational costs of evaluating the EPC strength at the GW level are high and thus represent strong limitations to a widespread application. We therefore discuss the accuracy of two less demanding alternatives on the MBPT level, namely the static Coulomb-hole plus screened-exchange (COHSEX) approximation and further the constant screening approach. In the latter, variations of the screened Coulomb potential W upon small changes of the atomic positions along the vibrational eigenmodes are neglected. We show that this latter approximation is most reliable, whereas the static COHSEX ansatz leads to substantial errors. These findings open the way for combining the present MBPT approach with efficient linear-response theories. C.F. gratefully acknowledges the Materials Theory Group, ETH Zurich for travel funding and the French CNRS and CEA for PhD funding. Computing time has been provided by the French GENCI-IDRIS supercomputing center under Contract No. i2012096655.

  6. Mathematical modeling and calculation of heating and melting of particles of the polymeric powder in flow channel of the sprayer

    NASA Astrophysics Data System (ADS)

    Fedyaev, V. L.; Morenko, I. V.; Siraev, A. R.; Galimov, E. R.; Gimranov, I. R.; Fazlyev, L. R.; Takhaviyev, M. S.

    2015-06-01

    Heating and melting of particles of polymeric powder in the central flow channel of spraying gun is investigated. Mathematical models of these processes taking into account convective and radiative-convective heat interaction of particles with environment is represented. Relations for calculating the temperature of the particles depending on the longitudinal coordinate, time of flight, operating and design parameters as well as thermophysical characteristics of the particles material and environment are given.

  7. Functional coupling of TRPV4 cationic channel and large conductance, calcium-dependent potassium channel in human bronchial epithelial cell lines.

    PubMed

    Fernández-Fernández, José M; Andrade, Yaniré N; Arniges, Maite; Fernandes, Jacqueline; Plata, Cristina; Rubio-Moscardo, Francisca; Vázquez, Esther; Valverde, Miguel A

    2008-10-01

    Calcium-dependent potassium channels are implicated in electrolyte transport, cell volume regulation and mechanical responses in epithelia, although the pathways for calcium entry and their coupling to the activation of potassium channels are not fully understood. We now show molecular evidence for the presence of TRPV4, a calcium permeable channel sensitive to osmotic and mechanical stress, and its functional coupling to the large conductance calcium-dependent potassium channel (BK(Ca)) in a human bronchial epithelial cell line (HBE). Reverse transcriptase polymerase chain reaction, intracellular calcium imaging and whole-cell patch-clamp experiments using HBE cells demonstrated the presence of TRPV4 messenger and Ca(2+) entry, and outwardly rectifying cationic currents elicited by the TRPV4 specific activator 4alpha-phorbol 12,13-didecanoate (4alphaPDD). Cell-attached and whole-cell patch-clamp of HBE cells exposed to 4alphaPDD, and hypotonic and high-viscosity solutions (related to mechanical stress) revealed the activation of BK(Ca) channels subsequent to extracellular Ca(2+) influx via TRPV4, an effect lost upon antisense-mediated knock-down of TRPV4. Further analysis of BK(Ca) modulation after TRPV4 activation showed that the Ca(2+) signal can be generated away from the BK(Ca) location at the plasma membrane, and it is not mediated by intracellular Ca(2+) release via ryanodine receptors. Finally, we have shown that, unlike the reported disengagement of TRPV4 and BK(Ca) in response to hypotonic solutions, cystic fibrosis bronchial epithelial cells (CFBE) preserve the functional coupling of TRPV4 and BK(Ca) in response to high-viscous solutions.

  8. Calculation of mutual information for nonlinear communication channel at large signal-to-noise ratio

    NASA Astrophysics Data System (ADS)

    Terekhov, I. S.; Reznichenko, A. V.; Turitsyn, S. K.

    2016-10-01

    Using the path-integral technique we examine the mutual information for the communication channel modeled by the nonlinear Schrödinger equation with additive Gaussian noise. The nonlinear Schrödinger equation is one of the fundamental models in nonlinear physics, and it has a broad range of applications, including fiber optical communications—the backbone of the internet. At large signal-to-noise ratio we present the mutual information through the path-integral, which is convenient for the perturbative expansion in nonlinearity. In the limit of small noise and small nonlinearity we derive analytically the first nonzero nonlinear correction to the mutual information for the channel.

  9. Tuning the allosteric regulation of artificial muscarinic and dopaminergic ligand-gated potassium channels by protein engineering of G protein-coupled receptors

    PubMed Central

    Moreau, Christophe J.; Revilloud, Jean; Caro, Lydia N.; Dupuis, Julien P.; Trouchet, Amandine; Estrada-Mondragón, Argel; Nieścierowicz, Katarzyna; Sapay, Nicolas; Crouzy, Serge; Vivaudou, Michel

    2017-01-01

    Ligand-gated ion channels enable intercellular transmission of action potential through synapses by transducing biochemical messengers into electrical signal. We designed artificial ligand-gated ion channels by coupling G protein-coupled receptors to the Kir6.2 potassium channel. These artificial channels called ion channel-coupled receptors offer complementary properties to natural channels by extending the repertoire of ligands to those recognized by the fused receptors, by generating more sustained signals and by conferring potassium selectivity. The first artificial channels based on the muscarinic M2 and the dopaminergic D2L receptors were opened and closed by acetylcholine and dopamine, respectively. We find here that this opposite regulation of the gating is linked to the length of the receptor C-termini, and that C-terminus engineering can precisely control the extent and direction of ligand gating. These findings establish the design rules to produce customized ligand-gated channels for synthetic biology applications. PMID:28145461

  10. Ab initio transport calculations of molecular wires with electron-phonon couplings

    NASA Astrophysics Data System (ADS)

    Hirose, Kenji; Kobayashi, Nobuhiko

    2009-03-01

    Understanding of electron transport through nanostructures becomes important with the advancement of fabrication process to construct atomic-scale devices. Due to the drastic change of transport properties by contact conditions to electrodes in local electric fields, first-principles calculation approaches are indispensable to understand and characterize the transport properties of nanometer-scale molecular devices. Here we study the transport properties of molecular wires between metallic electrodes, especially focusing on the effects of contacts to electrodes and of the electron-phonon interactions. We use an ab initio calculation method based on the scattering waves, which are obtained by the recursion-transfer-matrix (RTM) method, combined with non-equilibrium Green's function (NEGF) method including the electron-phonon scatterings. We find that conductance shows exponential behaviors as a function of the length of molecular wires due to tunneling process determined by the HOMO-LUMO energy gap. From the voltage drop behaviors inside the molecular wires, we show that the contact resistances are dominant source for the bias drop and thus are related to local heating. We will present the electron-phonon coupling effects at contact on the inelastic scattering and discuss on the local heating and local temperature, comparing them with those of metallic atomic wires.

  11. Intersubunit Physical Couplings Fostered By The Left Flipper Domain Facilitate Channel Opening Of P2X4 Receptors.

    PubMed

    Wang, Jin; Sun, Liang-Fei; Cui, Wen-Wen; Zhao, Wen-Shan; Ma, Xue-Fei; Li, Bin; Liu, Yan; Yang, Yang; Hu, You-Min; Huang, Li-Dong; Cheng, Xiao-Yang; Li, Lingyong; Lu, Xiang-Yang; Tian, Yun; Yu, Ye

    2017-03-16

    P2X receptors are ATP-gated trimeric channels with important roles in diverse pathophysiological functions. A detailed understanding of the mechanism underlying the gating process of these receptors is thus fundamentally important and may open new therapeutic avenues. The left flipper (LF) domain of P2X receptors is a flexible loop structure and its coordinated motions together with the dorsal fin (DF) domain are crucial for the channel gating of the P2X receptors. However, the mechanism underlying the crucial role of the LF domain in the channel gating remains obscure. Here, we propose that the ATP-induced allosteric changes of the LF domain enable it to foster intersubunit physical couplings among the DF and two lower body domains, which is pivotal for the channel gating of P2X4 receptors. Metadynamics analysis indicated that these newly established intersubunit couplings correlate well with the ATP-bound open state of the receptors. Moreover, weakening or strengthening these physical interactions with engineered intersubunit metal bridges remarkably decreased or increased the open probability of the receptors, respectively. Further disulfide crosslinking and covalent modification confirmed that the intersubunit physical couplings among the DF and two lower body domains fostered by the LF domain at the open state act as an integrated structural element that is stringently required for the channel gating of P2X4 receptors. Our observations provide new mechanistic insights into P2X receptor activation and will stimulate development of new allosteric modulators of P2X receptors.

  12. Benchmarking density-functional theory calculations of NMR shielding constants and spin-rotation constants using accurate coupled-cluster calculations.

    PubMed

    Teale, Andrew M; Lutnæs, Ola B; Helgaker, Trygve; Tozer, David J; Gauss, Jürgen

    2013-01-14

    Accurate sets of benchmark nuclear-magnetic-resonance shielding constants and spin-rotation constants are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the calculated coupled-cluster constants is established by a careful comparison with experimental data, taking into account zero-point vibrational corrections. Coupled-cluster basis-set convergence is analyzed and extrapolation techniques are employed to estimate basis-set-limit quantities, thereby establishing an accurate benchmark data set. Together with the set provided for rotational g-tensors and magnetizabilities in our previous work [O. B. Lutnæs, A. M. Teale, T. Helgaker, D. J. Tozer, K. Ruud, and J. Gauss, J. Chem. Phys. 131, 144104 (2009)], it provides a substantial source of consistently calculated high-accuracy data on second-order magnetic response properties. The utility of this benchmark data set is demonstrated by examining a wide variety of Kohn-Sham exchange-correlation functionals for the calculation of these properties. None of the existing approximate functionals provide an accuracy competitive with that provided by CCSD or CCSD(T) theory. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of Kohn-Sham calculations constrained to give the same electronic density. Routes to future improvements are discussed in light of this comparison.

  13. Benchmarking calculations of spectral densities for the diagonal and nondiagonal exciton-phonon coupling of tetracene crystal

    NASA Astrophysics Data System (ADS)

    Zhang, Jin; Zhu, Chaoyuan; Liang, WanZhen

    2017-08-01

    The spectral densities of diagonal and nondiagonal exciton-phonon (e-p) coupling for tetracene crystal have been calculated by the harmonic oscillator (HO) model and ground-state MD-based approaches. We find that classical MD-based approaches overestimate the coupling of exciton with high-frequency vibrational modes and predict the strongest e-p coupling appeared above 1500 cm-1 whereas HO model and AIMD-based approach predict it appeared at ∼ 1400 cm-1. Additionally, the calculated spectral densities of nondiagonal e-p coupling for three different dimers show that they are continuously distributed in the range of 0-150 cm-1 and are 2-3 order of magnitude smaller than the maxima of diagonal e-p coupling.

  14. Calculation of primary and secondary flow and boundary shear stresses in a meandering channel

    NASA Astrophysics Data System (ADS)

    Stoesser, Thorsten; Ruether, Nils; Olsen, Nils Reidar Boe

    2010-02-01

    Turbulent flow in a meandering channel is computed with two Computational Fluid Dynamics (CFD) codes solving the Navier-Stokes equations by employing different turbulence closure approaches. The first CFD code solves the steady Reynolds-Averaged Navier-Stokes equations (RANS) using an isotropic turbulence closure. The second code is based on the concept of Large Eddy Simulation (LES). LES resolves the large-scale turbulence structures in the flow and is known to outperform RANS models in flows in which large-scale structures dominate the statistics. The results obtained from the two codes are compared with experimental data from a physical model study. Both, LES and RANS simulation, predict the primary helical flow pattern in the meander as well as the occurrence of an outer-bank secondary cell. Computed primary as well as secondary flow velocities are in reasonably good agreement with experimental data. Evidence is given that the outer-bank secondary cell in a meander bend is the residual of the main secondary cell of the previous bend. However, the RANS code, regardless of the turbulence model employed, overpredicts the size and strength of the outer-bank secondary cell. Furthermore, only LES is able to uphold the outer-bank second secondary cell beyond the bend apex until the exit of the bend as turbulence anisotropy contributes to its persistence. The presence of multiple secondary cells has important consequences for the distribution of shear stresses along the wetted perimeter of the channel, and thereby the sediment transport in meandering channels. Consequently, even though LES is expected to compute the bed-shear stresses along the wetted perimeter of the channel with a higher degree of accuracy than the RANS model, comparisons between LES and RANS computed wall shear stresses agree well. These findings are useful for practitioners who need to rely on RANS model predictions of the flow in meandering channels at field scale.

  15. Strongly coupled fluid-particle flows in vertical channels. II. Turbulence modeling

    NASA Astrophysics Data System (ADS)

    Capecelatro, Jesse; Desjardins, Olivier; Fox, Rodney O.

    2016-03-01

    In Part I, simulations of strongly coupled fluid-particle flow in a vertical channel were performed with the purpose of understanding, in general, the fundamental physics of wall-bounded multiphase turbulence and, in particular, the roles of the spatially correlated and uncorrelated components of the particle velocity. The exact Reynolds-averaged (RA) equations for high-mass-loading suspensions were presented, and the unclosed terms that are retained in the context of fully developed channel flow were evaluated in an Eulerian-Lagrangian (EL) framework. Here, data from the EL simulations are used to validate a multiphase Reynolds-stress model (RSM) that predicts the wall-normal distribution of the two-phase, one-point turbulence statistics up to second order. It is shown that the anisotropy of the Reynolds stresses both near the wall and far away is a crucial component for predicting the distribution of the RA particle-phase volume fraction. Moreover, the decomposition of the phase-average (PA) particle-phase fluctuating energy into the spatially correlated and uncorrelated components is necessary to account for the boundary conditions at the wall. When these factors are properly accounted for in the RSM, the agreement with the EL turbulence statistics is satisfactory at first order (e.g., PA velocities) but less so at second order (e.g., PA turbulent kinetic energy). Finally, an algebraic stress model for the PA particle-phase pressure tensor and the Reynolds stresses is derived from the RSM using the weak-equilibrium assumption.

  16. Molecular dipole static polarisabilities and hyperpolarisabilities of conjugated oligomer chains calculated with the local π-electron coupled cluster theory

    NASA Astrophysics Data System (ADS)

    Ivanov, Vladimir V.; Zakharov, Anton B.; Adamowicz, Ludwik

    2013-12-01

    A new semi-empirical π-electron local coupled cluster theory has been developed to calculate static dipole polarisabilities and hyperpolarisabilities of extended π-conjugated systems. The key idea of the approach is the use of the ethylene molecular orbitals as the orbital basis set for π-conjugated compounds (the method is termed the Covalent Unbonded Molecules of Ethylene method, cue). Test calculations of some small model organic conjugated compounds demonstrate high accuracy of the version of the cue local coupled cluster theory developed in this work in comparison with the π-electron full configuration interaction (FCI) method. Calculations of different conjugated carbon-based oligomer chains (polyenes, polyynes, polyacenes, polybenzocyclobutadiene, etc.) demonstrate fast convergence (per π-electron) of the polarisability and hyperpolarisability values in the calculations when more classes of orbital excitations are included in the coupled cluster single and double (CCSD) excitation operator. The results show qualitatively correct dependence on the system size.

  17. Coupled-channel effects in elastic scattering and near-barrier fusion induced by weakly bound nuclei and exotic halo nuclei

    SciTech Connect

    Beck, C.; Keeley, N.

    2007-05-15

    The influence on fusion of coupling to the breakup process is investigated for reactions where at least one of the colliding nuclei has a sufficiently low binding energy for breakup to become an important process. Elastic scattering, excitation functions for sub- and near-barrier fusion cross sections, and breakup yields are analyzed for {sup 6,7}Li+{sup 59}Co. Continuum-discretized coupled-channels (CDCC) calculations describe well the data at and above the barrier. Elastic scattering with {sup 6}Li (as compared to {sup 7}Li) indicates the significant role of breakup for weakly bound projectiles. A study of {sup 4,6}He induced fusion reactions with a three-body CDCC method for the {sup 6}He halo nucleus is presented. The relative importance of breakup and bound-state structure effects on total fusion is discussed.

  18. The Open Gate of the KV1.2 Channel: Quantum Calculations Show the Key Role of Hydration

    PubMed Central

    Kariev, Alisher M.; Njau, Philipa; Green, Michael E.

    2014-01-01

    The open gate of the Kv1.2 voltage-gated potassium channel can just hold a hydrated K+ ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein. Water molecules not in the x-ray coordinates, and the ion itself, are placed by the calculation. The water molecules, including their orientation and hydrogen bonding, with and without an ion, are critical for the path of the ion, from the solution to the gate. A sequence of steps is postulated in which the potential experienced by the ion in the pore is influenced by the position of the ion. The gate structure, with and without the ion, has been optimized. The charges on the atoms and bond lengths have been calculated using natural bond orbital calculations, giving K+ ∼0.77 charges, rather than 1.0. The PVPV hinge sequence has been mutated in silico to PVVV (P407V in the 2A79 numbering). The water structure around the ion becomes discontinuous, separated into two sections, above and below the ion. PVPV conservation closely relates to maintaining the water structure. Finally, these results have implications concerning gating. PMID:24507595

  19. The open gate of the K(V)1.2 channel: quantum calculations show the key role of hydration.

    PubMed

    Kariev, Alisher M; Njau, Philipa; Green, Michael E

    2014-02-04

    The open gate of the Kv1.2 voltage-gated potassium channel can just hold a hydrated K(+) ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein. Water molecules not in the x-ray coordinates, and the ion itself, are placed by the calculation. The water molecules, including their orientation and hydrogen bonding, with and without an ion, are critical for the path of the ion, from the solution to the gate. A sequence of steps is postulated in which the potential experienced by the ion in the pore is influenced by the position of the ion. The gate structure, with and without the ion, has been optimized. The charges on the atoms and bond lengths have been calculated using natural bond orbital calculations, giving K(+) ~0.77 charges, rather than 1.0. The PVPV hinge sequence has been mutated in silico to PVVV (P407V in the 2A79 numbering). The water structure around the ion becomes discontinuous, separated into two sections, above and below the ion. PVPV conservation closely relates to maintaining the water structure. Finally, these results have implications concerning gating. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. Poisson-Nernst-Planck theory approach to the calculation of current through biological ion channels.

    PubMed

    Coalson, Rob D; Kurnikova, Maria G

    2005-03-01

    The Poisson-Nernst-Planck (PNP) theory of electro-diffusion is reviewed. Techniques for numerical solution of the three-dimensional PNP equations are summarized, and several illustrative applications to ion transport through protein channels are presented. Strengths and weaknesses of the theory are discussed, as well as attempts to improve it via increasingly realistic evaluation of the force acting on each ion due to the protein/membrane environment.

  1. Free energy calculation of water addition coupled to reduction of aqueous RuO4-.

    PubMed

    Tateyama, Yoshitaka; Blumberger, Jochen; Ohno, Takahisa; Sprik, Michiel

    2007-05-28

    Free energy calculations were carried out for water addition coupled reduction of aqueous ruthenate, RuO4-+H2O+e--->[RuO3(OH)2]2-, using Car-Parrinello molecular dynamics simulations. The full reaction is divided into the reduction of the tetrahedral monoanion, RuO4-+e--->RuO4(2-), followed by water addition, RuO4(2-)+H2O-->[RuO3(OH)2]2-. The free energy of reduction is computed from the fluctuations of the vertical energy gap using the MnO4-+e--->MnO(4)2- reaction as reference. The free energy for water addition is estimated using constrained molecular dynamics methods. While the description of this complex reaction, in principle, involves multiple reaction coordinates, we found that reversible transformation of the reactant into the product can be achieved by control of a single reaction coordinate consisting of a suitable linear combination of atomic distances. The free energy difference of the full reaction is computed to be -0.62 eV relative to the normal hydrogen electrode. This is in good agreement with the experimental value of -0.59 eV, lending further support to the hypothesis that, contrary to the ruthenate monoanion, the dianion is not tetrahedral but forms a trigonal-bipyramidal dihydroxo complex in aqueous solution. We construct an approximate two-dimensional free energy surface using the coupling parameter for reduction and the mechanical constraint for water addition as variables. Analyzing this surface we find that in the most favorable reaction pathway the reduction reaction precedes water addition. The latter takes place via the protonated complex [RuO3(OH)]- and subsequent transport of the created hydroxide ion to the fifth coordination site of Ru.

  2. Mass-producible microtags for security applications: calculated fabrication tolerances by rigorous coupled-wave analysis

    SciTech Connect

    Descour, M.R.; Sweatt, W.C.; Krenz, K.D.

    1998-04-01

    We develop a method for encoding phase and amplitude in microscopic computer-generated holograms (microtags) for security applications. An 8{times}8 cell phase-only and an 8{times}8 cell phase-and-amplitude microtag design are fabricated in photoresist using an extreme ultraviolet (13.4-nm) lithography (EUVL) tool. Each microtag measures 80{times}160{mu}m and contains features 0.2 {mu}m wide. Fraunhofer-zone diffraction patterns can be obtained from fabricated microtags without any intervening optics and compare very favorably with predicted diffraction patterns [Descour {ital et al.} (1996)]. We present the results of a rigorous coupled-wave analysis (RCWA) of microtags. Microtags are modeled as consisting of subwavelength gratings of a trapezoidal profile. Transverse-electric (TE) and TM readout polarizations are modeled. The analysis concerns the determination of optimal microtag-grating design parameter values and tolerances on those parameters. The parameters are grating wall-slope angle, grating duty cycle, grating depth, and metal coating thickness. Optimal microtag-grating parameter values result in maximum diffraction efficiency, which is calculated at 16{percent} for microtag gratings in air and 12{percent} for microtag gratings underneath a protective dielectric coating, within fabrication constraints. TM-polarized readout illumination is diffracted with higher efficiency than TE-polarized illumination by microtag gratings. {copyright} {ital 1998 Society of Photo-Optical Instrumentation Engineers.}{ital Key words:} computer-generated holograms; security and anticounterfeiting devices; grating fabrication tolerances; rigorous coupled-wave analysis. {copyright} {ital 1998} {ital Society of Photo-Optical Instrumentation Engineers}

  3. Study on Torque Calculation for Hybrid Magnetic Coupling and Influencing Factor Analysis

    NASA Astrophysics Data System (ADS)

    Wang, Shuang; Guo, Yong-cun; Wang, Peng-yu; Li, De-yong

    2017-03-01

    Specific to a problem that the present transmission of magnetic coupling torque was subjected to restrictions of its own structure, a hybrid magnetic coupling was proposed. Then, finite element method was adopted to carry out numerical calculations for its three-dimensional magnetic field to obtain three-dimensional magnetic field distribution of radial and axial configurations. Major influencing factors of its torque, such as lengths of axial and radial air gaps, thicknesses of axial and radial permanent magnets, the number of slots in axial copper rotor, thickness of axial and radial copper rotor, etc., were analyzed. The relevant results indicated that in certain conditions of shapes, ten magnetic poles of the axial permanent magnet rotor, nine of the radial permanent magnet rotor and nine slots from the axial copper rotor were used. Correspondingly, the axial copper rotor had a thickness of 20 mm and it was 5 mm for the radial copper rotor. Moreover, the maximum torque could reach 190 N.m approximately. If lengths of axial and radial air gaps increased, the torque may go down otherwise. Within a certain scope, the torque rose in the first place and then fell with increases in the permanent magnet thickness of axial permanent magnetic rotor, the number of axial and radial magnetic poles, the number of slots in axial copper rotor, and the thickness of axial copper rotor. Additionally, the number of slots in the axial copper rotor could not be equivalent to that of magnetic poles in axial permanent magnetic rotor. However, as the permanent magnet thickness of radial permanent magnetic rotor rose, the torque went up as well.

  4. Cooperative Nature of Gating Transitions in K+ Channels as seen from Dynamic Importance Sampling Calculations

    PubMed Central

    Denning, Elizabeth J.; Woolf, Thomas B.

    2009-01-01

    The growing dataset of K+ channel x-ray structures provides an excellent opportunity to begin a detailed molecular understanding of voltage-dependent gating. These structures, while differing in sequence, represent either a stable open or closed state. However, an understanding of the molecular details of gating will require models for the transitions and experimentally testable predictions for the gating transition. To explore these ideas, we apply Dynamic Importance Sampling (DIMS) to a set of homology models for the molecular conformations of K+ channels for four different sets of sequences and eight different states. In our results, we highlight the importance of particular residues upstream from the PVP region to the gating transition. This supports growing evidence that the PVP region is important for influencing the flexibility of the S6 helix and thus the opening of the gating domain. The results further suggest how gating on the molecular level depends on intra-subunit motions to influence the cooperative behavior of all four subunits of the K+ channel. We hypothesize that the gating process occurs in steps: first sidechain movement, then inter- S5-S6 subunit motions, and lastly the large-scale domain rearrangements. PMID:19950367

  5. Molecular origin of the cation selectivity in OmpF porin: single channel conductances vs. free energy calculation.

    PubMed

    Danelon, Christophe; Suenaga, Atsushi; Winterhalter, Mathias; Yamato, Ichiro

    2003-07-01

    Ion current through single outer membrane protein F (OmpF) trimers was recorded and compared to molecular dynamics simulation. Unidirectional insertion was revealed from the asymmetry in channel conductance. Single trimer conductance showed particularly high values at low symmetrical salt solution. The conductance values of various alkali metal ion solutions were proportional to the monovalent cation mobility values in the bulk phase, LiClchannels favored permeation of alkali metal ions over chloride and suggested size preference for smaller cations. These results suggest that there are specific interactions between the permeating cation and charged residues lining the channel walls. This hypothesis was supported by computational study which predicted that monovalent cations bind to Asp113 at low concentration. Here, free energy calculations revealed that the affinity of the alkali metal ions to its binding site increased with their atomic radii, Li(+) approximately Na(+)channel increases the translocation rate of cations under applied voltage by increasing their local concentration relative to the bulk solution.

  6. Gibbs energy calculation of electrolytic plasma channel with inclusions of copper and copper oxide with Al-base

    NASA Astrophysics Data System (ADS)

    Posuvailo, V. M.; Klapkiv, M. D.; Student, M. M.; Sirak, Y. Y.; Pokhmurska, H. V.

    2017-03-01

    The oxide ceramic coating with copper inclusions was synthesized by the method of plasma electrolytic oxidation (PEO). Calculations of the Gibbs energies of reactions between the plasma channel elements with inclusions of copper and copper oxide were carried out. Two methods of forming the oxide-ceramic coatings on aluminum base in electrolytic plasma with copper inclusions were established. The first method – consist in the introduction of copper into the aluminum matrix, the second - copper oxide. During the synthesis of oxide ceramic coatings plasma channel does not react with copper and copper oxide-ceramic included in the coating. In the second case is reduction of copper oxide in interaction with elements of the plasma channel. The content of oxide-ceramic layer was investigated by X-ray and X-ray microelement analysis. The inclusions of copper, CuAl2, Cu9Al4 in the oxide-ceramic coatings were found. It was established that in the spark plasma channels alongside with the oxidation reaction occurs also the reaction aluminothermic reduction of the metal that allows us to dope the oxide-ceramic coating by metal the isobaric-isothermal potential oxidation of which is less negative than the potential of the aluminum oxide.

  7. Dynamic Polarizability of the Helium Atom using a Variationally Stable Calculation within the Coupled Adiabatic Hyperspherical Approach^*

    NASA Astrophysics Data System (ADS)

    Masili, Mauro; Starace, Anthony F.

    2001-05-01

    Using a generalization(M. Masili and A. F. Starace, Phys. Rev. A 62), 033403 (2000). of the variationally stable method of Gao and Starace(B. Gao and A. F. Starace, Phys. Rev. Lett. 61), 404 (1988); Phys. Rev. A 39, 4550 (1989). for two-electron atoms and ions, which incorporates a coupled-channel adiabatic hyperspherical approach, we report results for the dynamic polarizability of the helium atom for frequencies below the single photon ionization threshold. Comparison of results of coupling one, two, three, and four adiabatic hyperspherical channels within each term level of the initial and intermediate states show good convergence. Comparisons are also given with results of prior work by others. ^*Supported by FAPESP (Brazilian agency) under Process No. 99/11363-8 and by the U.S. D.O.E, B.E.S., Div. Chem. Sci. under Grant No. DE-FG03-96ER14646.

  8. Use of label-free optical biosensors to detect modulation of potassium channels by G-protein coupled receptors.

    PubMed

    Fleming, Matthew R; Shamah, Steven M; Kaczmarek, Leonard K

    2014-02-10

    Ion channels control the electrical properties of neurons and other excitable cell types by selectively allowing ions to flow through the plasma membrane(1). To regulate neuronal excitability, the biophysical properties of ion channels are modified by signaling proteins and molecules, which often bind to the channels themselves to form a heteromeric channel complex(2,3). Traditional assays examining the interaction between channels and regulatory proteins require exogenous labels that can potentially alter the protein's behavior and decrease the physiological relevance of the target, while providing little information on the time course of interactions in living cells. Optical biosensors, such as the X-BODY Biosciences BIND Scanner system, use a novel label-free technology, resonance wavelength grating (RWG) optical biosensors, to detect changes in resonant reflected light near the biosensor. This assay allows the detection of the relative change in mass within the bottom portion of living cells adherent to the biosensor surface resulting from ligand induced changes in cell adhesion and spreading, toxicity, proliferation, and changes in protein-protein interactions near the plasma membrane. RWG optical biosensors have been used to detect changes in mass near the plasma membrane of cells following activation of G protein-coupled receptors (GPCRs), receptor tyrosine kinases, and other cell surface receptors. Ligand-induced changes in ion channel-protein interactions can also be studied using this assay. In this paper, we will describe the experimental procedure used to detect the modulation of Slack-B sodium-activated potassium (KNa) channels by GPCRs.

  9. Meson spectroscopy with unitary coupled-channels model for heavy-meson decay into three mesons

    SciTech Connect

    Satoshi Nakamura

    2012-04-01

    We develop a model for describing excited mesons decay into three mesons. The properties of the excited mesons can be extracted with this model. The model maintains the three-body unitarity that has been missed in previous data analyses based on the conventional isobar models. We study an importance of the three-body unitarity in extracting hadron properties from data. For this purpose, we use the unitary and isobar models to analyze the same pseudo data of {gamma}p {yields} {pi}{sup +}{pi}{sup +}{pi}{sup -}n, and extract the properties of excited mesons. We find a significant difference between the unitary and isobar models in the extracted properties of excited mesons, such as the mass, width and coupling strength to decay channels. Hadron properties such as quantum numbers (spin, parity, etc.), mass and (partial) width have been long studied as a subject called hadron spectroscopy. The hadron properties provide important information for understanding internal structure of the hadron and dynamics which governs it. The dynamics here is of course QCD in its nonperturbative regime. The hadron properties can be extracted from data through a careful analysis, in many cases, partial wave analysis (PWA). Thus it is essential for hadron spectroscopy to have a reliable theoretical analysis tool.

  10. Sodium-activated potassium channels are functionally coupled to persistent sodium currents.

    PubMed

    Hage, Travis A; Salkoff, Lawrence

    2012-02-22

    We report a novel coupled system of sodium-activated potassium currents (I(KNa)) and persistent sodium currents (I(NaP)), the components of which are widely distributed throughout the brain. Its existence and importance has not been previously recognized. Although I(KNa) was known to exist in many cell types, the source of Na(+) which activates I(KNa) remained a mystery. We now show in single membrane patches generated from the somas of rat neurons that sodium influx through I(NaP) is sufficient for activation of K(Na) channels, without substantial contribution from the transient sodium current or bulk [Na(+)](i). I(NaP) was found to be active at cell membrane resting potentials, a finding that may explain why I(KNa) can be evoked from negative holding potentials. These results show an unanticipated role for I(NaP) in activating a negative feedback system countering the excitable effects I(NaP); the interrelatedness of I(NaP) and I(KNa) suggests new ways neurons can tune their excitability.

  11. Coupled lattice-Boltzmann and finite-difference simulation of electroosmosis in microfluidic channels

    NASA Astrophysics Data System (ADS)

    Hlushkou, Dzmitry; Kandhai, Drona; Tallarek, Ulrich

    2004-10-01

    In this article we are concerned with an extension of the lattice-Boltzmann method for the numerical simulation of three-dimensional electroosmotic flow problems in porous media. Our description is evaluated using simple geometries as those encountered in open-channel microfluidic devices. In particular, we consider electroosmosis in straight cylindrical capillaries with a (non)uniform zeta-potential distribution for ratios of the capillary inner radius to the thickness of the electrical double layer from 10 to 100. The general case of heterogeneous zeta-potential distributions at the surface of a capillary requires solution of the following coupled equations in three dimensions: Navier-Stokes equation for liquid flow, Poisson equation for electrical potential distribution, and the Nernst-Planck equation for distribution of ionic species. The hydrodynamic problem has been treated with high efficiency by code parallelization through the lattice-Boltzmann method. For validation velocity fields were simulated in several microcapillary systems and good agreement with results predicted either theoretically or obtained by alternative numerical methods could be established. Results are also discussed with respect to the use of a slip boundary condition for the velocity field at the surface.

  12. Nuclear Astrophysics Studies with the Method of Continuum-Discretized Coupled-Channels

    SciTech Connect

    Ogata, K.; Yahiro, M.; Hashimoto, S.; Iseri, Y.; Kan, M.; Kamimura, M.

    2010-05-12

    The method of continuum-discretized coupled-channels (CDCC) is applied to two nuclear astrophysics studies. One is the determination of the astrophysical factor S{sub 17}(0) for the {sup 7}Be(p,gamma){sup 8}B reaction from the analysis of {sup 8}B breakup by {sup 208}Pb at 52 A MeV. We obtain S{sub 17}(0) = 20.9{sub -1.9}{sup +2.0} eV b, which is significantly larger than the previous one, S{sub 17}(0) = 18.9+-1.8 eV b, determined from an analysis with the virtual photon theory. The difference between the two values is found to be due to the contributions from nuclear breakup and higher-order processes. The other application of CDCC is the re-evaluation of the triple-alpha reaction rate by directly solving the three-body Schroedinger equation. The resonant and nonresonant processes are treated on the same footing. An accurate description of the alpha-alpha nonresonant states significantly quenches the Coulomb barrier between the first two alpha-particles and the third alpha-particle. Consequently, the alpha-alpha nonresonant continuum states give a markedly larger contribution at low temperatures than that reported in previous studies. We find an increase in triple-alpha reaction rate by 26 orders of magnitude around 10{sup 7} K compared with the rate of NACRE.

  13. TRPV4 channel is involved in the coupling of fluid viscosity changes to epithelial ciliary activity

    PubMed Central

    Andrade, Yaniré N.; Fernandes, Jacqueline; Vázquez, Esther; Fernández-Fernández, José M.; Arniges, Maite; Sánchez, Trinidad M.; Villalón, Manuel; Valverde, Miguel A.

    2005-01-01

    Autoregulation of the ciliary beat frequency (CBF) has been proposed as the mechanism used by epithelial ciliated cells to maintain the CBF and prevent the collapse of mucociliary transport under conditions of varying mucus viscosity. Despite the relevance of this regulatory response to the pathophysiology of airways and reproductive tract, the underlying cellular and molecular aspects remain unknown. Hamster oviductal ciliated cells express the transient receptor potential vanilloid 4 (TRPV4) channel, which is activated by increased viscous load involving a phospholipase A2–dependent pathway. TRPV4-transfected HeLa cells also increased their cationic currents in response to high viscous load. This mechanical activation is prevented in native ciliated cells loaded with a TRPV4 antibody. Application of the TRPV4 synthetic ligand 4α-phorbol 12,13-didecanoate increased cationic currents, intracellular Ca2+, and the CBF in the absence of a viscous load. Therefore, TRPV4 emerges as a candidate to participate in the coupling of fluid viscosity changes to the generation of the Ca2+ signal required for the autoregulation of CBF. PMID:15753126

  14. Extraction of Electromagnetic Transition Form Factors for Nucleon Resonances within a Dynamical Coupled-Channels Model

    SciTech Connect

    N. Suzuki, T. Sato, T.-S. H. Lee

    2010-10-01

    We explain the application of a recently developed analytic continuation method to extract the electromagnetic transition form factors for the nucleon resonances ($N^*$) within a dynamical coupled-channel model of meson-baryon reactions.Illustrative results of the obtained $N^*\\rightarrow \\gamma N$ transition form factors, defined at the resonance pole positions on the complex energy plane, for the well isolated $P_{33}$ and $D_{13}$, and the complicated $P_{11}$ resonances are presented. A formula has been developed to give an unified representation of the effects due to the first two $P_{11}$ poles, which are near the $\\pi\\Delta$ threshold, but are on different Riemann sheets. We also find that a simple formula, with its parameters determined in the Laurent expansions of $\\pi N \\rightarrow \\pi N$ and $\\gamma N \\rightarrow\\pi N$ amplitudes, can reproduce to a very large extent the exact solutions of the considered model at energies near the real parts of the extracted resonance positions. We indicate the differences between our results and those extracted from the approaches using the Breit-Wigner parametrization of resonant amplitudes to fit the data.

  15. The "K-pp" System Investigated with a Coupled-Channel Complex Scaling Method

    NASA Astrophysics Data System (ADS)

    Doté, Akinobu

    Nuclear systems with anti-kaons (kaonic nuclei) are expected to have exotic nature such as formation of a dense state, due to the strong attraction between an anti-kaon and a nucleon. In this article, the current theoretical studies of the most essential kaonic nucleus "K-pp" are reviewed and our study of "K-pp" based on a coupled-channel Complex Scaling Method is reported. With a new version of our chiral SU(3)-based potential constrained by a precise measurement of kaonic hydrogen atom (SIDDHARTA experiment), the "K-pp" state is found to be rather shallowly bound: BK - pp = 15-22 MeV and Γ M = 20-50 MeV. The "K-pp" seems to have another pole, and it might possibly have so-called a double-pole structure, similarly to the Λ (1405). Recent results of the K-pp search experiments (J-PARC E15 and E27) are discussed in comparison with several new theoretical studies.

  16. Coupled channel effect in elastic scattering and fusion for 6,7Li+28Si

    NASA Astrophysics Data System (ADS)

    Sinha, Mandira; Roy, Subinit; Basu, P.; Majumdar, H.; Santra, S.; Parkar, V. V.; Golda, K. S.; Kailas, S.

    2011-10-01

    The fusion excitation and elastic angular distribution were measured for 6,7Li+28Si from below to above Coulomb barrier (≤ 3Vb) energies. The barrier distribution derived from the fusion data was found to be broad and asymmetric at the sub-barrier region, compared to 1D BPM estimation. Effect of rotational coupling on fusion was found to be not so dominant. Phenomenological optical potential parameters, with surface and volume type imaginary potentials, were obtained from f tting of elastic scattering data and energy dependence of real and imaginary surface strengths were investigated around the barrier. CDCC calculations considering only breakup of projectile were performed for 6,7Li+28Si with the elastic scattering data, using the code FRESCO. The effects of breakup of projectile on elastic cross section do not agree with the energy dependence of real and imaginary strength with volume type imaginary potential around the barrier.

  17. Relativistic coupled-cluster calculations of transition properties in highly charged inert-gas ions

    NASA Astrophysics Data System (ADS)

    Nandy, D. K.

    2016-11-01

    We have carried out an extensive investigation of various spectroscopic properties of highly charged inert-gas ions using a relativistic coupled-cluster method through a one-electron detachment procedure. In particular, we have calculated the atomic states 2 s22 p53/2 2P, 2 s22 p51/2 2P, and 2 s 2 p61/2 2S in F-like inert-gas ions; 3 s23 p53/2 2P, 3 s23 p51/2 2P, and 3 s 3 p61/2 2S states in Cl-like Kr, Xe, and Rn; and 4 s24 p53/2 2P, 4 s24 p51/2 2P, and 4 s 4 p61/2 2S states in Br-like Xe and Rn. Starting from a single-reference Dirac-Hartree-Fock wave function, we construct our exact atomic states by including the dynamic correlation effects in an all-order perturbative fashion. Employing this method, we estimate the ionization potential energies of three low-lying orbitals present in their respective closed-shell configurations. Since the considered highly charged inert-gas ions exhibit huge relativistic effects, we have taken into account the corrections due to Breit interaction as well as from the dominant quantum electrodynamic correction such as vacuum polarization and self-energy effects in these systems. Using our calculated relativistic atomic wave functions and energies, we accurately determine various transition properties such as wavelengths, line strengths, oscillator strengths, transition probabilities, and lifetimes of the excited states.

  18. Closed state-coupled C-type inactivation in BK channels.

    PubMed

    Yan, Jiusheng; Li, Qin; Aldrich, Richard W

    2016-06-21

    Ion channels regulate ion flow by opening and closing their pore gates. K(+) channels commonly possess two pore gates, one at the intracellular end for fast channel activation/deactivation and the other at the selectivity filter for slow C-type inactivation/recovery. The large-conductance calcium-activated potassium (BK) channel lacks a classic intracellular bundle-crossing activation gate and normally show no C-type inactivation. We hypothesized that the BK channel's activation gate may spatially overlap or coexist with the C-type inactivation gate at or near the selectivity filter. We induced C-type inactivation in BK channels and studied the relationship between activation/deactivation and C-type inactivation/recovery. We observed prominent slow C-type inactivation/recovery in BK channels by an extreme low concentration of extracellular K(+) together with a Y294E/K/Q/S or Y279F mutation whose equivalent in Shaker channels (T449E/K/D/Q/S or W434F) caused a greatly accelerated rate of C-type inactivation or constitutive C-inactivation. C-type inactivation in most K(+) channels occurs upon sustained membrane depolarization or channel opening and then recovers during hyperpolarized membrane potentials or channel closure. However, we found that the BK channel C-type inactivation occurred during hyperpolarized membrane potentials or with decreased intracellular calcium ([Ca(2+)]i) and recovered with depolarized membrane potentials or elevated [Ca(2+)]i Constitutively open mutation prevented BK channels from C-type inactivation. We concluded that BK channel C-type inactivation is closed state-dependent and that its extents and rates inversely correlate with channel-open probability. Because C-type inactivation can involve multiple conformational changes at the selectivity filter, we propose that the BK channel's normal closing may represent an early conformational stage of C-type inactivation.

  19. Pion-eta scalar-isovector 3-coupled channel amplitude fitted to branching ratios and threshold plus subthreshold parameters

    NASA Astrophysics Data System (ADS)

    Kamiński, Robert; Bibrzycki, Łukasz

    2017-03-01

    The low energy (below 2 GeV) πη channel interaction amplitude becomes an object of interest mainly because of the search for exotic mesons in just beginning to collect data detector GlueX in JLab. Finding and interpretation of expected weak signals from these states require a comparison with a very accurate amplitude containing standard (qq¯) states i.e. a0(980) and a0(1450). The main problem in the determination of such amplitude is a total absence of data about the phases and inelasticities in the elastic and inelastic region. In addition, it is necessary to take into account the next two coupled higher channels - KK¯ and πη'. Presented here amplitude is based on separable potential model (working very well for the scalar-isoscalar ππ interactions) with only 9 free parameters. To determine such 3-coupled channel amplitude, the following information has been taken into account: experimental branching ratios and positions of both a0 resonances, theoretical couplings, scattering length from ChPT and value of squared radius of the πη form factor. Phase shifts, inelasticities and cross sections in all single and crossed channels are presented.

  20. Transonic Shock Oscillations and Wing Flutter Calculated with an Interactive Boundary Layer Coupling Method

    NASA Technical Reports Server (NTRS)

    Edwards, John W.

    1996-01-01

    A viscous-inviscid interactive coupling method is used for the computation of unsteady transonic flows involving separation and reattachment. A lag-entrainment integral boundary layer method is used with the transonic small disturbance potential equation in the CAP-TSDV (Computational Aeroelasticity Program - Transonic Small Disturbance) code. Efficient and robust computations of steady and unsteady separated flows, including steady separation bubbles and self-excited shock-induced oscillations are presented. The buffet onset boundary for the NACA 0012 airfoil is accurately predicted and shown computationally to be a Hopf bifurcation. Shock-induced oscillations are also presented for the 18 percent circular arc airfoil. The oscillation onset boundaries and frequencies are accurately predicted, as is the experimentally observed hysteresis of the oscillations with Mach number. This latter stability boundary is identified as a jump phenomenon. Transonic wing flutter boundaries are also shown for a thin swept wing and for a typical business jet wing, illustrating viscous effects on flutter and the effect of separation onset on the wing response at flutter. Calculations for both wings show limit cycle oscillations at transonic speeds in the vicinity of minimum flutter speed indices.

  1. Research on Structural Safety of the Stratospheric Airship Based on Multi-Physics Coupling Calculation

    NASA Astrophysics Data System (ADS)

    Ma, Z.; Hou, Z.; Zang, X.

    2015-09-01

    As a large-scale flexible inflatable structure by a huge inner lifting gas volume of several hundred thousand cubic meters, the stratospheric airship's thermal characteristic of inner gas plays an important role in its structural performance. During the floating flight, the day-night variation of the combined thermal condition leads to the fluctuation of the flow field inside the airship, which will remarkably affect the pressure acted on the skin and the structural safety of the stratospheric airship. According to the multi-physics coupling mechanism mentioned above, a numerical procedure of structural safety analysis of stratospheric airships is developed and the thermal model, CFD model, finite element code and criterion of structural strength are integrated. Based on the computation models, the distributions of the deformations and stresses of the skin are calculated with the variation of day-night time. The effects of loads conditions and structural configurations on the structural safety of stratospheric airships in the floating condition are evaluated. The numerical results can be referenced for the structural design of stratospheric airships.

  2. Calculated Coupling of Transmembrane Electron and Proton Transfer in Dihemic Quinol:Fumarate Reductase

    PubMed Central

    Haas, Alexander H.; Lancaster, C. Roy D.

    2004-01-01

    The quinol:fumarate reductase of Wolinella succinogenes binds a low- and a high-potential heme b group in its transmembrane subunit C. Both hemes are part of the electron transport chain between the two catalytic sites of this redox enzyme. The oxidation-reduction midpoint potentials of the hemes are well established but their assignment in the structure has not yet been determined. By simulating redox titrations, using continuum electrostatics calculations, it was possible to achieve an unequivocal assignment of the low- and high-potential hemes to the distal and proximal positions in the structure, respectively. Prominent features governing the differences in midpoint potential between the two hemes are the higher loss of reaction field energy for the proximal heme and the stronger destabilization of the oxidized form of the proximal heme due to several buried Arg and Lys residues. According to the so-called “E-pathway hypothesis”, quinol:fumarate reductase has previously been postulated to exhibit a novel coupling of transmembrane electron and proton transfer. Simulation of heme b reduction indicates that the protonation state of the conserved residue Glu C180, predicted to play a key role in this process, indeed depends on the redox state of the hemes. This result clearly supports the E-pathway hypothesis. PMID:15361415

  3. Multi-reference approach to the calculation of photoelectron spectra including spin-orbit coupling

    SciTech Connect

    Grell, Gilbert; Bokarev, Sergey I. Kühn, Oliver; Winter, Bernd; Seidel, Robert; Aziz, Emad F.; Aziz, Saadullah G.

    2015-08-21

    X-ray photoelectron spectra provide a wealth of information on the electronic structure. The extraction of molecular details requires adequate theoretical methods, which in case of transition metal complexes has to account for effects due to the multi-configurational and spin-mixed nature of the many-electron wave function. Here, the restricted active space self-consistent field method including spin-orbit coupling is used to cope with this challenge and to calculate valence- and core-level photoelectron spectra. The intensities are estimated within the frameworks of the Dyson orbital formalism and the sudden approximation. Thereby, we utilize an efficient computational algorithm that is based on a biorthonormal basis transformation. The approach is applied to the valence photoionization of the gas phase water molecule and to the core ionization spectrum of the [Fe(H{sub 2}O){sub 6}]{sup 2+} complex. The results show good agreement with the experimental data obtained in this work, whereas the sudden approximation demonstrates distinct deviations from experiments.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  5. Drainage beneath ice sheets: groundwater-channel coupling, and the origin of esker systems from former ice sheets

    NASA Astrophysics Data System (ADS)

    Boulton, G. S.; Hagdorn, M.; Maillot, P. B.; Zatsepin, S.

    2009-04-01

    The nature of the drainage system beneath ice sheets is crucial to their dynamic behaviour but remains problematic. An experimentally based theory of coupling between groundwater and major channel systems is applied to the esker systems in the area occupied the last ice sheet in Europe, which we regard as a fossil imprint of major longitudinal drainage channels. We conclude that the large-scale distribution and spacing of major eskers is consistent with the theory of groundwater control, in which esker spacing is partly controlled by the transmissivity of the bed. It is concluded that esker patterns reflect the large-scale organisation of the subglacial drainage pattern in which channel development is coupled to groundwater flow and to the ice sheet's dynamic regime. The theory is then used to deduce: basal meltwater recharge rates and their spatial variability from esker spacing in an area in which the ice sheet was actively streaming during its final retreat; patterns of palaeo-groundwater flow and head distribution; and the seasonally varying magnitude of discharge from stream tunnels at the retreating ice sheet margin. Major channel/esker systems appear to have been stable at least over several hundred of years during the retreat of the ice sheet, although major dynamic events are demonstrably associated with major shifts in the hydraulic regime. Modelling suggests: that glaciation can stimulate deep groundwater circulation cells that are spatially linked to channel locations, with groundwater flow predominantly transverse to ice flow; that the circulation pattern has the potential to create large-scale anomalies in groundwater chemistry; and that the spacing of channels will change through the glacial cycle, influencing water pressures in stream tunnels, subglacial hydraulic gradients and effective pressure. If the latter is reduced sufficiently, it could trigger enhanced bed deformation, thus coupling drainage to ice sheet movement. It suggests the

  6. Calculating branching ratio and spin-orbit coupling from first principles: A formalism and its application to iridates

    NASA Astrophysics Data System (ADS)

    Sim, Jae-Hoon; Yoon, Hongkee; Park, Sang Hyeon; Han, Myung Joon

    2016-09-01

    We present a simple technique to calculate spin-orbit coupling, , and branching ratio measured in x-ray absorption spectroscopy. Our method is for first-principles electronic structure calculation, and its implementation is straightforward for any of the standard formulations and codes. We applied this technique to several different large spin-orbit coupling iridates. The calculated and branching ratio of a prototype jeff=1 /2 Mott insulator, Sr2IrO4 , are in good agreement with recent experimental data over the wide range of Rh doping. Three different double-perovskite iridates (namely, Sr2MgIrO6 , Sr2ScIrO6 , and Sr2TiIrO6 ) are also well described. This technique can serve as a promising tool for studying large spin-orbit coupling materials from first principles and for understanding experiments.

  7. Complex image method for RF antenna-plasma inductive coupling calculation in planar geometry. Part I: basic concepts

    NASA Astrophysics Data System (ADS)

    Howling, A. A.; Guittienne, Ph; Jacquier, R.; Furno, I.

    2015-12-01

    The coupling between an inductive source and the plasma determines the power transfer efficiency and the reflected impedance in the primary circuit. Usually, the plasma coupling is analysed by means of a transformer equivalent circuit, where the plasma inductance and resistance are estimated using a global plasma model. This paper shows that, for planar RF antennas, the mutual inductance between the plasma and the primary circuit can be calculated using partial inductances and the complex image method, where the plasma coupling is determined in terms of the plasma skin depth and the distance to the plasma. To introduce the basic concepts, the mutual inductance is calculated here for a linear conductor parallel to the plasma surface. In the accompanying paper part II Guittienne et al (2015 Plasma Sources Sci. Technol. 24 065015), impedance measurements on a RF resonant planar plasma source are modeled using an impedance matrix where the plasma-antenna mutual impedances are calculated using the complex image method presented here.

  8. Broken symmetry approach to density functional calculation of magnetic anisotropy or zero field splittings for multinuclear complexes with antiferromagnetic coupling.

    PubMed

    van Wüllen, Christoph

    2009-10-29

    Antiferromagnetic coupling in multinuclear transition metal complexes usually leads to electronic ground states that cannot be described by a single Slater determinant and that are therefore difficult to describe by Kohn-Sham density functional methods. Density functional calculations in such cases are usually converged to broken symmetry solutions which break spin and, in many cases, also spatial symmetry. While a procedure exists to extract isotropic Heisenberg (exchange) coupling constants from such calculations, no such approach is yet established for the calculation of magnetic anisotropy energies or zero field splitting parameters. This work proposes such a procedure. The broken symmetry solutions are not only used to extract the exchange couplings but also single-ion D tensors which are then used to construct a (phenomenological) spin Hamiltonian, from which the magnetic anisotropy and the zero-field energy levels can be computed. The procedure is demonstrated for a bi- and a trinuclear Mn(III) model compound.

  9. Calculation of vibrational energy of molecule using coupled cluster linear response theory in bosonic representation: convergence studies.

    PubMed

    Banik, Subrata; Pal, Sourav; Prasad, M Durga

    2008-10-07

    Vibrational excited state energies have been calculated using vibrational coupled cluster linear response theory (CCLRT). The method has been implemented on formaldehyde and water molecule. Convergence studies have been shown with varying the cluster operator from S(4) to S(6) as well as the excitation operator from four bosons to six bosons. A good agreement with full configuration interaction results has been observed with S(6) truncation at coupled-cluster method level and six bosonic excitations at CCLRT level.

  10. Electron collisions with phenol: Total, integral, differential, and momentum transfer cross sections and the role of multichannel coupling effects on the elastic channel

    SciTech Connect

    Costa, Romarly F. da; Oliveira, Eliane M. de; Lima, Marco A. P.; Bettega, Márcio H. F.; Varella, Márcio T. do N.; Jones, Darryl B.; Brunger, Michael J.; Blanco, Francisco; Colmenares, Rafael; and others

    2015-03-14

    We report theoretical and experimental total cross sections for electron scattering by phenol (C{sub 6}H{sub 5}OH). The experimental data were obtained with an apparatus based in Madrid and the calculated cross sections with two different methodologies, the independent atom method with screening corrected additivity rule (IAM-SCAR), and the Schwinger multichannel method with pseudopotentials (SMCPP). The SMCPP method in the N{sub open}-channel coupling scheme, at the static-exchange-plus-polarization approximation, is employed to calculate the scattering amplitudes at impact energies ranging from 5.0 eV to 50 eV. We discuss the multichannel coupling effects in the calculated cross sections, in particular how the number of excited states included in the open-channel space impacts upon the convergence of the elastic cross sections at higher collision energies. The IAM-SCAR approach was also used to obtain the elastic differential cross sections (DCSs) and for correcting the experimental total cross sections for the so-called forward angle scattering effect. We found a very good agreement between our SMCPP theoretical differential, integral, and momentum transfer cross sections and experimental data for benzene (a molecule differing from phenol by replacing a hydrogen atom in benzene with a hydroxyl group). Although some discrepancies were found for lower energies, the agreement between the SMCPP data and the DCSs obtained with the IAM-SCAR method improves, as expected, as the impact energy increases. We also have a good agreement among the present SMCPP calculated total cross section (which includes elastic, 32 inelastic electronic excitation processes and ionization contributions, the latter estimated with the binary-encounter-Bethe model), the IAM-SCAR total cross section, and the experimental data when the latter is corrected for the forward angle scattering effect [Fuss et al., Phys. Rev. A 88, 042702 (2013)].

  11. Rotational excitation of symmetric top molecules by collisions with atoms: Close coupling, coupled states, and effective potential calculations for NH3-He

    NASA Technical Reports Server (NTRS)

    Green, S.

    1976-01-01

    The formalism for describing rotational excitation in collisions between symmetric top rigid rotors and spherical atoms is presented both within the accurate quantum close coupling framework and also the coupled states approximation of McGuire and Kouri and the effective potential approximation of Rabitz. Calculations are reported for thermal energy NH3-He collisions, treating NH3 as a rigid rotor and employing a uniform electron gas (Gordon-Kim) approximation for the intermolecular potential. Coupled states are found to be in nearly quantitative agreement with close coupling results while the effective potential method is found to be at least qualitatively correct. Modifications necessary to treat the inversion motion in NH3 are discussed.

  12. Channels

    NASA Image and Video Library

    2015-11-20

    Today's VIS image shows a number of unnamed channels located on the northeastern margin of Terra Sabaea. Orbit Number: 61049 Latitude: 33.5036 Longitude: 58.6967 Instrument: VIS Captured: 2015-09-18 12:54 http://photojournal.jpl.nasa.gov/catalog/PIA20097

  13. Coupled radiation effects in thermochemical nonequilibrium shock-capturing flowfield calculations

    NASA Astrophysics Data System (ADS)

    Hartung, Lin C.; Mitcheltree, Robert A.; Gnoffo, Peter A.

    1992-07-01

    Lunar and Mars return conditions are examined using the LAURA flowfield code and the LORAN radiation code to assess the effect of radiative coupling on axisymmetric thermochemical nonequilibrium flows. Coupling of the two codes is achieved iteratively. Special treatment required to couple radiation in a shock-capturing method is discussed. Results indicate that while coupling effects are generally the same as occur in equilibrium flows, under certain conditions radiation can modify the chemical kinetics of a nonequilibrium flow and thus alter relaxation processes. Coupling effects are found to be small for all cases considered, except for a five meter diameter aerobrake returning from Mars at 13.6 km/sec.

  14. Coupled Radiation Effects in Thermochemical Nonequilibrium Shock-Capturing Flowfield Calculations

    NASA Technical Reports Server (NTRS)

    Hartung, Lin C.; Mitcheltree, Robert A.; Gnoffo, Peter A.

    1993-01-01

    Lunar and Mars return conditions are examined using the LAURA flow field code and the LORAN radiation code to assess the effect of radiative coupling on axisymmetric thermochemical nonequilibrium flows. Coupling of the two codes is achieved iteratively. Special treatment required to couple radiation in a shock-capturing method is discussed. Results indicate that while coupling effects are generally the same as occur in equilibrium flows, under certain conditions radiation can modify the chemical kinetics of a nonequilibrium flow and thus alter relaxation processes. Coupling effects are found to be small for all cases considered, except for a five meter diameter aerobrake returning from Mars at 13.6 kilometers per second.

  15. Application of Brownian motion theory to the analysis of membrane channel ionic trajectories calculated by molecular dynamics.

    PubMed Central

    Jakobsson, E; Chiu, S W

    1988-01-01

    This paper shows how Brownian motion theory can be used to analyze features of individual ion trajectories in channels as calculated by molecular dynamics, and that its use permits more precise determinations of diffusion coefficients than would otherwise be possible. We also show how a consideration of trajectories of single particles can distinguish between effects due to the magnitude of the diffusion coefficient and effects due to barriers and wells in the potential profile, effects which can not be distinguished by consideration of average fluxes. PMID:2465032

  16. Measurement of mode coupling distribution along a few-mode fiber using a synchronous multi-channel OTDR.

    PubMed

    Nakazawa, Masataka; Yoshida, Masato; Hirooka, Toshihiko

    2014-12-15

    We describe the nondestructive measurement of mode coupling along a few-mode fiber using a synchronous multi-channel optical time-domain reflectometer (OTDR). By installing a few-mode fiber (FMF) coupler made with a phase mask method, we excite the LP01 mode in an FMF under the test as an input mode, and then we detect backward Rayleigh scattered LP11a or LP11b modes, which were generated as a result of the mode coupling through the coupler. The mode coupling distribution between the LP01 and LP11a,b modes along the test FMF was successfully measured with a 10-m spatial resolution by obtaining the ratio between the backscattered LP01 mode and LP11a or LP11b. The value of the mode coupling obtained with the present method agreed well with that obtained with the conventional transmission method.

  17. Effect of metal ions on radical type and proton-coupled electron transfer channel: sigma-radical vs pi-radical and sigma-channel vs pi-channel in the imide units.

    PubMed

    Chen, Xiaohua; Xing, Dianxiang; Zhang, Liang; Cukier, Robert I; Bu, Yuxiang

    2009-12-01

    The mechanism of proton transfer (PT)/electron transfer (ET) in imide units, and its regulation by hydrated metal ions, was explored theoretically using density functional theory in a representative model (a nearly planar and cisoid complex between uracil and its N(3)-dehydrogenated radical, UU). In UU (sigma-radical), PT/ET normally occurs via a seven-center, cyclic proton-coupled sigma-electron sigma-channel transfer (PC(sigma)E(sigma)T) mechanism (3.8 kcal/mol barrier height) with a N(3)-->N(3') PT and an O(4)-->O(4') ET. Binding of hydrated metal ions to the dioxygen sites (O(2)/O(2') or/and O(4)/O(4')) of UU may significantly affect its PT/ET cooperative reactivity by changing the radical type (sigma-radical <--> pi-radical) and ET channel (sigma-channel <--> pi-channel), leading to different mechanisms, ranging from PC(sigma)E(sigma)T, to proton-coupled pi-electron sigma-channel transfer (PC(pi)E(sigma)T) to proton-coupled pi-electron pi-channel transfer (PC(pi)E(pi)T). This change originates from an alteration of the ordering of the UU moiety SOMO/HDMO (the singly occupied molecular orbital and the highest doubly occupied molecular orbital), induced by binding of the hydrated metal ions. It is a consequence of three associated factors: the asymmetric reactant structure, electron cloud redistribution, and fixing role of metal ions to structural backbone. The findings regarding the modulation of the PT/ET pathway via hydrated metal ions may provide valuable information for a greater understanding of PT/ET cooperative mechanisms, and an alternative way for designing imide-based molecular devices, such as molecular switches and molecular wires.

  18. Singularity method applied to the classical Helmholtz flow coupling procedure with boundary layer calculation

    NASA Astrophysics Data System (ADS)

    Legallais, Ph.; Hureau, J.

    1994-06-01

    A free streamline wake model based on singularity distribution is proposed in order to treat the flow past an arbitrary curved obstacle with Helmholtz's wake. The slipping condition gives the vortex distribution on the obstacle and the steady evolution condition is written on the first part of the free streamlines in order to find their locations, the geometry of the second part being fixed by an asymptotic study. The validity of the method is judged by comparing results with those obtained by a formulation, to be used as a standard, which encloses conformal mapping and is an adaptation of Levi-Civita's method. Good agreement leads us to envisage extending the method to multi-element systems. Correlatively, we show a coupling procedure with a boundary layer calculation. Applied to the circular cylinder, it allows to bring out the existence of sub-and supercritical ranges. Although the latter is well predicted for the separation angle and the drag coefficient, the former is only approximately approached, with an overestimate of the critical Reynolds number as an immediate consequence. Nous mettons en œuvre une méthode de singularités pour calculer l'écoulement autour d'un obstacle à paroi courbe quelconque en présence d'un sillage de Helmholtz. La répartition de densité tourbillonnaire sur la paroi baignée de l'obstacle est calculée par l'application de la condition de glissement. La condition d'évolution stationnaire est écrite sur la première partie des lignes de glissement afin de déterminer leur position, la géométrie de la seconde partie provenant d'une étude asymptotique. Nous jugeons de la validité de la méthode en comparant les résultats avec ceux obtenus par une méthode étalon utilisant la transformation conforme, et qui est une adaptation de la méthode de Levi-Civita. Le bon accord entre les deux nous permet d'envisager l'extension de la méthode au cas multi-obstacles. Nous proposons ensuite une procédure de couplage avec un calcul

  19. Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

    NASA Astrophysics Data System (ADS)

    Oberhofer, Harald; Blumberger, Jochen

    2010-12-01

    We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q-) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, ( {< {| {H_ab } |^2 } > } )^{1/2} = 6.7 {mH}, is significantly higher than the value obtained for the minimum energy structure, | {H_ab } | = 3.8 {mH}. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q- in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

  20. Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set.

    PubMed

    Oberhofer, Harald; Blumberger, Jochen

    2010-12-28

    We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q(-)) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, (<|H(ab)|(2)>)(1/2)=6.7 mH, is significantly higher than the value obtained for the minimum energy structure, |H(ab)|=3.8 mH. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q(-) in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

  1. CPM{P,N} methods extended for the solution of coupled channel Schrödinger equations

    NASA Astrophysics Data System (ADS)

    Ledoux, V.; Van Daele, M.; Vanden Berghe, G.

    2006-03-01

    The successful CPM {P,N} methods for the one-dimensional time-independent Schrödinger problem are generalized to the coupled channel case. The derivation of the formulae is discussed and a MAPLE program code is included which allows to determine the analytic expressions of the perturbation corrections needed to construct methods of different orders. Some numerical illustrations are given showing the accuracy, the robustness and the CPU-time gain of the proposed algorithms over the sixth order LILIX method which was presented in [L.Gr. Ixaru, LILIX—A package for the solution of the coupled channel Schrödinger equation, Comput. Phys. Comm. 147 (2002) 834-852].

  2. Protein translocation channel of mitochondrial inner membrane and matrix-exposed import motor communicate via two-domain coupling protein.

    PubMed

    Banerjee, Rupa; Gladkova, Christina; Mapa, Koyeli; Witte, Gregor; Mokranjac, Dejana

    2015-12-29

    The majority of mitochondrial proteins are targeted to mitochondria by N-terminal presequences and use the TIM23 complex for their translocation across the mitochondrial inner membrane. During import, translocation through the channel in the inner membrane is coupled to the ATP-dependent action of an Hsp70-based import motor at the matrix face. How these two processes are coordinated remained unclear. We show here that the two domain structure of Tim44 plays a central role in this process. The N-terminal domain of Tim44 interacts with the components of the import motor, whereas its C-terminal domain interacts with the translocation channel and is in contact with translocating proteins. Our data suggest that the translocation channel and the import motor of the TIM23 complex communicate through rearrangements of the two domains of Tim44 that are stimulated by translocating proteins.

  3. Utrophin suppresses low frequency oscillations and coupled gating of mechanosensitive ion channels in dystrophic skeletal muscle.

    PubMed

    Lansman, Jeffry B

    2015-01-01

    An absence of utrophin in muscle from mdx mice prolongs the open time of single mechanosensitive channels. On a time scale much longer than the duration of individual channel activations, genetic depletion of utrophin produces low frequency oscillations of channel open probability. Oscillatory channel opening occurred in the dystrophin/utrophin mutants, but was absent in wild-type and mdx fibers. By contrast, small conductance channels showed random gating behavior when present in the same patch. Applying a negative pressure to a patch on a DKO fiber produced a burst of mode II activity, but channels subsequently closed and remained silent for tens of seconds during the maintained pressure stimulus. In addition, simultaneous opening of multiple MS channels could be frequently observed in recordings from patches on DKO fibers, but only rarely in wild-type and mdx muscle. A model which accounts for the single-channel data is proposed in which utrophin acts as gating spring which maintains the mechanical stability a caveolar-like compartment. The state of this compartment is suggested to be dynamic; its continuity with the extracellular surface varying over seconds to minutes. Loss of the mechanical stability of this compartment contributes to pathogenic Ca(2+) entry through MS channels in Duchenne dystrophy.

  4. The foot structure from the type 1 ryanodine receptor is required for functional coupling to store-operated channels.

    PubMed

    Sampieri, Alicia; Diaz-Muñoz, Mauricio; Antaramian, Anaid; Vaca, Luis

    2005-07-01

    In the present study we have explored structural determinants of the functional interaction between skeletal muscle ryanodine receptor (RyR1) and transient receptor potential channel 1 (TRPC1) channels expressed in Chinese hamster ovary cells. We have illustrated a functional interaction between TRPC1 channels and RyR1 for the regulation of store-operated calcium entry (SOCE) initiated after releasing calcium from a caffeine-sensitive intracellular calcium pool. RNA interference experiments directed to reduce the amount of TRPC1 protein indicate that RyR1 associates to at least two different types of store-operated channels (SOCs), one dependent and one independent of TRPC1. In contrast, bradykinin-induced SOCE is completely dependent on the presence of TRPC1 protein, as we have previously illustrated. Removing the foot structure from RyR1 results in normal caffeine-induced release of calcium from internal stores but abolishes the activation of SOCE, indicating that this structure is require for functional coupling to SOCs. The footless RyR1 protein shows a different cellular localization when compared with wild type RyR1. The later protein shows a higher percentage of colocalization with FM-464, a marker of plasma membrane. The implications of the foot structure for the functional and physical coupling to TRPC and SOCs is discussed.

  5. RGS2 modulates coupling between GABAB receptors and GIRK channels in dopamine neurons of the ventral tegmental area.

    PubMed

    Labouèbe, Gwenaël; Lomazzi, Marta; Cruz, Hans G; Creton, Cyril; Luján, Rafael; Li, Meng; Yanagawa, Yuchio; Obata, Kunihiko; Watanabe, Masahiko; Wickman, Kevin; Boyer, Stephanie B; Slesinger, Paul A; Lüscher, Christian

    2007-12-01

    Agonists of GABA(B) receptors exert a bi-directional effect on the activity of dopamine (DA) neurons of the ventral tegmental area, which can be explained by the fact that coupling between GABA(B) receptors and G protein-gated inwardly rectifying potassium (GIRK) channels is significantly weaker in DA neurons than in GABA neurons. Thus, low concentrations of agonists preferentially inhibit GABA neurons and thereby disinhibit DA neurons. This disinhibition might confer reinforcing properties on addictive GABA(B) receptor agonists such as gamma-hydroxybutyrate (GHB) and its derivatives. Here we show that, in DA neurons of mice, the low coupling efficiency reflects the selective expression of heteromeric GIRK2/3 channels and is dynamically modulated by a member of the regulator of G protein signaling (RGS) protein family. Moreover, repetitive exposure to GHB increases the GABA(B) receptor-GIRK channel coupling efficiency through downregulation of RGS2. Finally, oral self-administration of GHB at a concentration that is normally rewarding becomes aversive after chronic exposure. On the basis of these results, we propose a mechanism that might underlie tolerance to GHB.

  6. A coupled biophysical model for the distribution of the great scallop Pecten maximus in the English Channel

    NASA Astrophysics Data System (ADS)

    Le Goff, Clément; Lavaud, Romain; Cugier, Philippe; Jean, Fred; Flye-Sainte-Marie, Jonathan; Foucher, Eric; Desroy, Nicolas; Fifas, Spyros; Foveau, Aurélie

    2017-03-01

    In this paper we used a modelling approach integrating both physical and biological constraints to understand the biogeographical distribution of the great scallop Pecten maximus in the English Channel during its whole life cycle. A 3D bio-hydrodynamical model (ECO-MARS3D) providing environmental conditions was coupled to (i) a population dynamics model and (ii) an individual ecophysiological model (Dynamic Energy Budget model). We performed the coupling sequentially, which underlined the respective role of biological and physical factors in defining P. maximus distribution in the English Channel. Results show that larval dispersion by hydrodynamics explains most of the scallop distribution and enlighten the main known hotspots for the population, basically corresponding to the main fishing areas. The mechanistic description of individual bioenergetics shows that food availability and temperature control growth and reproduction and explain how populations may maintain themselves in particular locations. This last coupling leads to more realistic densities and distributions of adults in the English Channel. The results of this study improves our knowledge on the stock and distribution dynamics of P. maximus, and provides grounds for useful tools to support management strategies.

  7. Extension of the Source-Sink Potential (SSP) approach for multi-channel conductance calculations

    NASA Astrophysics Data System (ADS)

    Rocheleau, Philippe; Ernzerhof, Matthias

    2010-03-01

    In molecular electronics, molecules are connected to macroscopic contacts and the current passing through is studied as a function of the applied voltage. We focus on modeling the transmission of electrons through such a molecular electronic device (MED). Based on a simple H"uckel Hamiltonian to describe the π electrons in conjugated systems, the SSP method [1,2,3] employs complex potentials to replace the wavefunction of the infinite contacts in a rigorous way. The initial SSP approach [4] was limited to two one-dimensional contacts, here we extend the approach to multiple channels, i.e., to two-dimensional contacts including transverse modes. We describe the development of the method and illustrate it with applications. References:[1] F. Goyer, M. Ernzerhof and M. Zhuang, J. Chem. Phys., 126, (2007) 144104.[2] M. Ernzerhof, J. Chem. Phys., 127, (2007) 204709.[3] B.T. Pickup and P.W. Fowler, Chem. Phys. Lett., 459, (2008) 198-202.[4] P. Rocheleau and M. Ernzerhof, J. Chem. Phys., 130 (17) (2009).

  8. CAL3JHH: a Java program to calculate the vicinal coupling constants (3 J H,H) of organic molecules

    NASA Astrophysics Data System (ADS)

    Aguirre-Valderrama, Alonso; Dobado, José A.

    2008-12-01

    Here, we present a free web-accessible application, developed in the JAVA programming language for the calculation of vicinal coupling constant (3 J H,H) of organic molecules with the H-Csp3-Csp3-H fragment. This JAVA applet is oriented to assist chemists in structural and conformational analyses, allowing the user to calculate the averaged 3 J H,H values among conformers, according to its Boltzmann populations. Thus, the CAL3JHH program uses the Haasnoot-Leeuw-Altona equation, and, by reading the molecule geometry from a protein data bank (PDB) file format or from multiple pdb files, automatically detects all the coupled hydrogens, evaluating the data needed for this equation. Moreover, a "Graphical viewer" menu allows the display of the results on the 3D molecule structure, as well as the plotting of the Newman projection for the couplings.

  9. CAL3JHH: a Java program to calculate the vicinal coupling constants (3J H,H) of organic molecules.

    PubMed

    Aguirre-Valderrama, Alonso; Dobado, José A

    2008-12-01

    Here, we present a free web-accessible application, developed in the JAVA programming language for the calculation of vicinal coupling constant (3J(H,H)) of organic molecules with the H-Csp3-Csp3-H fragment. This JAVA applet is oriented to assist chemists in structural and conformational analyses, allowing the user to calculate the averaged 3J(H,H) values among conformers, according to its Boltzmann populations. Thus, the CAL3JHH program uses the Haasnoot-Leeuw-Altona equation, and, by reading the molecule geometry from a protein data bank (PDB) file format or from multiple pdb files, automatically detects all the coupled hydrogens, evaluating the data needed for this equation. Moreover, a "Graphical viewer" menu allows the display of the results on the 3D molecule structure, as well as the plotting of the Newman projection for the couplings.

  10. Complete one-loop calculation of electroweak supersymmetric effects in t-channel single top production at CERN LHC

    SciTech Connect

    Beccaria, M.; Calame, C. M. Carloni; Macorini, G.; Verzegnassi, C.; Mirabella, E.; Piccinini, F.; Renard, F. M.

    2008-06-01

    We have computed the complete one-loop electroweak effects in the minimal supersymmetric standard model for single top (and single antitop) production in the t channel at hadron colliders, generalizing a previous analysis performed for the dominant dt final state and fully including QED effects. The results are quite similar for all processes. The overall standard model one-loop effect is small, of the few percent size. This is due to a compensation of weak and QED contributions that are of opposite sign. The genuine supersymmetry contribution is generally quite modest in the minimal supergravity scenario. The experimental observables would therefore only practically depend, in this framework, on the Cabibbo-Kobayashi-Maskawa Wtb coupling.

  11. Tight coupling of rubidium conductance and inactivation in human KCNQ1 potassium channels.

    PubMed

    Seebohm, Guiscard; Sanguinetti, Michael C; Pusch, Michael

    2003-10-15

    KCNQ1 K+ channels in humans are important for repolarization of cardiac action potentials and for K+ secretion in the inner ear. The pore-forming channel subunits form heteromeric complexes with small regulatory subunits of the KCNE family, in particular with KCNE1 to form channels that conduct a slow delayed rectifier K+ current, IKs. This association leads to alteration of biophysical properties, including a slowing of activation, a suppression of inactivation and an increase of the apparent single-channel conductance. In addition, inward Rb+ currents conducted by homomeric KCNQ1 channels are about threefold larger than K+ currents, whereas heteromeric KCNQ1-KCNE1 channels have smaller inward Rb+ currents compared to K+ currents. We determined inactivation properties and compared K+ vs. Rb+ inward currents for channels formed by co-assembly of KCNQ1 with KCNE1, KCNE3 and KCNE5, and for homomeric KCNQ1 channels with point mutations in the pore helix S5 or S6 transmembrane domains. Several of the channels with point mutations eliminated the apparent inactivation of KCNQ1, as described previously (Seebohm et al. 2001). We found that the extent of inactivation and the ratio of Rb+/K+ currents were positively correlated. Since the effect of Rb+ on the current size has been shown previously to be related to a fast 'flickery' process, our results suggest that inactivation of KCNQ1 channels is related to a fast flicker of the open channel. A kinetic model incorporating two open states, no explicit inactivated state and a fast flicker that is different for the two open states is able to account for the apparent inactivation and the correlation of inactivation and large Rb+ currents. We conclude that an association between KCNQ1 and KCNE subunits or removal of inactivation by mutation of KCNQ1 stabilizes the open conformation of the pore principally by altering an interaction between the pore helix and the selectivity filter and with S5/S6 domains.

  12. Analyzing and Interpreting NMR Spin-Spin Coupling Constants Using Molecular Orbital Calculations

    ERIC Educational Resources Information Center

    Autschbach, Jochen; Le Guennic, Boris

    2007-01-01

    Molecular orbital plots are used to analyze and interpret NMR spin-spin coupling constants, also known as J coupling constants. Students have accepted the concept of contributions to molecular properties from individual orbitals without the requirement to provide explicit equations.

  13. Analyzing and Interpreting NMR Spin-Spin Coupling Constants Using Molecular Orbital Calculations

    ERIC Educational Resources Information Center

    Autschbach, Jochen; Le Guennic, Boris

    2007-01-01

    Molecular orbital plots are used to analyze and interpret NMR spin-spin coupling constants, also known as J coupling constants. Students have accepted the concept of contributions to molecular properties from individual orbitals without the requirement to provide explicit equations.

  14. A toxin from the spider Phoneutria nigriventer that blocks calcium channels coupled to exocytosis

    PubMed Central

    Guatimosim, C; Romano-Silva, M A; Cruz, J S; Beirão, P S L; Kalapothakis, E; Moraes-Santos, T; Cordeiro, M N; Diniz, C R; Gomez, M V; Prado, M A M

    1997-01-01

    The aim of the present experiments was to investigate the pharmacological action of a toxin from the spider Phoneutria nigriventer, Tx3-3, on the function of calcium channels that control exocytosis of synaptic vesicles. Tx3-3, in confirmation of previous work, diminished the intracellular calcium increase induced by membrane depolarization with KCl (25 mM) in rat cerebrocortical synaptosomes. The toxin was very potent (IC50 0.9 nM) at inhibiting calcium channels that regulate calcium entry in synaptosomes. In addition, Tx3-3 blocked the exocytosis of synaptic vesicles, as measured with the fluorescent dye FM1-43. Using ω-toxins that interact selectively with distinct neuronal calcium channels, we investigated whether the target of Tx3-3 overlaps with known channels that mediate exocytosis. The results indicate that the main population of voltage-sensitive calcium channels altered by Tx3-3 can also be inhibited by ω-agatoxin IVA, an antagonist of P/Q calcium channels. ω-conotoxin GVIA, which inhibits N type calcium channels did not decrease significantly the entry of calcium or exocytosis of synaptic vesicles in depolarized synaptosomes. It is concluded that Tx3-3 potently inhibits ω-agatoxin IVA-sensitive calcium channels, which are involved in controlling exocytosis in rat brain cortical synaptosomes. PMID:9351520

  15. Role of K2P channels in stimulus-secretion coupling

    PubMed Central

    Kim, Donghee; Kang, Dawon

    2014-01-01

    Two-pore domain K+ (K2P) channels are involved in a variety of physiological processes by virtue of their high basal activity and sensitivity to various biological stimuli. One of these processes is secretion of hormones and transmitters in response to stimuli such as hypoxia, acidosis and receptor agonists. The rise in intracellular [Ca2+] ([Ca2+]i) that is critical for the secretory event can be achieved by several mechanisms: (a) Inhibition of resting (background) K+ channels, (b) activation of Na+/Ca2+-permeable channels and (c) release of Ca2+ from intracellular stores. Here, we discuss the role of TASK and TREK in stimulus-secretion mechanisms in carotid body chemoreceptor cells and adrenal medullary/cortical cells. Studies show that stimuli such as hypoxia and acidosis cause cell depolarization and transmitter/hormone secretion by inhibition of TASK or TREK. Subsequent elevation of [Ca2+]i produced by opening of voltage-dependent Ca2+ channels then activates a Na+-permeable cation channel, presumably to help sustain the depolarization and [Ca2+]i. Agonists such as angiotensin II may elevate [Ca2+]i via multiple mechanisms involving both inhibition of TASK/TREK and Ca2+ release from internal stores to cause aldosterone secretion. Thus, inhibition of resting (background) K+ channels and subsequent activation of voltage-gated Ca2+ channels and Na+-permeable non-selective cation channels may be a common ionic mechanism that lead to hormone and transmitter secretion. PMID:25476848

  16. Calculation of vibronic couplings for phenoxyl/phenol and benzyl/toluene self-exchange reactions: implications for proton-coupled electron transfer mechanisms.

    PubMed

    Skone, Jonathan H; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2006-12-27

    The vibronic couplings for the phenoxyl/phenol and the benzyl/toluene self-exchange reactions are calculated with a semiclassical approach, in which all electrons and the transferring hydrogen nucleus are treated quantum mechanically. In this formulation, the vibronic coupling is the Hamiltonian matrix element between the reactant and product mixed electronic-proton vibrational wavefunctions. The magnitude of the vibronic coupling and its dependence on the proton donor-acceptor distance can significantly impact the rates and kinetic isotope effects, as well as the temperature dependences, of proton-coupled electron transfer reactions. Both of these self-exchange reactions are vibronically nonadiabatic with respect to a solvent environment at room temperature, but the proton tunneling is electronically nonadiabatic for the phenoxyl/phenol reaction and electronically adiabatic for the benzyl/toluene reaction. For the phenoxyl/phenol system, the electrons are unable to rearrange fast enough to follow the proton motion on the electronically adiabatic ground state, and the excited electronic state is involved in the reaction. For the benzyl/toluene system, the electrons can respond virtually instantaneously to the proton motion, and the proton moves on the electronically adiabatic ground state. For both systems, the vibronic coupling decreases exponentially with the proton donor-acceptor distance for the range of distances studied. When the transferring hydrogen is replaced with deuterium, the magnitude of the vibronic coupling decreases and the exponential decay with distance becomes faster. Previous studies designated the phenoxyl/phenol reaction as proton-coupled electron transfer and the benzyl/toluene reaction as hydrogen atom transfer. In addition to providing insights into the fundamental physical differences between these two types of reactions, the present analysis provides a new diagnostic for differentiating between the conventionally defined hydrogen atom

  17. Graded Ca2+/calmodulin-dependent coupling of voltage-gated CaV1.2 channels

    PubMed Central

    Dixon, Rose E; Moreno, Claudia M; Yuan, Can; Opitz-Araya, Ximena; Binder, Marc D; Navedo, Manuel F; Santana, Luis F

    2015-01-01

    In the heart, reliable activation of Ca2+ release from the sarcoplasmic reticulum during the plateau of the ventricular action potential requires synchronous opening of multiple CaV1.2 channels. Yet the mechanisms that coordinate this simultaneous opening during every heartbeat are unclear. Here, we demonstrate that CaV1.2 channels form clusters that undergo dynamic, reciprocal, allosteric interactions. This ‘functional coupling’ facilitates Ca2+ influx by increasing activation of adjoined channels and occurs through C-terminal-to-C-terminal interactions. These interactions are initiated by binding of incoming Ca2+ to calmodulin (CaM) and proceed through Ca2+/CaM binding to the CaV1.2 pre-IQ domain. Coupling fades as [Ca2+]i decreases, but persists longer than the current that evoked it, providing evidence for ‘molecular memory’. Our findings suggest a model for CaV1.2 channel gating and Ca2+-influx amplification that unifies diverse observations about Ca2+ signaling in the heart, and challenges the long-held view that voltage-gated channels open and close independently. DOI: http://dx.doi.org/10.7554/eLife.05608.001 PMID:25714924

  18. Line coupling effects in the isotropic Raman spectra of N{sub 2}: A quantum calculation at room temperature

    SciTech Connect

    Thibault, Franck; Boulet, Christian; Ma, Qiancheng

    2014-01-28

    We present quantum calculations of the relaxation matrix for the Q branch of N{sub 2} at room temperature using a recently proposed N{sub 2}-N{sub 2} rigid rotor potential. Close coupling calculations were complemented by coupled states studies at high energies and provide about 10 200 two-body state-to state cross sections from which the needed one-body cross-sections may be obtained. For such temperatures, convergence has to be thoroughly analyzed since such conditions are close to the limit of current computational feasibility. This has been done using complementary calculations based on the energy corrected sudden formalism. Agreement of these quantum predictions with experimental data is good, but the main goal of this work is to provide a benchmark relaxation matrix for testing more approximate methods which remain of a great utility for complex molecular systems at room (and higher) temperatures.

  19. Line Coupling Effects in the Isotropic Raman Spectra of N2: A Quantum Calculation at Room Temperature

    NASA Technical Reports Server (NTRS)

    Thibault, Franck; Boulet, Christian; Ma, Qiancheng

    2014-01-01

    We present quantum calculations of the relaxation matrix for the Q branch of N2 at room temperature using a recently proposed N2-N2 rigid rotor potential. Close coupling calculations were complemented by coupled states studies at high energies and provide about 10200 two-body state-to state cross sections from which the needed one-body cross-sections may be obtained. For such temperatures, convergence has to be thoroughly analyzed since such conditions are close to the limit of current computational feasibility. This has been done using complementary calculations based on the energy corrected sudden formalism. Agreement of these quantum predictions with experimental data is good, but the main goal of this work is to provide a benchmark relaxation matrix for testing more approximate methods which remain of a great utility for complex molecular systems at room (and higher) temperatures.

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

    NASA Astrophysics Data System (ADS)

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

    2017-09-01

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

  1. Solution of the coupled-channel schrödinger equation using constant, linear and quadratic reference potentials

    NASA Astrophysics Data System (ADS)

    Mattson, Timothy G.; Anderson, Roger W.

    Systems of coupled second order differential equations arise in many problems in molecular quantum physics. In this paper we investigate approximate potential methods that solve these differential equations. A series method for the evaluation of the propagators is developed for the multichannel Schrödinger equation where the reference potential is expressed as a polynomial. The case of a linear approximate potential is treated in detail and the results are compared with the Magnus and Bessel methods which approximate the potential as a constant in each interval. The importance of fitting the potentials at the zeroes of a Legendre polynomial is shown. Optimum fitting of the potential results in second and fourth order global convergence respectively for constant and linear fits. Richardson extrapolation is used to increase the accuracy of the low order methods. Explicit formulae are presented for the first order perturbative corrections to the Magnus propagators. The importance of adding the leading terms in the second order perturbative correction to the first order corrections is shown. Useful formulae are derived from the perturbation analysis to guide variable step size determination. A simple series correction is also presented to improve the accuracy of the Magnus method. The application of the various propagators to the two channel Olson-Smith problem show that the Bessel propagators are the most efficient for moderate accuracy (> 10-3 root mean square fractional error in inelastic differential cross sections) calculations. The first order perturbatively corrected Magnus method (with leading second order terms) is the most efficient for higher accuracy calculations. The zeroth order Gordon methods, where the potential in an interval is assumed to be diagonal with linear or quadratic elements, are less efficient than the simple Magnus method. The methods developed in this paper are compared with the log derivative method and the most efficient of ovr methods

  2. The numerical calculation for the coupling of multiple propeller discrete noise and its interaction with the fuselage boundary

    NASA Astrophysics Data System (ADS)

    Wang, Tongqing; Sheng, Yuansheng; Zhou, Sheng

    This paper presents a numerical method for calculating multiple subsonic propeller discrete noise with the influence of rigid fuselage boundary condition of arbitrary shape, the method described unites the multiple propeller discrete noise coupling effect with the effect caused by its interaction with the fuselage boundary. The interaction of the discrete noise of the Y12 scaled propeller model with a cylindrical fuselage model boundary was calculated. The interpretation of every terms of the governing equation and the discussion of the calculation results illustrated that the mathematical model is acceptable. Substantially, the method can be used to calculate the interaction of any known harmonic sound sources and rigid boundary. The calculation results explain the propeller's sychronizer role, and its applicable principles.

  3. 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.

  4. Impact of improved light calculations on predicted phytoplankton growth and heating in an idealized upwelling-downwelling channel geometry

    NASA Astrophysics Data System (ADS)

    Mobley, Curtis D.; Chai, Fei; Xiu, Peng; Sundman, Lydia K.

    2015-02-01

    Ocean ecosystem models require accurate calculations of both hydrodynamics and biology; those calculations in turn require accurate calculation of in-water irradiance. Ecosystem models now achieve great accuracy in their hydrodynamical predictions, and the biological modules are becoming correspondingly sophisticated. The optical calculations are however often oversimplified, to the possible detriment of the physical and biological predictions. We used a recently developed, extremely fast radiative transfer code, EcoLight-S, to study differences in ecosystem and thermal development in an idealized upwelling-downwelling system when simple versus accurate irradiance calculations are used. The use of accurate irradiances gave up to 57% differences in chlorophyll concentrations after two weeks of simulated time, compared to predictions based on irradiances obtained using a simple exponential attenuation formula. Accurate irradiance calculations increased sea surface temperatures and decreased temperatures at depth, leading to increased stratification. Use of EcoLight-S couples the physical and biological calculations so that biology feeds back to physics, and vice versa. EcoLight-S outputs ancillary quantities such as remote sensing reflectance and in-water spectral irradiance, which can be used to validate ecosystem predictions using remotely sensed ocean color imagery or optical measurements from buoys or gliders, without the need to convert such measurements to chlorophyll values. After optimization, the ecosystem model total run times with EcoLight-S were less than 20% more than for the analytical irradiance models. We also found that the use of 24 h average irradiances gave factor-of-two differences in chlorophyll concentrations compared to the use of a diel irradiance pattern with the same 24 h average value.

  5. Landscape response to rare flood events: a feedback cycle in channel-hillslope coupling

    NASA Astrophysics Data System (ADS)

    Golly, Antonius; Turowski, Jens; Hovius, Niels; Badoux, Alexandre

    2017-04-01

    Fluvial channels and the surrounding landscapes are in a permanent feedback relation, exchanging mass and energy. Only rarely we get the opportunity to observe the processes at work and study the underlying cause and effect relations. This is especially difficult, since processes can be highly non-linear, and the response to a trigger may occur after a lag time such that their correspondence is not immediately obvious. In the Erlenbach, a mountain stream in the Swiss Prealps, we study the mechanistic relations between in-channel hydrology, channel morphology, external climatic forcing and the surrounding sediment sources to identify relevant controls of sediment input and their characteristic scales. Here, we present time-lapse observations of a suspended slow-moving landslide complex with a direct connection to the channel. The channel-hillslope system was in a stable system state for several months. Only after a flood event, in which a channel step was eroded at the base of the hillslope, the hillslope was destabilized through debuttressing. As a consequence, the landslide was reactivated and entered a sustained phase of integral motion. The response phase ended when the landslide material reached the channel and formed a new channel step, re-buttressing the hillslope. The observations reveal that, at least in the Erlenbach, sediment input from the hillslopes is not a uniform process controlled by precipitation only. Instead, a perturbation of the system in form of the erosion of an alluvial channel step was necessary to initiate the feedback cycle. The observation illustrates the importance of a thorough identification of the process mechanics to understand the sediment dynamics and the formation of landscapes on long time-scales.

  6. Transport of logs coupled to channel morphodynamics in a laboratory experiment

    NASA Astrophysics Data System (ADS)

    Tal, M.; Metivier, F.; Piégay, H.; Limare, A.

    2009-12-01

    Wood introduced to a river obstructs the flow and alters the channel hydraulics, exerting a first-order control on channel morphology across a wide range of scales, from channel roughness and surface grain size to the creation of in-channel features, channel patterns, and the formation of floodplains and valley bottom landforms. Much of our understanding of the behavior of wood in rivers is based on studies in relatively pristine systems which are characterized by riparian forests with trees that are very large compared to the size of individual channels. In such systems a single tree introduced into the channel can remain there for several decades and have significant effects on the local geomorphology. The most important impact of historical river and riparian forest management has been a reduction in the quantity and size of wood input, leading to decreased wood storage and increased mobility. Wood in a river increases the risk of flooding and is an obstacle for navigation. As such, river management laws in populated areas typically mandate wholesale removal of woody debris. However, wood has been shown to provide important ecological benefits by increasing the complexity of channel morphology necessary to support a diverse aquatic ecosystem. In order to inform management practices that balance societal needs, public safety, and the ecological health of river systems, it is necessary to characterize how wood is transferred through a system. We are using a physical model to quantify the spatial and temporal dynamics of woody debris storage and transfer through a reach and relating transport dynamics to channel morphodynamics. We use a Moiré contouring method to measure bed topography and flow depth and perform particle tracking on individual logs.

  7. Quantum calculations on water in the KcsA channel cavity with permeant and non-permeant ions

    SciTech Connect

    Kariev, Alisher M.; Green, Michael E.

    2009-04-30

    Different ions in the pore of the KcsA channel behave differently, and we relate this to their solvation. We show that the selectivity is dependent, in part, on the solvation in the cavity (sometimes referred to as the vestibule, it is the region containing water molecules between the intracellular gate and the selectivity filter at the extracellular end of the pore). We have shown earlier that potassium is more dependent at the upper end of the cavity region on solvation by the threonines there, while sodium ion has more water molecules as ligands. In addition, sodium ion is placed asymmetrically, while potassium is nearly exactly symmetric with respect to the four-fold symmetry of the channel. We have now extended these calculations to rubidium and cesium ions, and find that rubidium solvation resembles that of potassium (and both are permeant ions), while cesium resembles sodium (and both are non-permeant), in terms of the geometry of up to eight hydrating, and four non-hydrating, water molecules. In each case, a maximum of 12 water molecules are relevant to the calculation. The placement of the water molecules in the two cases is essentially the same as found from the electron density in the X-ray structure of Zhou and MacKinnon. For Na+ and K+, we show that energy decreases from bulk to the cavity to the lowest position in the selectivity filter (accurate energy could not be calculated for the heavier ions). A separate calculation shows that fixing the Na+ ion at the position of the K+ minimum, followed by re-optimization produced a significantly modified system, not something that could be produced by thermal fluctuations. Moving the K+ into the Na+ position in the upper cavity led to a small increase in energy, ≈ 3 kBT, but was accompanied by large shifts in the positions of hydrating waters, which would create a major kinetic barrier. Therefore, thermal fluctuations could not invalidate the conclusions of the main calculations.

  8. Intracellular calcium level is an important factor influencing ion channel modulations by PLC-coupled metabotropic receptors in hippocampal neurons.

    PubMed

    Sugawara, Yuto; Echigo, Ryousuke; Kashima, Kousuke; Minami, Hanae; Watanabe, Megumi; Nishikawa, Yuiko; Muranishi, Miho; Yoneda, Mitsugu; Ohno-Shosaku, Takako

    2013-05-28

    Signaling pathways involving phospholipase C (PLC) are involved in various neural functions. Understanding how these pathways are regulated will lead to a better understanding of their roles in neural functions. Previous studies demonstrated that receptor-driven PLCβ activation depends on intracellular Ca(2+) concentration ([Ca(2+)]i), suggesting the possibility that PLCβ-dependent cellular responses are basically Ca(2+) dependent. To test this possibility, we examined whether modulations of ion channels driven by PLC-coupled metabotropic receptors are sensitive to [Ca(2+)]i using cultured hippocampal neurons. Muscarinic activation triggered an inward current at -100 mV (the equilibrium potential for K(+)) in a subpopulation of neurons. This current response was suppressed by pirenzepine (an M1-preferring antagonist), PLC inhibitor, non-selective cation channel blocker, and lowering [Ca(2+)]i. Using the neurons showing no response at -100 mV, effects of muscarinic activation on K(+) channels were examined at -40 mV. Muscarinic activation induced a transient decrease of the holding outward current. This current response was mimicked and occluded by XE991, an M-current K(+) channel blocker, suppressed by pirenzepine, PLC inhibitor and lowering [Ca(2+)]i, and enhanced by elevating [Ca(2+)]i. Similar results were obtained when group I metabotropic glutamate receptors were activated instead of muscarinic receptors. These results clearly show that ion channel modulations driven by PLC-coupled metabotropic receptors are dependent on [Ca(2+)]i, supporting the hypothesis that cellular responses induced by receptor-driven PLCβ activation are basically Ca(2+) dependent.

  9. On the calculation of resonances by means of analytic continuation in coupling constant

    NASA Astrophysics Data System (ADS)

    Horáček, J.; Paidarová, I.

    2010-11-01

    The method of analytic continuation in the coupling constant in combination with the use of statistical Padé approximation designed to determine resonance parameters is introduced. It is shown that standard quantum chemistry codes provide accurate data which can be used for the process of analytic continuation in coupling constant. Resonance parameters, both the energy and the width, can be inferred for real molecules with accuracy comparable to other more elaborated methods.

  10. Resonances in SN2 reactions: Two-mode quantum calculations for Cl-+CH3Br on a coupled-cluster potential energy surface

    NASA Astrophysics Data System (ADS)

    Schmatz, Stefan; Botschwina, Peter; Hauschildt, Jan; Schinke, Reinhard

    2002-12-01

    An effective two-dimensional potential energy surface has been constructed for the SN2 reaction Cl-+CH3Br→ClCH3+Br- from coupled-cluster calculations with a large basis set. In the quantum dynamics calculations Radau coordinates were employed to describe the Cl-C and C-Br stretching modes. Making use of the filter diagonalization method and an optical potential, bound states as well as resonance states up to energies far above the dissociation threshold have been calculated. The resonance widths fluctuate over several orders of magnitude. In addition to a majority of Feshbach-type resonances there are also exceedingly long-lived shape resonances, which can only decay by tunneling. Owing to a smaller width of the potential barrier and a larger density of states, tunneling through the barrier is more important for Cl-+CH3Br than for Cl-+CH3Cl despite the larger total mass of this system. Excitation of the C-Br stretching vibration enhances the tunneling probability of the entrance channel complex.

  11. Relativistic coupled-cluster calculations of {sup 20}Ne, {sup 40}Ar, {sup 84}Kr, and {sup 129}Xe: Correlation energies and dipole polarizabilities

    SciTech Connect

    Mani, B. K.; Angom, D.; Latha, K. V. P.

    2009-12-15

    We have carried out a detailed and systematic study of the correlation energies of inert gas atoms Ne, Ar, Kr, and Xe using relativistic many-body perturbation theory and relativistic coupled-cluster theory. In the relativistic coupled-cluster calculations, we implement perturbative triples and include these in the correlation energy calculations. We then calculate the dipole polarizability of the ground states using perturbed coupled-cluster theory.

  12. Neutron/gamma coupled library generation and gamma transport calculation with KARMA 1.2

    SciTech Connect

    Hong, S. G.; Kim, K. S.; Cho, J. Y.; Lee, K. H.

    2012-07-01

    KAERI has developed a lattice transport calculation code KARMA and its multi-group cross section library generation system. Recently, the multi-group cross section library generation system has included a gamma cross section generation capability and KARMA also has been improved to include a gamma transport calculation module. This paper addresses the multi-group gamma cross section generation capability for the KARMA 1.2 code and the preliminary test results of the KARMA 1.2 gamma transport calculations. The gamma transport calculation with KARMA 1.2 gives the gamma flux, gamma smeared power, and gamma energy deposition distributions. The results of the KARMA gamma calculations were compared with those of HELIOS and they showed that KARMA 1.2 gives reasonable gamma transport calculation results. (authors)

  13. Treating Subvalence Correlation Effects in Domain Based Pair Natural Orbital Coupled Cluster Calculations: An Out-of-the-Box Approach.

    PubMed

    Bistoni, Giovanni; Riplinger, Christoph; Minenkov, Yury; Cavallo, Luigi; Auer, Alexander A; Neese, Frank

    2017-07-11

    The validity of the main approximations used in canonical and domain based pair natural orbital coupled cluster methods (CCSD(T) and DLPNO-CCSD(T), respectively) in standard chemical applications is discussed. In particular, we investigate the dependence of the results on the number of electrons included in the correlation treatment in frozen-core (FC) calculations and on the main threshold governing the accuracy of DLPNO all-electron (AE) calculations. Initially, scalar relativistic orbital energies for the ground state of the atoms from Li to Rn in the periodic table are calculated. An energy criterion is used for determining the orbitals that can be excluded from the correlation treatment in FC coupled cluster calculations without significant loss of accuracy. The heterolytic dissociation energy (HDE) of a series of metal compounds (LiF, NaF, AlF3, CaF2, CuF, GaF3, YF3, AgF, InF3, HfF4, and AuF) is calculated at the canonical CCSD(T) level, and the dependence of the results on the number of correlated electrons is investigated. Although for many of the studied reactions subvalence correlation effects contribute significantly to the HDE, the use of an energy criterion permits a conservative definition of the size of the core, allowing FC calculations to be performed in a black-box fashion while retaining chemical accuracy. A comparison of the CCSD and the DLPNO-CCSD methods in describing the core-core, core-valence, and valence-valence components of the correlation energy is given. It is found that more conservative thresholds must be used for electron pairs containing at least one core electron in order to achieve high accuracy in AE DLPNO-CCSD calculations relative to FC calculations. With the new settings, the DLPNO-CCSD method reproduces canonical CCSD results in both AE and FC calculations with the same accuracy.

  14. RIM - binding proteins (RBPs) couple Rab3 - interacting molecules (RIMs) to voltage - gated Ca2+ channels

    PubMed Central

    Hibino, H.; Pironkova, R.; Onwumere, O.; Vologodskaia, M.; Hudspeth, A. J.; Lesage, F.

    2007-01-01

    Summary Ca2+ influx through voltage-gated channels initiates the exocytotic fusion of synaptic vesicles to the plasma membrane. Here we show that RIM-binding proteins (RBPs), which associate with Ca2+ channels in hair cells, photoreceptors, and neurons, interact with α1D (L-type) and α1B (N-type) Ca2+-channel subunits. RBPs contain three Src homology 3 domains that bind to proline-rich motifs in α1 subunits and Rab3-interacting molecules (RIMs). Overexpression in PC12 cells of fusion proteins that suppress the interactions of RBPs with RIMs and α1 augments the exocytosis triggered by depolarization. RBPs may regulate the strength of synaptic transmission by creating a functional link between the synaptic-vesicle tethering apparatus, which includes RIMs and Rab3, and the fusion machinery, which includes Ca2+ channels and the SNARE complex. PMID:11988172

  15. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

    NASA Astrophysics Data System (ADS)

    Roemelt, Michael

    2015-07-01

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.

  16. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

    SciTech Connect

    Roemelt, Michael

    2015-07-28

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.

  17. Tight coupling of rubidium conductance and inactivation in human KCNQ1 potassium channels

    PubMed Central

    Seebohm, Guiscard; Sanguinetti, Michael C; Pusch, Michael

    2003-01-01

    KCNQ1 K+ channels in humans are important for repolarization of cardiac action potentials and for K+ secretion in the inner ear. The pore-forming channel subunits form heteromeric complexes with small regulatory subunits of the KCNE family, in particular with KCNE1 to form channels that conduct a slow delayed rectifier K+ current, Iks. This association leads to alteration of biophysical properties, including a slowing of activation, a suppression of inactivation and an increase of the apparent single-channel conductance. In addition, inward Rb+ currents conducted by homomeric KCNQ1 channels are about threefold larger than K+ currents, whereas heteromeric KCNQ1-KCNE1 channels have smaller inward Rb+ currents compared to K+ currents. We determined inactivation properties and compared K+vs. Rb+ inward currents for channels formed by co-assembly of KCNQ1 with KCNE1, KCNE3 and KCNE5, and for homomeric KCNQ1 channels with point mutations in the pore helix S5 or S6 transmembrane domains. Several of the channels with point mutations eliminated the apparent inactivation of KCNQ1, as described previously (Seebohm et al. 2001). We found that the extent of inactivation and the ratio of Rb+/K+ currents were positively correlated. Since the effect of Rb+ on the current size has been shown previously to be related to a fast ‘flickery’ process, our results suggest that inactivation of KCNQ1 channels is related to a fast flicker of the open channel. A kinetic model incorporating two open states, no explicit inactivated state and a fast flicker that is different for the two open states is able to account for the apparent inactivation and the correlation of inactivation and large Rb+ currents. We conclude that an association between KCNQ1 and KCNE subunits or removal of inactivation by mutation of KCNQ1 stabilizes the open conformation of the pore principally by altering an interaction between the pore helix and the selectivity filter and with S5/S6 domains. PMID:14561821

  18. Continuum electrostatic calculations of the pKa of ionizable residues in an ion channel: dynamic vs. static input structure.

    PubMed

    Aguilella-Arzo, M; Aguilella, V M

    2010-04-01

    We have computed the pK(a)'s of the ionizable residues of a protein ion channel, the Staphylococcus aureus toxin alpha-hemolysin, by using two types of input structures, namely the crystal structure of the heptameric alpha-hemolysin and a set of over four hundred snapshots from a 4.38 ns Molecular Dynamics simulation of the protein inserted in a phospholipid planar bilayer. The comparison of the dynamic picture provided by the Molecular Simulation with the static one based on the X-ray crystal structure of the protein embedded in a lipid membrane allows analyzing the influence of the fluctuations in the protein structure on its ionization properties. We find that the use of the dynamic structure provides interesting information about the sensitivity of the computed pK(a) of a given residue to small changes in the local structure. The calculated pK(a) are consistent with previous indirect estimations obtained from single-channel conductance and selectivity measurements.

  19. Phosphoinositide 3-kinase isoforms selectively couple receptors to vascular L-type Ca(2+) channels.

    PubMed

    Macrez, N; Mironneau, C; Carricaburu, V; Quignard, J F; Babich, A; Czupalla, C; Nürnberg, B; Mironneau, J

    2001-10-12

    Heterodimeric class I phosphoinositide 3-kinase (PI3K) has been shown to be involved in the stimulation of voltage-gated Ca(2+) channels by various mediators. In this study, we bring evidences that vascular L-type Ca(2+) channels can be modulated by both tyrosine kinase-regulated class Ia and G protein-regulated class Ib PI3Ks. Purified recombinant PI3Ks increased the peak Ca(2+) channel current density when applied intracellularly. Furthermore, PI3Kalpha-, beta-, and delta-mediated stimulations of Ca(2+) channel currents were increased by preactivation by a phosphotyrosyl peptide, whereas PI3Kgamma- and beta-mediated effects were increased by Gbetagamma. In freshly isolated and cultured vascular myocytes, angiotensin II and Gbetagamma stimulated L-type Ca(2+) channel current. In contrast, platelet-derived growth factor (PDGF)-BB and the phosphotyrosyl peptide did not stimulate Ca(2+) channel current in freshly isolated cells despite the presence of endogenous PDGF receptors and PI3Kalpha and PI3Kgamma. Interestingly, when endogenous PI3Kbeta expression arose in cultured myocytes, both PDGF and phosphotyrosyl peptide stimulated Ca(2+) channels through PI3Kbeta, as revealed by the inhibitory effect of an anti-PI3Kbeta antibody. These results suggest that endogenous PI3Kbeta but not PI3Kalpha is specifically involved in PDGF receptor-induced stimulation of Ca(2+) channels and that different isoforms of PI3K regulate physiological increases of Ca(2+) influx in vascular myocytes stimulated by vasoconstrictor or growth factor.

  20. Effect of the coupling channel on the excitation of hydrogenic atoms by the impact of protons and antiprotons

    NASA Astrophysics Data System (ADS)

    Tantawi, Reda S.

    2014-02-01

    Excitation of hydrogenic atoms H, He+ and Li++ initially in the 2p excited state to the n = 3 states by impact of protons and antiprotons is studied using the single-center atomic orbital close-coupling formalism in its impact parameter approach. The calculations cover the incident energy range from 1 to 1000 keV, in which the straight-line trajectory description of nuclear motion is applicable and the inertial confinement plasma research is of main interest. The influences of couplings between the n = 2 states, as well as the back coupling to the 2p initial state, on the excitation processes are investigated. Including the back couplings is found to be more important in the case of proton scattering than in the case of antiproton, and neglecting couplings between the n = 2 states is found to increase the effect of the sign of the projectile's charge. The calculated cross sections for the H atom are compared with those obtained by previous theoretical calculations.

  1. Climate variability and predictability associated with the Indo-Pacific Oceanic Channel Dynamics in the CCSM4 Coupled System Model

    NASA Astrophysics Data System (ADS)

    Yuan, Dongliang; Xu, Peng; Xu, Tengfei

    2017-01-01

    An experiment using the Community Climate System Model (CCSM4), a participant of the Coupled Model Intercomparison Project phase-5 (CMIP5), is analyzed to assess the skills of this model in simulating and predicting the climate variabilities associated with the oceanic channel dynamics across the Indo-Pacific Oceans. The results of these analyses suggest that the model is able to reproduce the observed lag correlation between the oceanic anomalies in the southeastern tropical Indian Ocean and those in the cold tongue in the eastern equatorial Pacific Ocean at a time lag of 1 year. This success may be largely attributed to the successful simulation of the interannual variations of the Indonesian Throughflow, which carries the anomalies of the Indian Ocean Dipole (IOD) into the western equatorial Pacific Ocean to produce subsurface temperature anomalies, which in turn propagate to the eastern equatorial Pacific to generate ENSO. This connection is termed the "oceanic channel dynamics" and is shown to be consistent with the observational analyses. However, the model simulates a weaker connection between the IOD and the interannual variability of the Indonesian Throughflow transport than found in the observations. In addition, the model overestimates the westerly wind anomalies in the western-central equatorial Pacific in the year following the IOD, which forces unrealistic upwelling Rossby waves in the western equatorial Pacific and downwelling Kelvin waves in the east. This assessment suggests that the CCSM4 coupled climate system has underestimated the oceanic channel dynamics and overestimated the atmospheric bridge processes.

  2. Mechanism for selectivity-inactivation coupling in KcsA potassium channels.

    PubMed

    Cheng, Wayland W L; McCoy, Jason G; Thompson, Ameer N; Nichols, Colin G; Nimigean, Crina M

    2011-03-29

    Structures of the prokaryotic K(+) channel, KcsA, highlight the role of the selectivity filter carbonyls from the GYG signature sequence in determining a highly selective pore, but channels displaying this sequence vary widely in their cation selectivity. Furthermore, variable selectivity can be found within the same channel during a process called C-type inactivation. We investigated the mechanism for changes in selectivity associated with inactivation in a model K(+) channel, KcsA. We found that E71A, a noninactivating KcsA mutant in which a hydrogen-bond behind the selectivity filter is disrupted, also displays decreased K(+) selectivity. In E71A channels, Na(+) permeates at higher rates as seen with and flux measurements and analysis of intracellular Na(+) block. Crystal structures of E71A reveal that the selectivity filter no longer assumes the "collapsed," presumed inactivated, conformation in low K(+), but a "flipped" conformation, that is also observed in high K(+), high Na(+), and even Na(+) only conditions. The data reveal the importance of the E71-D80 interaction in both favoring inactivation and maintaining high K(+) selectivity. We propose a molecular mechanism by which inactivation and K(+) selectivity are linked, a mechanism that may also be at work in other channels containing the canonical GYG signature sequence.

  3. Mechanism for Selectivity-inactivation Coupling in KcsA Potassium Channels

    SciTech Connect

    W Cheng; J McCoy; A Thompson; C Nichols; C Nimigean

    2011-12-31

    Structures of the prokaryotic K{sup +} channel, KcsA, highlight the role of the selectivity filter carbonyls from the GYG signature sequence in determining a highly selective pore, but channels displaying this sequence vary widely in their cation selectivity. Furthermore, variable selectivity can be found within the same channel during a process called C-type inactivation. We investigated the mechanism for changes in selectivity associated with inactivation in a model K{sup +} channel, KcsA. We found that E71A, a noninactivating KcsA mutant in which a hydrogen-bond behind the selectivity filter is disrupted, also displays decreased K{sup +} selectivity. In E71A channels, Na{sup +} permeates at higher rates as seen with {sup 86}Rb{sup +} and {sup 22}Na{sup +} flux measurements and analysis of intracellular Na{sup +} block. Crystal structures of E71A reveal that the selectivity filter no longer assumes the 'collapsed,' presumed inactivated, conformation in low K{sup +}, but a 'flipped' conformation, that is also observed in high K{sup +}, high Na{sup +}, and even Na{sup +} only conditions. The data reveal the importance of the E71-D80 interaction in both favoring inactivation and maintaining high K{sup +} selectivity. We propose a molecular mechanism by which inactivation and K{sup +} selectivity are linked, a mechanism that may also be at work in other channels containing the canonical GYG signature sequence.

  4. An integrated model coupling open-channel flow, turbidity current and flow exchanges between main river and tributaries in Xiaolangdi Reservoir, China

    NASA Astrophysics Data System (ADS)

    Wang, Zenghui; Xia, Junqiang; Li, Tao; Deng, Shanshan; Zhang, Junhua

    2016-12-01

    The ever growing importance of sustainable management of reservoir sedimentation has promoted the development and applications of turbidity current models. However, there are few effective and practical models in literature for turbidity currents in a reservoir where the impounded area involves both the main river and its many tributaries. An integrated numerical model coupling open-channel flow, turbidity current and flow exchanges between main river and tributaries is proposed, which can simulate the complex flow and sediment transport in a reservoir where these three physical processes coexist. The model consists of two sets of governing equations for the open-channel flow and turbidity current, which are based on the modified St. Venant equations by taking into account the effect of lateral flow exchanges. These two sets of equations are solved in the finite volume method framework and the solutions are executed in an alternating calculation mode. Different methods are respectively proposed to calculate the discharge of flow exchange caused by free surface gradient and turbidity current intrusion. For the surface-gradient driven flow exchange, a storage cell method, which re-defines the relationship between water level and representative cross-sectional area, is used to update the water level at confluence. For the turbidity current intrusion, a discharge formula is proposed based on the analysis of the energy and momentum transformation in the intruding turbid water body. This formula differs from previous ones in that the effect of tributary bed slope is considered. Two events of water-sediment regulation conducted in the Xiaolangdi Reservoir in 2004 and 2006 were simulated to test the ability of this model. The predicted reservoir drawdown process, the turbidity current evolution and the sediment venting efficiency were in close agreement with the measurements. The necessity to couple the flow exchanges was demonstrated by comparing the performance of the

  5. On the Usage of Locally Dense Basis Sets in the Calculation of NMR Indirect Nuclear Spin-Spin Coupling Constants

    NASA Astrophysics Data System (ADS)

    Sanchez, Marina; Provasi, Patricio F.; Aucar, Gustavo A.; Sauer, Stephan P. A.

    Locally dense basis sets (calculations of vicinal fluorine-fluorine indirect nuclear spin-spin couplings in several saturated and unsaturated fluorinated hydrocarbons. We find that the choice of the basis set for each atom belonging to our studied model compounds depends on its location with respect to the coupled fluorine atoms and on the cis/trans or synperiplanar/antiperiplanar conformation of the molecule. Carbon atoms in the bonding path connecting the coupled fluorine atoms have to be described with better basis sets than the carbon atoms outside this path. For the hydrogen atoms directly connected to the coupling pathway in molecules with trans or antiperiplanar conformations and for all hydrogen atoms not directly connected to the coupling pathway one can employ a minimal basis set with only one s-function. Employing these type of LDBSs we can reduce the number of necessary basis functions by about 30% without losing more than about 1 Hz in accuracy. The analysis of the four contributions to the vicinal fluorine-fluorine coupling constants shows that the non-contact orbital paramagnetic term is the most important contribution followed by the also non-contact spin-dipolar term. The Fermi contact term is the largest contribution only in the synperiplanar conformations of 1,2-difluoroethane and -propane.

  6. A Novel Field-Circuit FEM Modeling and Channel Gain Estimation for Galvanic Coupling Real IBC Measurements.

    PubMed

    Gao, Yue-Ming; Wu, Zhu-Mei; Pun, Sio-Hang; Mak, Peng-Un; Vai, Mang-I; Du, Min

    2016-04-02

    Existing research on human channel modeling of galvanic coupling intra-body communication (IBC) is primarily focused on the human body itself. Although galvanic coupling IBC is less disturbed by external influences during signal transmission, there are inevitable factors in real measurement scenarios such as the parasitic impedance of electrodes, impedance matching of the transceiver, etc. which might lead to deviations between the human model and the in vivo measurements. This paper proposes a field-circuit finite element method (FEM) model of galvanic coupling IBC in a real measurement environment to estimate the human channel gain. First an anisotropic concentric cylinder model of the electric field intra-body communication for human limbs was developed based on the galvanic method. Then the electric field model was combined with several impedance elements, which were equivalent in terms of parasitic impedance of the electrodes, input and output impedance of the transceiver, establishing a field-circuit FEM model. The results indicated that a circuit module equivalent to external factors can be added to the field-circuit model, which makes this model more complete, and the estimations based on the proposed field-circuit are in better agreement with the corresponding measurement results.

  7. A Novel Field-Circuit FEM Modeling and Channel Gain Estimation for Galvanic Coupling Real IBC Measurements

    PubMed Central

    Gao, Yue-Ming; Wu, Zhu-Mei; Pun, Sio-Hang; Mak, Peng-Un; Vai, Mang-I; Du, Min

    2016-01-01

    Existing research on human channel modeling of galvanic coupling intra-body communication (IBC) is primarily focused on the human body itself. Although galvanic coupling IBC is less disturbed by external influences during signal transmission, there are inevitable factors in real measurement scenarios such as the parasitic impedance of electrodes, impedance matching of the transceiver, etc. which might lead to deviations between the human model and the in vivo measurements. This paper proposes a field-circuit finite element method (FEM) model of galvanic coupling IBC in a real measurement environment to estimate the human channel gain. First an anisotropic concentric cylinder model of the electric field intra-body communication for human limbs was developed based on the galvanic method. Then the electric field model was combined with several impedance elements, which were equivalent in terms of parasitic impedance of the electrodes, input and output impedance of the transceiver, establishing a field-circuit FEM model. The results indicated that a circuit module equivalent to external factors can be added to the field-circuit model, which makes this model more complete, and the estimations based on the proposed field-circuit are in better agreement with the corresponding measurement results. PMID:27049386

  8. Remodeling excitation-contraction coupling of hypertrophied ventricular myocytes is dependent on T-type calcium channels expression.

    PubMed

    Takebayashi, Satoshi; Li, Yulong; Kaku, Toshihiko; Inagaki, Shuichiro; Hashimoto, Yutaka; Kimura, Kazuhiro; Miyamoto, Shinji; Hadama, Tetsuo; Ono, Katsushige

    2006-06-30

    We utilized Wistar rats with monocrotaline (MCT)-induced right ventricular hypertrophy (RVH) in order to evaluate the T-type Ca2+ channel current (ICaT) for myocardial contraction. RT-PCR provides that mRNA for T-type Ca2+ channel alpha1-subunits in hypertrophied myocytes was significantly higher than those in control rats (alpha1G; 264+/-36%, alpha1H; 191+/-34%; P<0.05). By whole-cell patch-clamp study, ICaT was recorded only in hypertrophied myocytes but not in control myocytes. The application of 50 nmol/L nifedipine reduced the twitch tension of the right ventricles equally in the control and RVH rats. On the other hand, 0.5 micromol/L mibefradil, a T-type Ca2+ channel blocker, strongly inhibited the twitch tension of the RVH muscle (control 6.4+/-0.8% vs. RVH 20.0+/-2.3% at 5 Hz; P<0.01). In conclusion, our results indicate the functional expression of T-type Ca2+ channels in the hypertrophied heart and their contribution to the remodeling of excitation-contraction coupling in the cardiac myocyte.

  9. Electromechanical coupling and design considerations in single-layer MoS2 suspended-channel transistors and resonators

    NASA Astrophysics Data System (ADS)

    Yang, Rui; Islam, Arnob; Feng, Philip X.-L.

    2015-11-01

    We report on the analysis of electromechanical coupling effects in suspended doubly-clamped single-layer MoS2 structures, and the designs of suspended-channel field-effect transistors (FETs) and vibrating-channel nanoelectromechanical resonators. In DC gating scenario, signal transduction processes including electrostatic actuation, deflection, straining on bandgap, mobility, carrier density and their intricate cross-interactions, have been analyzed considering strain-enhanced mobility (by up to 4 times), to determine the transfer characteristics. In AC gating scenario and resonant operations (using 100 MHz and 1 GHz devices as relevant targets), we demonstrate that the vibrating-channel MoS2 devices can offer enhanced signals (than the zero-bandgap graphene counterparts), thanks to the resonant straining effects on electron transport of the semiconducting channel. We also show dependence of signal intensity and signal-to-background ratio (SBR) on device geometries and scaling effects, with SBR enhancement by a factor of ~8 for resonance signal, which provide guidelines toward designing future devices with desirable parameters.

  10. Hydrodynamic Coupling in Microbially Mediated Fracture Mineralization: Formation of Self-Organized Groundwater Flow Channels

    NASA Astrophysics Data System (ADS)

    Lunn, R. J.; El Mountassir, G.; MacLachlan, E.; Moir, H.

    2013-12-01

    Evidence of fossilized microorganisms embedded within mineral veins and mineral-filled fractures has been observed in a wide range of geological environments. Microorganisms can act as sites for mineral nucleation and also contribute to mineral precipitation by inducing local geochemical changes. In this study, we explore fundamental controls on microbially induced mineralization in rock fractures. Specifically, we systematically investigate the influence of hydrodynamics (velocity, flow rate, aperture) on microbially mediated calcite precipitation. We use a case study of microbially induced calcite precipitation as a model biomineralization system to investigate potential feedback mechanisms between the temporally varying patterns of mineral precipitation within a fracture and the resulting variations in the local velocity field. Fractures are represented as a series of precision-etched parallel channels between a pair of sealed Perspex plates. Multiple channels are designed to maintain a constant flow rate, whilst independently adjusting channel aperture and width to explore the effects of aperture and fluid velocity on biomineral precipitation. Our experimental results demonstrate that a feedback mechanism exists between the gradual reduction in fracture aperture due to precipitation, and its effect on the local fluid velocity. This feedback results in mineral fill distributions that focus flow into a small number of self-organizing channels that remain open, ultimately controlling the final aperture profile that governs flow within the fracture. This feedback mechanism exists because precipitation on the fracture walls (as opposed to in solution) requires the bacteria to be transported to the fracture surface. Bacteria settle out of a quiescent solution at a velocity that is dependent on individual floc size and density. This settling velocity competes with the bed shear velocity, inhibiting deposition via entrainment. As precipitation progresses, the flow

  11. Calculation of coupled secular oscillation frequencies and axial secular frequency in a nonlinear ion trap by a homotopy method.

    PubMed

    Doroudi, Alireza

    2009-11-01

    In this paper the homotopy perturbation method is used for calculation of the frequencies of the coupled secular oscillations and axial secular frequencies of a nonlinear ion trap. The motion of the ion in a rapidly oscillating field is transformed to the motion in an effective potential. The equations of ion motion in the effective potential are in the form of a Duffing-like equation. The homotopy perturbation method is used for solving the resulted system of coupled nonlinear differential equations and the resulted axial equation for obtaining the expressions for ion secular frequencies as a function of nonlinear field parameters and amplitudes of oscillations. The calculated axial secular frequencies are compared with the results of Lindstedt-Poincare method and the exact results.

  12. Hanle precession in the presence of energy-dependent coupling between localized states and an epitaxial graphene spin channel

    NASA Astrophysics Data System (ADS)

    van den Berg, J. J.; Kaverzin, A.; van Wees, B. J.

    2016-12-01

    Hanle spin precession measurements are a common method to extract the spin transport properties of graphene. In epitaxial graphene on silicon carbide, these measurements show unexpected behavior, due to presumed localized states in the carbon buffer layer that is present between the channel and the substrate. As a consequence, the Hanle curve narrows in its magnetic field dependence and can show an unconventional shape, which has been experimentally observed and modeled in previous studies. Here, we extend the previously developed model by assuming that the localized states are charge traps, that have a power-law distribution of trapping times. Our simulations show that the energy dependence of these trapping times can be extracted from the temperature evolution of the Hanle curve, which was previously observed in experiments. Our extended model gives better insight into what processes play a role when a spin channel is coupled to localized states and their relation to the experimental observations.

  13. Calculation of the heavy-hadron axial couplings g1, g2, and g3 using lattice QCD

    SciTech Connect

    Will Detmold, David Lin, Stefan Meinel

    2012-06-01

    In a recent paper [arXiv:1109.2480] we have reported on a lattice QCD calculation of the heavy-hadron axial couplings g{sub 1}, g{sub 2}, and g{sub 3}. These quantities are low-energy constants of heavy-hadron chiral perturbation theory (HH{chi}PT) and are related to the B*B{pi}, {Sigma}{sub b}*{Sigma}{sub b}{pi}, and {Sigma}{sub b}{sup (*)}{Lambda}{sub b}{pi} couplings. In the following, we discuss important details of the calculation and give further results. To determine the axial couplings, we explicitly match the matrix elements of the axial current in QCD with the corresponding matrix elements in HH{chi}PT. We construct the ratios of correlation functions used to calculate the matrix elements in lattice QCD, and study the contributions from excited states. We present the complete numerical results and discuss the data analysis in depth. In particular, we demonstrate the convergence of SU(4|2) HH{chi}PT for the axial current matrix elements at pion masses up to about 400 MeV and show the impact of the nonanalytic loop contributions. Finally, we present additional predictions for strong and radiative decay widths of charm and bottom baryons.

  14. Irreversibility analysis of hydromagnetic flow of couple stress fluid with radiative heat in a channel filled with a porous medium

    NASA Astrophysics Data System (ADS)

    Eegunjobi, A. S.; Makinde, O. D.

    Numerical analysis of the intrinsic irreversibility of a mixed convection hydromagnetic flow of an electrically conducting couple stress fluid through upright channel filled with a saturated porous medium and radiative heat transfer was carried out. The thermodynamics first and second laws were employed to examine the problem. We obtained the dimensionless nonlinear differential equations and solves numerically with shooting procedure joined with a fourth order Runge-Kutta-Fehlberg integration scheme. The temperature and velocity obtained, used to analyse the entropy generation rate together with some various physical parameters of the flow. Our results are presented graphically and talk over.

  15. Strong coupling between a permalloy ferromagnetic contact and helical edge channel in a narrow HgTe quantum well

    SciTech Connect

    Kononov, A.; Egorov, S. V.; Kvon, Z. D.; Mikhailov, N. N.; Dvoretsky, S. A.; Deviatov, E. V.

    2016-11-15

    We experimentally investigate spin-polarized electron transport between a permalloy ferromagnet and the edge of a two-dimensional electron system with band inversion, realized in a narrow, 8 nm wide, HgTe quantum well. In zero magnetic field, we observe strong asymmetry of the edge potential distribution with respect to the ferromagnetic ground lead. This result indicates that the helical edge channel, specific for the structures with band inversion even at the conductive bulk, is strongly coupled to the ferromagnetic side contact, possibly due to the effects of proximity magnetization. This allows selective and spin-sensitive contacting of helical edge states.

  16. Second-law analysis for buoyancy-driven hydromagnetic couple stress fluid flow through a porous channel

    NASA Astrophysics Data System (ADS)

    Kareem, Semiu O.; Adesanya, Samuel O.; Vincent, Uchechukwu E.

    2016-08-01

    This paper examines the combined effects of the buoyancy force and of the magnetic field on the entropy generation rate in the flow of a couple stress fluid through a porous vertical channel. The flow's dynamical equations were non-dimensionalised and solved via the application of the Adomian decomposition method (ADM). Variations of some thermo-physical parameters were conducted and discussed, with regard to the physics of the fluid. Our result shows that the entropy generation rate increases as the buoyancy increases in the fluid. In addition, the irreversibility in the flow system results mainly from the fluid's viscosity, ohmic heating, and the buoyancy.

  17. Coupled Motions between Pore and Voltage-Sensor Domains: A Model for Shaker B, a Voltage-Gated Potassium Channel

    PubMed Central

    Treptow, Werner; Maigret, Bernard; Chipot, Christophe; Tarek, Mounir

    2004-01-01

    A high-resolution crystal structure of KvAP, an archeabacterial voltage-gated potassium (Kv) channel, complexed with a monoclonal Fab fragment has been recently determined. Based on this structure, a mechanism for the activation (opening) of Kv channels has been put forward. This mechanism has since been criticized, suggesting that the resolved structure is not representative of the family of voltage-gated potassium channels. Here, we propose a model of the transmembrane domain of Shaker B, a well-characterized Kv channel, built by homology modeling and docking calculations. In this model, the positively charged S4 helices are oriented perpendicular to the membrane and localized in the groove between segments S5 and S6 of adjacent subunits. The structure and the dynamics of the full atomistic model embedded in a hydrated lipid bilayer were investigated by means of two large-scale molecular dynamics simulations under transmembrane-voltage conditions known to induce, respectively, the resting state (closed) and the activation (opening) of voltage-gated channels. Upon activation, the model undergoes conformational changes that lead to an increase of the hydration of the charged S4 helices, correlated with an upward translation and a tilting of the latter, concurrently with movements of the S5 helices and the activation gate. Although small, these conformational changes ultimately result in an alteration of the ion-conduction pathway. Our findings support the transporter model devised by Bezanilla and collaborators, and further underline the crucial role played by internal hydration in the activation of the channel. PMID:15454436

  18. Calculations of Motions and Loads Resulting from Gust Disturbances Acting Upon Aircraft in Coupled Flight

    DTIC Science & Technology

    1949-07-18

    Republic Aviation Corporation Report...Investigation of F-64 and B-50 Wing-Tip to Wing-Tip/Coupling Republic Aviation Corporation Report No. EDR-F905-1, July 15/ 1949 $-1-72 „,Ptairc <g) mi...U ! s -£- 3^ St—S —J Hf%^-~5 is tn eiiii Q ffi- 5]1 ******ID. CMICKIr RCVISKD REPUBLIC AVIATION -« CORPORATION

  19. A spreadsheet-coupled SOLGAS: A computerized thermodynamic equilibrium calculation tool. Revision 1

    SciTech Connect

    Trowbridge, L.D.; Leitnaker, J.M.

    1995-07-01

    SOLGAS, an early computer program for calculating equilibrium in a chemical system, has been made more user-friendly, and several ``bells and whistles`` have been added. The necessity to include elemental species has been eliminated. The input of large numbers of starting conditions has been automated. A revised spreadsheet-based format for entering data, including non-ideal binary and ternary mixtures, simplifies and reduces chances for error. Calculational errors by SOLGAS are flagged, and several programming errors are corrected. Auxiliary programs are available to assemble and partially automate plotting of large amounts of data. Thermodynamic input data can be changed on line. The program can be operated with or without a co-processor. Copies of the program, suitable for the IBM-PC or compatibles with at least 384 bytes of low RAM, are available from the authors. This user manual contains appendices with examples of the use of SOLGAS. These range from elementary examples, such as, the relationships among water, ice, and water vapor, to more complex systems: phase diagram calculation of UF{sub 4} and UF{sub 6} system; burning UF{sub 4} in fluorine; thermodynamic calculation of the Cl-F-O-H system; equilibria calculations in the CCl{sub 4}--CH{sub 3}OH system; and limitations applicable to aqueous solutions. An appendix also contains the source code.

  20. Self-consistent calculation of the coupling constant in the Gross-Pitaevskii equation

    SciTech Connect

    Cherny, A.Yu.; Brand, J.

    2004-10-01

    A method is proposed for a self-consistent evaluation of the coupling constant in the Gross-Pitaevskii equation without involving a pseudopotential replacement. A renormalization of the coupling constant occurs due to medium effects and the trapping potential, e.g., in quasi-1D or quasi-2D systems. It is shown that a simplified version of the Hartree-Fock-Bogoliubov approximation leads to a variational problem for both the condensate and a two-body wave function describing the behavior of a pair of bosons in the Bose-Einstein condensate. The resulting coupled equations are free of unphysical divergences. Particular cases of this scheme that admit analytical estimations are considered and compared to the literature. In addition to the well-known cases of low-dimensional trapping, crossover regimes can be studied. The values of the kinetic, interaction, external, and release energies in low dimensions are also evaluated and contributions due to short-range correlations are found to be substantial.

  1. Quantum chemistry calculations for molecules coupled to reservoirs: Formalism, implementation, and application to benzenedithiol

    NASA Astrophysics Data System (ADS)

    Arnold, A.; Weigend, F.; Evers, F.

    2007-05-01

    Modern quantum chemistry calculations are usually implemented for isolated systems—big molecules or atom clusters; total energy and particle number are fixed. However, in many situations, like quantum transport calculations or molecules in a electrochemical environment, the molecule can exchange particles (and energy) with a reservoir. Calculations for such cases require to switch from the canonical to a grand canonical description, where one fixes the chemical potential rather than particle number. To achieve this goal, the authors propose an implementation in standard quantum chemistry packages. An application to the nonlinear charge transport through 1,4-benzenedithiol will be presented. They explain the leading finite bias effect on the transmission as a consequence of a nonequilibrium Stark effect and discuss the relation to earlier work.

  2. A recombinant inwardly rectifying potassium channel coupled to GTP- binding proteins

    PubMed Central

    1996-01-01

    GTP-binding (G) proteins have been shown to mediate activation of inwardly rectifying potassium (K+) channels in cardiac, neuronal and neuroendocrine cells. Here, we report functional expression of a recombinant inwardly rectifying channel which we call KGP (or hpKir3.4), to signify that it is K+ selective, G-protein-gated and isolated from human pancreas. KGP expression in Xenopus oocytes resulted in sizeable basal (or agonist-independent) currents while coexpression with a G-protein-linked receptor, yielded additional agonist-induced currents. Coexpression of KGP and hGIRK1 (a human brain homolog of GIRK1/Kir3.1) produced much larger basal currents than those observed with KGP or hGIRK1 alone, and upon coexpression with receptor, similarly large agonist-induced currents could be obtained. Pertussis toxin treatment significantly diminished agonist-dependent currents due to either KGP or KGP/hGIRK1 expression. Interestingly, PTX also significantly reduced basal KGP or KGP/hGIRK1 currents, suggesting that basal activity is largely the result of G-protein gating as well. When the two channels were coexpressed with receptor, the relative increase in current elicited by agonist was similar whether KGP and hGIRK1 were expressed alone or together. When in vitro translated or when expressed in Xenopus oocytes or CHO mammalian cells, KGP gave rise to a nonglycosylated 45-kD protein. Antibodies directed against either KGP or hGIRK1 coprecipitated both proteins coexpressed in oocytes, providing evidence for the heteromeric assembly of the two channels and suggesting that the current potentiation seen with coexpression of the two channel subunits is due to specific interactions between them. An endogenous oocyte protein similar in size to KGP was also coprecipitated with hGIRK1. PMID:8868049

  3. Ab initio calculation of electron-phonon coupling in monoclinic β-Ga2O3 crystal

    NASA Astrophysics Data System (ADS)

    Ghosh, Krishnendu; Singisetti, Uttam

    2016-08-01

    The interaction between electrons and vibrational modes in monoclinic β-Ga2O3 is theoretically investigated using ab-initio calculations. The large primitive cell of β-Ga2O3 gives rise to 30 phonon modes all of which are taken into account in transport calculation. The electron-phonon interaction is calculated under density functional perturbation theory and then interpolated using Wannier-Fourier interpolation. The long-range interaction elements between electrons and polar optical phonon (POP) modes are calculated separately using the Born effective charge tensor. The direction dependence of the long-range POP coupling in a monoclinic crystal is explored and is included in the transport calculations. Scattering rate calculations are done using the Fermi golden rule followed by solving the Boltzmann transport equation using the Rode's method to estimate low field mobility. A room temperature mobility of 115 cm2/V s is observed. Comparison with recent experimentally reported mobility is done for a wide range of temperatures (30 K-650 K). It is also found that the POP interaction dominates the electron mobility under low electric field conditions. The relative contribution of the different POP modes is analyzed and the mode 21 meV POP is found to have the highest impact on low field electron mobility at room temperature.

  4. Ab initio calculation of electron–phonon coupling in monoclinic β-Ga{sub 2}O{sub 3} crystal

    SciTech Connect

    Ghosh, Krishnendu Singisetti, Uttam

    2016-08-15

    The interaction between electrons and vibrational modes in monoclinic β-Ga{sub 2}O{sub 3} is theoretically investigated using ab-initio calculations. The large primitive cell of β-Ga{sub 2}O{sub 3} gives rise to 30 phonon modes all of which are taken into account in transport calculation. The electron-phonon interaction is calculated under density functional perturbation theory and then interpolated using Wannier–Fourier interpolation. The long-range interaction elements between electrons and polar optical phonon (POP) modes are calculated separately using the Born effective charge tensor. The direction dependence of the long-range POP coupling in a monoclinic crystal is explored and is included in the transport calculations. Scattering rate calculations are done using the Fermi golden rule followed by solving the Boltzmann transport equation using the Rode's method to estimate low field mobility. A room temperature mobility of 115 cm{sup 2}/V s is observed. Comparison with recent experimentally reported mobility is done for a wide range of temperatures (30 K–650 K). It is also found that the POP interaction dominates the electron mobility under low electric field conditions. The relative contribution of the different POP modes is analyzed and the mode 21 meV POP is found to have the highest impact on low field electron mobility at room temperature.

  5. Implementation and validation of fully relativistic GW calculations: Spin–orbit coupling in molecules, nanocrystals, and solids

    DOE PAGES

    Scherpelz, Peter; Govoni, Marco; Hamada, Ikutaro; ...

    2016-06-22

    We present an implementation of G0W0 calculations including spin–orbit coupling (SOC) enabling investigations of large systems, with thousands of electrons, and we discuss results for molecules, solids, and nanocrystals. Using a newly developed set of molecules with heavy elements (called GW-SOC81), we find that, when based upon hybrid density functional calculations, fully relativistic (FR) and scalar-relativistic (SR) G0W0 calculations of vertical ionization potentials both yield excellent performance compared to experiment, with errors below 1.9%. We demonstrate that while SR calculations have higher random errors, FR calculations systematically underestimate the VIP by 0.1 to 0.2 eV. We further verify that SOCmore » effects may be well approximated at the FR density functional level and then added to SR G0W0 results for a broad class of systems. We also address the use of different root-finding algorithms for the G0W0 quasiparticle equation and the significant influence of including d electrons in the valence partition of the pseudopotential for G0W0 calculations. Lastly, we present statistical analyses of our data, highlighting the importance of separating definitive improvements from those that may occur by chance due to a limited number of samples. We suggest the statistical analyses used here will be useful in the assessment of the accuracy of a large variety of electronic structure methods« less

  6. Implementation and Validation of Fully Relativistic GW Calculations: Spin-Orbit Coupling in Molecules, Nanocrystals, and Solids.

    PubMed

    Scherpelz, Peter; Govoni, Marco; Hamada, Ikutaro; Galli, Giulia

    2016-08-09

    We present an implementation of G0W0 calculations including spin-orbit coupling (SOC) enabling investigations of large systems, with thousands of electrons, and we discuss results for molecules, solids, and nanocrystals. Using a newly developed set of molecules with heavy elements (called GW-SOC81), we find that, when based upon hybrid density functional calculations, fully relativistic (FR) and scalar-relativistic (SR) G0W0 calculations of vertical ionization potentials both yield excellent performance compared to experiment, with errors below 1.9%. We demonstrate that while SR calculations have higher random errors, FR calculations systematically underestimate the VIP by 0.1 to 0.2 eV. We further verify that SOC effects may be well approximated at the FR density functional level and then added to SR G0W0 results for a broad class of systems. We also address the use of different root-finding algorithms for the G0W0 quasiparticle equation and the significant influence of including d electrons in the valence partition of the pseudopotential for G0W0 calculations. Finally, we present statistical analyses of our data, highlighting the importance of separating definitive improvements from those that may occur by chance due to a limited number of samples. We suggest the statistical analyses used here will be useful in the assessment of the accuracy of a large variety of electronic structure methods.

  7. H-H, C-H, and C-C NMR spin-spin coupling constants calculated by the FP-INDO method for aromatic hydrocarbons

    NASA Technical Reports Server (NTRS)

    Long, S. A. T.; Memory, J. D.

    1978-01-01

    The FP-INDO (finite perturbation-intermediate neglect of differential overlap) method is used to calculate the H-H, C-H, and C-C coupling constants in hertz for molecules of six different benzenoid hydrocarbons: benzene, naphthalene, biphenyl, anthracene, phenanthrene, and pyrene. The calculations are based on both the actual and the average molecular geometries. It is found that only the actual molecular geometries can always yield the correct relative order of values for the H-H coupling constants. For the calculated C-C coupling constants, as for the calculated C-H coupling constants, the signs are positive (negative) for an odd (even) number of bonds connecting the two nuclei. Agreements between the calculated and experimental values of the coupling constants for all six molecules are comparable to those reported previously for other molecules.

  8. H-H, C-H, and C-C NMR spin-spin coupling constants calculated by the FP-INDO method for aromatic hydrocarbons

    NASA Technical Reports Server (NTRS)

    Long, S. A. T.; Memory, J. D.

    1978-01-01

    The FP-INDO (finite perturbation-intermediate neglect of differential overlap) method is used to calculate the H-H, C-H, and C-C coupling constants in hertz for molecules of six different benzenoid hydrocarbons: benzene, naphthalene, biphenyl, anthracene, phenanthrene, and pyrene. The calculations are based on both the actual and the average molecular geometries. It is found that only the actual molecular geometries can always yield the correct relative order of values for the H-H coupling constants. For the calculated C-C coupling constants, as for the calculated C-H coupling constants, the signs are positive (negative) for an odd (even) number of bonds connecting the two nuclei. Agreements between the calculated and experimental values of the coupling constants for all six molecules are comparable to those reported previously for other molecules.

  9. Determining the Structure of Oxalate Anion Using Infrared and Raman Spectroscopy Coupled with Gaussian Calculations

    ERIC Educational Resources Information Center

    Peterson, Karen I.; Pullman, David P.

    2016-01-01

    A laboratory project for the upper-division physical chemistry laboratory is described, and it combines IR and Raman spectroscopies with Gaussian electronic structure calculations to determine the structure of the oxalate anion in solid alkali oxalates and in aqueous solution. The oxalate anion has two limiting structures whose vibrational spectra…

  10. Determining the Structure of Oxalate Anion Using Infrared and Raman Spectroscopy Coupled with Gaussian Calculations

    ERIC Educational Resources Information Center

    Peterson, Karen I.; Pullman, David P.

    2016-01-01

    A laboratory project for the upper-division physical chemistry laboratory is described, and it combines IR and Raman spectroscopies with Gaussian electronic structure calculations to determine the structure of the oxalate anion in solid alkali oxalates and in aqueous solution. The oxalate anion has two limiting structures whose vibrational spectra…

  11. Interrogation of the intersubunit interface of the open Hv1 proton channel with a probe of allosteric coupling

    PubMed Central

    Hong, Liang; Singh, Vikrant; Wulff, Heike; Tombola, Francesco

    2015-01-01

    The Hv1 voltage-gated proton channel is a dimeric complex consisting of two voltage-sensing domains (VSDs), each containing a gated proton permeation pathway. Dimerization is controlled by a cytoplasmic coiled-coil domain. The transitions from the closed to the open state in the two VSDs are known to occur cooperatively; however, the underlying mechanism is poorly understood. Intersubunit interfaces play a critical role in allosteric processes; but, such interfaces have not been determined in the open Hv1 channel. Here we show that 2-guanidinothiazole derivatives block the two Hv1 VSDs in a cooperative way, and use one of the compounds as a probe of allosteric coupling between open subunits. We find that the extracellular ends of the first transmembrane segments of the VSDs form the intersubunit interface that mediates coupling between binding sites, while the coiled-coil domain does not directly participate in the process. We also find strong evidence that the channel’s proton selectivity filter controls blocker binding cooperativity. PMID:26365828

  12. Particle-vibration coupling: Recent advances in microscopic calculations with the Skyrme Hamiltonian

    SciTech Connect

    Colò, G.; Baldo, M.; Bortignon, P. F.; Rizzo, D.; Bocchi, G.

    2016-11-15

    In this contribution, we report some recent progress in our understanding of particle-vibration coupling (PVC) in nuclei. In particular, we first review the formal development that has allowed some of us to deduce the PVC equations within the Green’s functionmethod. Applications are then discussed, both in the case of single-particle states and giant resonances in magic nuclei. We also present a new model that extends the PVC ansatz and is meant to account for the complete low-lying spectra of odd nuclei.

  13. Particle-vibration coupling: Recent advances in microscopic calculations with the Skyrme Hamiltonian

    NASA Astrophysics Data System (ADS)

    Colò, G.; Baldo, M.; Bortignon, P. F.; Rizzo, D.; Bocchi, G.

    2016-11-01

    In this contribution, we report some recent progress in our understanding of particle-vibration coupling (PVC) in nuclei. In particular, we first review the formal development that has allowed some of us to deduce the PVC equations within the Green's functionmethod. Applications are then discussed, both in the case of single-particle states and giant resonances in magic nuclei. We also present a new model that extends the PVC ansatz and is meant to account for the complete low-lying spectra of odd nuclei.

  14. A fully coupled Navier-Stokes solver for calculation of turbulent incompressible free surface flow past a ship hull

    NASA Astrophysics Data System (ADS)

    Alessandrini, B.; Delhommeau, G.

    1999-01-01

    This paper deals with the calculation of free surface flow of viscous incompressible fluid around the hull of a boat moving with rectilinear motion. An original method used to avoid a large part of the theoretical problems connected with free surface boundary conditions in three-dimensional Navier-Stokes-Reynolds equations is proposed here. The linearised system of convective equations for velocities, pressure and free surface elevation unknowns is discretised by finite differences and two methods to solve the fully coupled resulting matrix are presented here. The non-linear convergence of fully coupled algorithm is compared with the velocity-pressure weakly coupled algorithm SIMPLER. Turbulence is taken into account through Reynolds decomposition and k- or k- model to close the equations. These two models are implemented without wall function and numerical calculations are performed up to the viscous sub-layer. Numerical results and comparisons with experiments are presented on the Series 60 CB=0.60 ship model for a Reynolds number Rn=4.5×106 and a Froude number Fn=0.316. Copyright

  15. Protein translocation channel of mitochondrial inner membrane and matrix-exposed import motor communicate via two-domain coupling protein

    PubMed Central

    Banerjee, Rupa; Gladkova, Christina; Mapa, Koyeli; Witte, Gregor; Mokranjac, Dejana

    2015-01-01

    The majority of mitochondrial proteins are targeted to mitochondria by N-terminal presequences and use the TIM23 complex for their translocation across the mitochondrial inner membrane. During import, translocation through the channel in the inner membrane is coupled to the ATP-dependent action of an Hsp70-based import motor at the matrix face. How these two processes are coordinated remained unclear. We show here that the two domain structure of Tim44 plays a central role in this process. The N-terminal domain of Tim44 interacts with the components of the import motor, whereas its C-terminal domain interacts with the translocation channel and is in contact with translocating proteins. Our data suggest that the translocation channel and the import motor of the TIM23 complex communicate through rearrangements of the two domains of Tim44 that are stimulated by translocating proteins. DOI: http://dx.doi.org/10.7554/eLife.11897.001 PMID:26714107

  16. Amyloid precursor protein modulates Nav1.6 sodium channel currents through a Go-coupled JNK pathway

    PubMed Central

    Li, Shao; Wang, Xi; Ma, Quan-Hong; Yang, Wu-lin; Zhang, Xiao-Gang; Dawe, Gavin S.; Xiao, Zhi-Cheng

    2016-01-01

    Amyloid precursor protein (APP), commonly associated with Alzheimer’s disease, also marks axonal degeneration. In the recent studies, we demonstrated that APP aggregated at nodes of Ranvier (NORs) in myelinated central nervous system (CNS) axons and interacted with Nav1.6. However, the physiological function of APP remains unknown. In this study, we described reduced sodium current densities in APP knockout hippocampal neurons. Coexpression of APP or its intracellular domains containing a VTPEER motif with Nav1.6 sodium channels in Xenopus oocytes resulted in an increase in peak sodium currents, which was enhanced by constitutively active Go mutant and blocked by a dominant negative mutant. JNK and CDK5 inhibitor attenuated increases in Nav1.6 sodium currents induced by overexpression of APP. Nav1.6 sodium currents were increased by APPT668E (mutant Thr to Glu) and decreased by T668A (mutant Thr to ALa) mutant, respectively. The cell surface expression of Nav1.6 sodium channels in the white matter of spinal cord and the spinal conduction velocity is decreased in APP, p35 and JNK3 knockout mice. Therefore, APP modulates Nav1.6 sodium channels through a Go-coupled JNK pathway, which is dependent on phosphorylation of APP at Thr668. PMID:28008944

  17. Structural characteristics of gap junctions. I. Channel number in coupled and uncoupled conditions

    PubMed Central

    1988-01-01

    Gap junctions between crayfish lateral axons were studied by combining anatomical and electrophysiological measurements to determine structural changes associated during uncoupling by axoplasmic acidification. In basal conditions, the junctional resistance, Rj, was approximately 60-80 k omega and the synapses appeared as two adhering membranes; 18-20-nm overall thickness, containing transverse densities (channels) spanning both membranes and the narrow extracellular gap (4- 6 nm). In freeze-fracture replicas, the synapses contained greater than 3 X 10(3) gap junction plaques having a total of approximately 3.5 X 10(5) intramembrane particles. "Single" gap junction particles represented approximately 10% of the total number of gap junction particles present in the synapse. Therefore, in basal conditions, most of the gap junction particles were organized in plaques. Moreover, correlations of the total number of gap junction particles with Rj suggested that most of the junctional particles in plaques corresponded to conducting channels. Upon acidification of the axoplasm to pH 6.7- 6.8, the junctional resistance increased to approximately 300 k omega and action potentials failed to propagate across the septum. Morphological measurements showed that the total number of gap junction particles in plaques decreased approximately 11-fold to 3.1 X 10(4) whereas the number of single particles dispersed in the axolemmae increased significantly. Thin sections of these synapses showed that the width of the extracellular gap increased from 4-6 nm in basal conditions to 10-20 nm under conditions where axoplasmic pH was 6.7- 6.8. These observations suggest that single gap junction particles dispersed in the synapse most likely represent hemi-channels produced by the dissasembly of channels previously arranged in plaques. PMID:3372591

  18. Conformational change opening the CFTR chloride channel pore coupled to ATP-dependent gating.

    PubMed

    Wang, Wuyang; Linsdell, Paul

    2012-03-01

    Opening and closing of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel are controlled by ATP binding and hydrolysis by its nucleotide binding domains (NBDs). This is presumed to control opening of a single "gate" within the permeation pathway, however, the location of such a gate has not been described. We used patch clamp recording to monitor access of cytosolic cysteine reactive reagents to cysteines introduced into different transmembrane (TM) regions in a cysteine-less form of CFTR. The rate of modification of Q98C (TM1) and I344C (TM6) by both [2-sulfonatoethyl] methanethiosulfonate (MTSES) and permeant Au(CN)(2)(-) ions was reduced when ATP concentration was reduced from 1mM to 10μM, and modification by MTSES was accelerated when 2mM pyrophosphate was applied to prevent channel closure. Modification of K95C (TM1) and V345C (TM6) was not affected by these manoeuvres. We also manipulated gating by introducing the mutations K464A (in NBD1) and E1371Q (in NBD2). The rate of modification of Q98C and I344C by both MTSES and Au(CN)(2)(-) was decreased by K464A and increased by E1371Q, whereas modification of K95C and V345C was not affected. These results suggest that access from the cytoplasm to K95 and V345 is similar in open and closed channels. In contrast, modifying ATP-dependent channel gating alters access to Q98 and I344, located further into the pore. We propose that ATP-dependent gating of CFTR is associated with the opening and closing of a gate within the permeation pathway at the level of these pore-lining amino acids.

  19. A coupled wavenumber integration approach for calculating the wavefield in large-scale laterally varying structures

    NASA Astrophysics Data System (ADS)

    Lucifredi, Irena; Ishii, Miaki

    2012-01-01

    This paper presents implementation techniques for the coupled wavenumber integration approach that is occasionally used in the underwater acoustics community to address larger scale problems in seismo-acoustics. This numerically efficient method is suitable for detailed wavefield representation of the long, thin waveguide propagating geometries such as those within subducting plate. It therefore represents an attractive alternative to ray-based solutions and finite element methods when thin layers with strong velocity contrast are expected. This wavefield modelling technique is based upon range-dependent wavenumber integration combined with Kirchhoff approximation. Examples of the details of the propagating wavefield with a dipping slab-like structure and the effects of low-velocity layers (LVLs) are presented. These results include the propagation of the wavefield through the wedge and through very LVLs as a function of setups of different complexity as well as a function of horizontal range. By identifying the existence of a sediment-like layer, the presence of a source within and the effects of the changes in the receiver range location, we demonstrate the ability of the coupled wavenumber technique to capture the physics associated with LVLs configuration, and provide classification features for effective identification of these, often intricate, subducted slab structure characteristic.

  20. Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivation

    NASA Astrophysics Data System (ADS)

    Conti, Luca; Renhorn, Jakob; Gabrielsson, Anders; Turesson, Fredrik; Liin, Sara I.; Lindahl, Erik; Elinder, Fredrik

    2016-06-01

    Voltage-gated potassium channels open at depolarized membrane voltages. A prolonged depolarization causes a rearrangement of the selectivity filter which terminates the conduction of ions – a process called slow or C-type inactivation. How structural rearrangements in the voltage-sensor domain (VSD) cause alteration in the selectivity filter, and vice versa, are not fully understood. We show that pulling the pore domain of the Shaker potassium channel towards the VSD by a Cd2+ bridge accelerates C-type inactivation. Molecular dynamics simulations show that such pulling widens the selectivity filter and disrupts the K+ coordination, a hallmark for C-type inactivation. An engineered Cd2+ bridge within the VSD also affect C-type inactivation. Conversely, a pore domain mutation affects VSD gating-charge movement. Finally, C-type inactivation is caused by the concerted action of distant amino acid residues in the pore domain. All together, these data suggest a reciprocal communication between the pore domain and the VSD in the extracellular portion of the channel.