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Sample records for zeta basis set

  1. Segmented all-electron Gaussian basis sets of double and triple zeta qualities for Fr, Ra, and Ac

    NASA Astrophysics Data System (ADS)

    Campos, C. T.; de Oliveira, A. Z.; Ferreira, I. B.; Jorge, F. E.; Martins, L. S. C.

    2017-05-01

    Segmented all-electron basis sets of valence double and triple zeta qualities plus polarization functions for the elements Fr, Ra, and Ac are generated using non-relativistic and Douglas-Kroll-Hess (DKH) Hamiltonians. The sets are augmented with diffuse functions with the purpose to describe appropriately the electrons far from the nuclei. At the DKH-B3LYP level, first atomic ionization energies and bond lengths, dissociation energies, and polarizabilities of a sample of diatomics are calculated. Comparison with theoretical and experimental data available in the literature is carried out. It is verified that despite the small sizes of the basis sets, they are yet reliable.

  2. Benchmark calculations with correlated molecular wavefunctions. XIII. Potential energy curves for He2, Ne2 and Ar2 using correlation consistent basis sets through augmented sextuple zeta

    NASA Astrophysics Data System (ADS)

    van Mourik, Tanja

    1999-02-01

    The potential energy curves of the rare gas dimers He2, Ne2, and Ar2 have been computed using correlation consistent basis sets ranging from singly augmented aug-cc-pVDZ sets through triply augmented t-aug-cc-pV6Z sets, with the augmented sextuple basis sets being reported herein. Several methods for including electron correlation were investigated, namely Moller-Plesset perturbation theory (MP2, MP3 and MP4) and coupled cluster theory [CCSD and CCSD(T)]. For He2CCSD(T)/d-aug-cc-pV6Z calculations yield a well depth of 7.35cm-1 (10.58K), with an estimated complete basis set (CBS) limit of 7.40cm-1 (10.65K). The latter is smaller than the 'exact' well depth (Aziz, R. A., Janzen, A. R., and Moldover, M. R., 1995, Phys. Rev. Lett., 74, 1586) by about 0.2cm-1 (0.35K). The Ne well depth, computed with the CCSD(T)/d-aug-cc-pV6Z method, is 28.31cm-1 and the estimated CBS limit is 28.4cm-1, approximately 1cm-1 smaller than the empirical potential of Aziz, R. A., and Slaman, M., J., 1989, Chem. Phys., 130, 187. Inclusion of core and core-valence correlation effects has a negligible effect on the Ne well depth, decreasing it by only 0.04cm-1. For Ar2, CCSD(T)/ d-aug-cc-pV6Z calculations yield a well depth of 96.2cm-1. The corresponding HFDID potential of Aziz, R. A., 1993, J. chem. Phys., 99, 4518 predicts of D of 99.7cm-1. Inclusion of core and core-valence effects in Ar increases the well depth and decreases the discrepancy by approximately 1cm-1.

  3. High quality Gaussian basis sets for fourth-row atoms

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Faegri, Knut, Jr.

    1992-01-01

    Energy optimized Gaussian basis sets of triple-zeta quality for the atoms Rb-Xe have been derived. Two series of basis sets are developed: (24s 16p 10d) and (26s 16p 10d) sets which were expanded to 13d and 19p functions as the 4d and 5p shells become occupied. For the atoms lighter than Cd, the (24s 16p 10d) sets with triple-zeta valence distributions are higher in energy than the corresponding double-zeta distribution. To ensure a triple-zeta distribution and a global energy minimum, the (26s 16p 10d) sets were derived. Total atomic energies from the largest basis sets are between 198 and 284 (mu)E(sub H) above the numerical Hartree-Fock energies.

  4. Molecular basis of length polymorphism in the human zeta-globin gene complex.

    PubMed Central

    Goodbourn, S E; Higgs, D R; Clegg, J B; Weatherall, D J

    1983-01-01

    The length polymorphism between the human zeta-globin gene and its pseudogene is caused by an allele-specific variation in the copy number of a tandemly repeating 36-base-pair sequence. This sequence is related to a tandemly repeated 14-base-pair sequence in the 5' flanking region of the human insulin gene, which is known to cause length polymorphism, and to a repetitive sequence in intervening sequence (IVS) 1 of the pseudo-zeta-globin gene. Evidence is presented that the latter is also of variable length, probably because of differences in the copy number of the tandem repeat. The homology between the three length polymorphisms may be an indication of the presence of a more widespread group of related sequences in the human genome, which might be useful for generalized linkage studies. PMID:6308667

  5. Some considerations about Gaussian basis sets for electric property calculations

    NASA Astrophysics Data System (ADS)

    Arruda, Priscilla M.; Canal Neto, A.; Jorge, F. E.

    Recently, segmented contracted basis sets of double, triple, and quadruple zeta valence quality plus polarization functions (XZP, X = D, T, and Q, respectively) for the atoms from H to Ar were reported. In this work, with the objective of having a better description of polarizabilities, the QZP set was augmented with diffuse (s and p symmetries) and polarization (p, d, f, and g symmetries) functions that were chosen to maximize the mean dipole polarizability at the UHF and UMP2 levels, respectively. At the HF and B3LYP levels of theory, electric dipole moment and static polarizability for a sample of molecules were evaluated. Comparison with experimental data and results obtained with a similar size basis set, whose diffuse functions were optimized for the ground state energy of the anion, was done.

  6. Estimating the CCSD basis-set limit energy from small basis sets: basis-set extrapolations vs additivity schemes

    NASA Astrophysics Data System (ADS)

    Spackman, Peter R.; Karton, Amir

    2015-05-01

    Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/Lα two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol-1. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol-1.

  7. Estimating the CCSD basis-set limit energy from small basis sets: basis-set extrapolations vs additivity schemes

    SciTech Connect

    Spackman, Peter R.; Karton, Amir, E-mail: amir.karton@uwa.edu.au

    Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/L{sup α} two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/ormore » second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol{sup –1}. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol{sup –1}.« less

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

    SciTech Connect

    Claudino, Daniel; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu; Gargano, Ricardo

    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 newmore » 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 〈r{sup n}〉 (−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.« less

  9. On the optimization of Gaussian basis sets

    NASA Astrophysics Data System (ADS)

    Petersson, George A.; Zhong, Shijun; Montgomery, John A.; Frisch, Michael J.

    2003-01-01

    A new procedure for the optimization of the exponents, αj, of Gaussian basis functions, Ylm(ϑ,φ)rle-αjr2, is proposed and evaluated. The direct optimization of the exponents is hindered by the very strong coupling between these nonlinear variational parameters. However, expansion of the logarithms of the exponents in the orthonormal Legendre polynomials, Pk, of the index, j: ln αj=∑k=0kmaxAkPk((2j-2)/(Nprim-1)-1), yields a new set of well-conditioned parameters, Ak, and a complete sequence of well-conditioned exponent optimizations proceeding from the even-tempered basis set (kmax=1) to a fully optimized basis set (kmax=Nprim-1). The error relative to the exact numerical self-consistent field limit for a six-term expansion is consistently no more than 25% larger than the error for the completely optimized basis set. Thus, there is no need to optimize more than six well-conditioned variational parameters, even for the largest sets of Gaussian primitives.

  10. On the performance of large Gaussian basis sets for the computation of total atomization energies

    NASA Technical Reports Server (NTRS)

    Martin, J. M. L.

    1992-01-01

    The total atomization energies of a number of molecules have been computed using an augmented coupled-cluster method and (5s4p3d2f1g) and 4s3p2d1f) atomic natural orbital (ANO) basis sets, as well as the correlation consistent valence triple zeta plus polarization (cc-pVTZ) correlation consistent valence quadrupole zeta plus polarization (cc-pVQZ) basis sets. The performance of ANO and correlation consistent basis sets is comparable throughout, although the latter can result in significant CPU time savings. Whereas the inclusion of g functions has significant effects on the computed Sigma D(e) values, chemical accuracy is still not reached for molecules involving multiple bonds. A Gaussian-1 (G) type correction lowers the error, but not much beyond the accuracy of the G1 model itself. Using separate corrections for sigma bonds, pi bonds, and valence pairs brings down the mean absolute error to less than 1 kcal/mol for the spdf basis sets, and about 0.5 kcal/mol for the spdfg basis sets. Some conclusions on the success of the Gaussian-1 and Gaussian-2 models are drawn.

  11. Basis set construction for molecular electronic structure theory: natural orbital and Gauss-Slater basis for smooth pseudopotentials.

    PubMed

    Petruzielo, F R; Toulouse, Julien; Umrigar, C J

    2011-02-14

    A simple yet general method for constructing basis sets for molecular electronic structure calculations is presented. These basis sets consist of atomic natural orbitals from a multiconfigurational self-consistent field calculation supplemented with primitive functions, chosen such that the asymptotics are appropriate for the potential of the system. Primitives are optimized for the homonuclear diatomic molecule to produce a balanced basis set. Two general features that facilitate this basis construction are demonstrated. First, weak coupling exists between the optimal exponents of primitives with different angular momenta. Second, the optimal primitive exponents for a chosen system depend weakly on the particular level of theory employed for optimization. The explicit case considered here is a basis set appropriate for the Burkatzki-Filippi-Dolg pseudopotentials. Since these pseudopotentials are finite at nuclei and have a Coulomb tail, the recently proposed Gauss-Slater functions are the appropriate primitives. Double- and triple-zeta bases are developed for elements hydrogen through argon. These new bases offer significant gains over the corresponding Burkatzki-Filippi-Dolg bases at various levels of theory. Using a Gaussian expansion of the basis functions, these bases can be employed in any electronic structure method. Quantum Monte Carlo provides an added benefit: expansions are unnecessary since the integrals are evaluated numerically.

  12. Correlation consistent basis sets for the atoms In–Xe

    SciTech Connect

    Mahler, Andrew; Wilson, Angela K., E-mail: akwilson@unt.edu

    In this work, the correlation consistent family of Gaussian basis sets has been expanded to include all-electron basis sets for In–Xe. The methodology for developing these basis sets is described, and several examples of the performance and utility of the new sets have been provided. Dissociation energies and bond lengths for both homonuclear and heteronuclear diatomics demonstrate the systematic convergence behavior with respect to increasing basis set quality expected by the family of correlation consistent basis sets in describing molecular properties. Comparison with recently developed correlation consistent sets designed for use with the Douglas-Kroll Hamiltonian is provided.

  13. Atomization Energies of SO and SO2; Basis Set Extrapolation Revisted

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Ricca, Alessandra; Arnold, James (Technical Monitor)

    1998-01-01

    The addition of tight functions to sulphur and extrapolation to the complete basis set limit are required to obtain accurate atomization energies. Six different extrapolation procedures are tried. The best atomization energies come from the series of basis sets that yield the most consistent results for all extrapolation techniques. In the variable alpha approach, alpha values larger than 4.5 or smaller than 3, appear to suggest that the extrapolation may not be reliable. It does not appear possible to determine a reliable basis set series using only the triple and quadruple zeta based sets. The scalar relativistic effects reduce the atomization of SO and SO2 by 0.34 and 0.81 kcal/mol, respectively, and clearly must be accounted for if a highly accurate atomization energy is to be computed. The magnitude of the core-valence (CV) contribution to the atomization is affected by missing diffuse valence functions. The CV contribution is much more stable if basis set superposition errors are accounted for. A similar study of SF, SF(+), and SF6 shows that the best family of basis sets varies with the nature of the S bonding.

  14. Optimization of selected molecular orbitals in group basis sets.

    PubMed

    Ferenczy, György G; Adams, William H

    2009-04-07

    We derive a local basis equation which may be used to determine the orbitals of a group of electrons in a system when the orbitals of that group are represented by a group basis set, i.e., not the basis set one would normally use but a subset suited to a specific electronic group. The group orbitals determined by the local basis equation minimize the energy of a system when a group basis set is used and the orbitals of other groups are frozen. In contrast, under the constraint of a group basis set, the group orbitals satisfying the Huzinaga equation do not minimize the energy. In a test of the local basis equation on HCl, the group basis set included only 12 of the 21 functions in a basis set one might ordinarily use, but the calculated active orbital energies were within 0.001 hartree of the values obtained by solving the Hartree-Fock-Roothaan (HFR) equation using all 21 basis functions. The total energy found was just 0.003 hartree higher than the HFR value. The errors with the group basis set approximation to the Huzinaga equation were larger by over two orders of magnitude. Similar results were obtained for PCl(3) with the group basis approximation. Retaining more basis functions allows an even higher accuracy as shown by the perfect reproduction of the HFR energy of HCl with 16 out of 21 basis functions in the valence basis set. When the core basis set was also truncated then no additional error was introduced in the calculations performed for HCl with various basis sets. The same calculations with fixed core orbitals taken from isolated heavy atoms added a small error of about 10(-4) hartree. This offers a practical way to calculate wave functions with predetermined fixed core and reduced base valence orbitals at reduced computational costs. The local basis equation can also be used to combine the above approximations with the assignment of local basis sets to groups of localized valence molecular orbitals and to derive a priori localized orbitals. An

  15. Gaussian basis sets for use in correlated molecular calculations. XI. Pseudopotential-based and all-electron relativistic basis sets for alkali metal (K-Fr) and alkaline earth (Ca-Ra) elements

    NASA Astrophysics Data System (ADS)

    Hill, J. Grant; Peterson, Kirk A.

    2017-12-01

    New correlation consistent basis sets based on pseudopotential (PP) Hamiltonians have been developed from double- to quintuple-zeta quality for the late alkali (K-Fr) and alkaline earth (Ca-Ra) metals. These are accompanied by new all-electron basis sets of double- to quadruple-zeta quality that have been contracted for use with both Douglas-Kroll-Hess (DKH) and eXact 2-Component (X2C) scalar relativistic Hamiltonians. Sets for valence correlation (ms), cc-pVnZ-PP and cc-pVnZ-(DK,DK3/X2C), in addition to outer-core correlation [valence + (m-1)sp], cc-p(w)CVnZ-PP and cc-pwCVnZ-(DK,DK3/X2C), are reported. The -PP sets have been developed for use with small-core PPs [I. S. Lim et al., J. Chem. Phys. 122, 104103 (2005) and I. S. Lim et al., J. Chem. Phys. 124, 034107 (2006)], while the all-electron sets utilized second-order DKH Hamiltonians for 4s and 5s elements and third-order DKH for 6s and 7s. The accuracy of the basis sets is assessed through benchmark calculations at the coupled-cluster level of theory for both atomic and molecular properties. Not surprisingly, it is found that outer-core correlation is vital for accurate calculation of the thermodynamic and spectroscopic properties of diatomic molecules containing these elements.

  16. Localized basis sets for unbound electrons in nanoelectronics.

    PubMed

    Soriano, D; Jacob, D; Palacios, J J

    2008-02-21

    It is shown how unbound electron wave functions can be expanded in a suitably chosen localized basis sets for any desired range of energies. In particular, we focus on the use of Gaussian basis sets, commonly used in first-principles codes. The possible usefulness of these basis sets in a first-principles description of field emission or scanning tunneling microscopy at large bias is illustrated by studying a simpler related phenomenon: The lifetime of an electron in a H atom subjected to a strong electric field.

  17. Hybrid Grid and Basis Set Approach to Quantum Chemistry DMRG

    NASA Astrophysics Data System (ADS)

    Stoudenmire, Edwin Miles; White, Steven

    We present a new approach for using DMRG for quantum chemistry that combines the advantages of a basis set with that of a grid approximation. Because DMRG scales linearly for quasi-one-dimensional systems, it is feasible to approximate the continuum with a fine grid in one direction while using a standard basis set approach for the transverse directions. Compared to standard basis set methods, we reach larger systems and achieve better scaling when approaching the basis set limit. The flexibility and reduced costs of our approach even make it feasible to incoporate advanced DMRG techniques such as simulating real-time dynamics. Supported by the Simons Collaboration on the Many-Electron Problem.

  18. Consistent structures and interactions by density functional theory with small atomic orbital basis sets.

    PubMed

    Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

    2015-08-07

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods

  19. Communication: A novel implementation to compute MP2 correlation energies without basis set superposition errors and complete basis set extrapolation.

    PubMed

    Dixit, Anant; Claudot, Julien; Lebègue, Sébastien; Rocca, Dario

    2017-06-07

    By using a formulation based on the dynamical polarizability, we propose a novel implementation of second-order Møller-Plesset perturbation (MP2) theory within a plane wave (PW) basis set. Because of the intrinsic properties of PWs, this method is not affected by basis set superposition errors. Additionally, results are converged without relying on complete basis set extrapolation techniques; this is achieved by using the eigenvectors of the static polarizability as an auxiliary basis set to compactly and accurately represent the response functions involved in the MP2 equations. Summations over the large number of virtual states are avoided by using a formalism inspired by density functional perturbation theory, and the Lanczos algorithm is used to include dynamical effects. To demonstrate this method, applications to three weakly interacting dimers are presented.

  20. Point Set Denoising Using Bootstrap-Based Radial Basis Function.

    PubMed

    Liew, Khang Jie; Ramli, Ahmad; Abd Majid, Ahmad

    2016-01-01

    This paper examines the application of a bootstrap test error estimation of radial basis functions, specifically thin-plate spline fitting, in surface smoothing. The presence of noisy data is a common issue of the point set model that is generated from 3D scanning devices, and hence, point set denoising is one of the main concerns in point set modelling. Bootstrap test error estimation, which is applied when searching for the smoothing parameters of radial basis functions, is revisited. The main contribution of this paper is a smoothing algorithm that relies on a bootstrap-based radial basis function. The proposed method incorporates a k-nearest neighbour search and then projects the point set to the approximated thin-plate spline surface. Therefore, the denoising process is achieved, and the features are well preserved. A comparison of the proposed method with other smoothing methods is also carried out in this study.

  1. Correlation consistent basis sets for actinides. I. The Th and U atoms

    SciTech Connect

    Peterson, Kirk A., E-mail: kipeters@wsu.edu

    New correlation consistent basis sets based on both pseudopotential (PP) and all-electron Douglas-Kroll-Hess (DKH) Hamiltonians have been developed from double- to quadruple-zeta quality for the actinide atoms thorium and uranium. Sets for valence electron correlation (5f6s6p6d), cc − pV nZ − PP and cc − pV nZ − DK3, as well as outer-core correlation (valence + 5s5p5d), cc − pwCV nZ − PP and cc − pwCV nZ − DK3, are reported (n = D, T, Q). The -PP sets are constructed in conjunction with small-core, 60-electron PPs, while the -DK3 sets utilized the 3rd-order Douglas-Kroll-Hess scalar relativistic Hamiltonian. Bothmore » series of basis sets show systematic convergence towards the complete basis set limit, both at the Hartree-Fock and correlated levels of theory, making them amenable to standard basis set extrapolation techniques. To assess the utility of the new basis sets, extensive coupled cluster composite thermochemistry calculations of ThF{sub n} (n = 2 − 4), ThO{sub 2}, and UF{sub n} (n = 4 − 6) have been carried out. After accurately accounting for valence and outer-core correlation, spin-orbit coupling, and even Lamb shift effects, the final 298 K atomization enthalpies of ThF{sub 4}, ThF{sub 3}, ThF{sub 2}, and ThO{sub 2} are all within their experimental uncertainties. Bond dissociation energies of ThF{sub 4} and ThF{sub 3}, as well as UF{sub 6} and UF{sub 5}, were similarly accurate. The derived enthalpies of formation for these species also showed a very satisfactory agreement with experiment, demonstrating that the new basis sets allow for the use of accurate composite schemes just as in molecular systems composed only of lighter atoms. The differences between the PP and DK3 approaches were found to increase with the change in formal oxidation state on the actinide atom, approaching 5-6 kcal/mol for the atomization enthalpies of ThF{sub 4} and ThO{sub 2}. The DKH3 atomization energy of ThO{sub 2} was calculated to be smaller than

  2. Correlation consistent basis sets for actinides. I. The Th and U atoms.

    PubMed

    Peterson, Kirk A

    2015-02-21

    New correlation consistent basis sets based on both pseudopotential (PP) and all-electron Douglas-Kroll-Hess (DKH) Hamiltonians have been developed from double- to quadruple-zeta quality for the actinide atoms thorium and uranium. Sets for valence electron correlation (5f6s6p6d), cc - pV nZ - PP and cc - pV nZ - DK3, as well as outer-core correlation (valence + 5s5p5d), cc - pwCV nZ - PP and cc - pwCV nZ - DK3, are reported (n = D, T, Q). The -PP sets are constructed in conjunction with small-core, 60-electron PPs, while the -DK3 sets utilized the 3rd-order Douglas-Kroll-Hess scalar relativistic Hamiltonian. Both series of basis sets show systematic convergence towards the complete basis set limit, both at the Hartree-Fock and correlated levels of theory, making them amenable to standard basis set extrapolation techniques. To assess the utility of the new basis sets, extensive coupled cluster composite thermochemistry calculations of ThFn (n = 2 - 4), ThO2, and UFn (n = 4 - 6) have been carried out. After accurately accounting for valence and outer-core correlation, spin-orbit coupling, and even Lamb shift effects, the final 298 K atomization enthalpies of ThF4, ThF3, ThF2, and ThO2 are all within their experimental uncertainties. Bond dissociation energies of ThF4 and ThF3, as well as UF6 and UF5, were similarly accurate. The derived enthalpies of formation for these species also showed a very satisfactory agreement with experiment, demonstrating that the new basis sets allow for the use of accurate composite schemes just as in molecular systems composed only of lighter atoms. The differences between the PP and DK3 approaches were found to increase with the change in formal oxidation state on the actinide atom, approaching 5-6 kcal/mol for the atomization enthalpies of ThF4 and ThO2. The DKH3 atomization energy of ThO2 was calculated to be smaller than the DKH2 value by ∼1 kcal/mol.

  3. A new basis set for molecular bending degrees of freedom.

    PubMed

    Jutier, Laurent

    2010-07-21

    We present a new basis set as an alternative to Legendre polynomials for the variational treatment of bending vibrational degrees of freedom in order to highly reduce the number of basis functions. This basis set is inspired from the harmonic oscillator eigenfunctions but is defined for a bending angle in the range theta in [0:pi]. The aim is to bring the basis functions closer to the final (ro)vibronic wave functions nature. Our methodology is extended to complicated potential energy surfaces, such as quasilinearity or multiequilibrium geometries, by using several free parameters in the basis functions. These parameters allow several density maxima, linear or not, around which the basis functions will be mainly located. Divergences at linearity in integral computations are resolved as generalized Legendre polynomials. All integral computations required for the evaluation of molecular Hamiltonian matrix elements are given for both discrete variable representation and finite basis representation. Convergence tests for the low energy vibronic states of HCCH(++), HCCH(+), and HCCS are presented.

  4. Density functional theory calculations of the lowest energy quintet and triplet states of model hemes: role of functional, basis set, and zero-point energy corrections.

    PubMed

    Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman

    2008-04-24

    We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results

  5. Basis set study of classical rotor lattice dynamics.

    PubMed

    Witkoskie, James B; Wu, Jianlan; Cao, Jianshu

    2004-03-22

    The reorientational relaxation of molecular systems is important in many phenomenon and applications. In this paper, we explore the reorientational relaxation of a model Brownian rotor lattice system with short range interactions in both the high and low temperature regimes. In this study, we use a basis set expansion to capture collective motions of the system. The single particle basis set is used in the high temperature regime, while the spin wave basis is used in the low temperature regime. The equations of motion derived in this approach are analogous to the generalized Langevin equation, but the equations render flexibility by allowing nonequilibrium initial conditions. This calculation shows that the choice of projection operators in the generalized Langevin equation (GLE) approach corresponds to defining a specific inner-product space, and this inner-product space should be chosen to reveal the important physics of the problem. The basis set approach corresponds to an inner-product and projection operator that maintain the orthogonality of the spherical harmonics and provide a convenient platform for analyzing GLE expansions. The results compare favorably with numerical simulations, and the formalism is easily extended to more complex systems. (c) 2004 American Institute of Physics

  6. Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr

    NASA Astrophysics Data System (ADS)

    Feng, Rulin; Peterson, Kirk A.

    2017-08-01

    New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP0 for PuO2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal

  7. Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr.

    PubMed

    Feng, Rulin; Peterson, Kirk A

    2017-08-28

    New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO 2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP 0 for PuO 2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal

  8. Sensitivity of the Properties of Ruthenium “Blue Dimer” to Method, Basis Set, and Continuum Model

    SciTech Connect

    Ozkanlar, Abdullah; Clark, Aurora E.

    2012-05-23

    The ruthenium “blue dimer” [(bpy)2RuIIIOH2]2O4+ is best known as the first well-defined molecular catalyst for water oxidation. It has been subject to numerous computational studies primarily employing density functional theory. However, those studies have been limited in the functionals, basis sets, and continuum models employed. The controversy in the calculated electronic structure and the reaction energetics of this catalyst highlights the necessity of benchmark calculations that explore the role of density functionals, basis sets, and continuum models upon the essential features of blue-dimer reactivity. In this paper, we report Kohn-Sham complete basis set (KS-CBS) limit extrapolations of the electronic structuremore » of “blue dimer” using GGA (BPW91 and BP86), hybrid-GGA (B3LYP), and meta-GGA (M06-L) density functionals. The dependence of solvation free energy corrections on the different cavity types (UFF, UA0, UAHF, UAKS, Bondi, and Pauling) within polarizable and conductor-like polarizable continuum model has also been investigated. The most common basis sets of double-zeta quality are shown to yield results close to the KS-CBS limit; however, large variations are observed in the reaction energetics as a function of density functional and continuum cavity model employed.« less

  9. Correlation consistent basis sets for lanthanides: The atoms La–Lu

    SciTech Connect

    Lu, Qing; Peterson, Kirk A., E-mail: kipeters@wsu.edu

    Using the 3rd-order Douglas-Kroll-Hess (DKH3) Hamiltonian, all-electron correlation consistent basis sets of double-, triple-, and quadruple-zeta quality have been developed for the lanthanide elements La through Lu. Basis sets designed for the recovery of valence correlation (defined here as 4f5s5p5d6s), cc-pVnZ-DK3, and outer-core correlation (valence + 4s4p4d), cc-pwCVnZ-DK3, are reported (n = D, T, and Q). Systematic convergence of both Hartree-Fock and correlation energies towards their respective complete basis set (CBS) limits are observed. Benchmark calculations of the first three ionization potentials (IPs) of La through Lu are reported at the DKH3 coupled cluster singles and doubles with perturbative triples,more » CCSD(T), level of theory, including effects of correlation down through the 4s electrons. Spin-orbit coupling is treated at the 2-component HF level. After extrapolation to the CBS limit, the average errors with respect to experiment were just 0.52, 1.14, and 4.24 kcal/mol for the 1st, 2nd, and 3rd IPs, respectively, compared to the average experimental uncertainties of 0.03, 1.78, and 2.65 kcal/mol, respectively. The new basis sets are also used in CCSD(T) benchmark calculations of the equilibrium geometries, atomization energies, and heats of formation for Gd{sub 2}, GdF, and GdF{sub 3}. Except for the equilibrium geometry and harmonic frequency of GdF, which are accurately known from experiment, all other calculated quantities represent significant improvements compared to the existing experimental quantities. With estimated uncertainties of about ±3 kcal/mol, the 0 K atomization energies (298 K heats of formation) are calculated to be (all in kcal/mol): 33.2 (160.1) for Gd{sub 2}, 151.7 (−36.6) for GdF, and 447.1 (−295.2) for GdF{sub 3}.« less

  10. An efficient basis set representation for calculating electrons in molecules

    DOE PAGES

    Jones, Jeremiah R.; Rouet, Francois -Henry; Lawler, Keith V.; ...

    2016-04-27

    The method of McCurdy, Baertschy, and Rescigno, is generalised to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules. It uses a basis set of product sinc functions arrayed on a Cartesian grid, and yields 1 kcal/mol precision for valence transition energies with a grid resolution of approximately 0.1 bohr. The Coulomb matrix elements are replaced with matrix elements obtained from the kinetic energy operator. A resolution-of-the-identity approximation renders the primitive one- and two-electron matrix elements diagonal; in other words, the Coulomb operator is local with respect to the grid indices. Themore » calculation of contracted two-electron matrix elements among orbitals requires only O( Nlog (N)) multiplication operations, not O( N 4), where N is the number of basis functions; N = n 3 on cubic grids. The representation not only is numerically expedient, but also produces energies and properties superior to those calculated variationally. Absolute energies, absorption cross sections, transition energies, and ionisation potentials are reported for 1- (He +, H + 2), 2- (H 2, He), 10- (CH 4), and 56-electron (C 8H 8) systems.« less

  11. Basis sets for the calculation of core-electron binding energies

    NASA Astrophysics Data System (ADS)

    Hanson-Heine, Magnus W. D.; George, Michael W.; Besley, Nicholas A.

    2018-05-01

    Core-electron binding energies (CEBEs) computed within a Δ self-consistent field approach require large basis sets to achieve convergence with respect to the basis set limit. It is shown that supplementing a basis set with basis functions from the corresponding basis set for the element with the next highest nuclear charge (Z + 1) provides basis sets that give CEBEs close to the basis set limit. This simple procedure provides relatively small basis sets that are well suited for calculations where the description of a core-ionised state is important, such as time-dependent density functional theory calculations of X-ray emission spectroscopy.

  12. Basis set expansion for inverse problems in plasma diagnostic analysis

    SciTech Connect

    Jones, B.; Ruiz, C. L.

    A basis set expansion method [V. Dribinski, A. Ossadtchi, V. A. Mandelshtam, and H. Reisler, Rev. Sci. Instrum. 73, 2634 (2002)] is applied to recover physical information about plasma radiation sources from instrument data, which has been forward transformed due to the nature of the measurement technique. This method provides a general approach for inverse problems, and we discuss two specific examples relevant to diagnosing fast z pinches on the 20–25 MA Z machine [M. E. Savage, L. F. Bennett, D. E. Bliss, W. T. Clark, R. S. Coats, J. M. Elizondo, K. R. LeChien, H. C. Harjes, J. M.more » Lehr, J. E. Maenchen, D. H. McDaniel, M. F. Pasik, T. D. Pointon, A. C. Owen, D. B. Seidel, D. L. Smith, B. S. Stoltzfus, K. W. Struve, W. A. Stygar, L. K. Warne, J. R. Woodworth, C. W. Mendel, K. R. Prestwich, R. W. Shoup, D. L. Johnson, J. P. Corley, K. C. Hodge, T. C. Wagoner, and P. E. Wakeland, in Proceedings of the Pulsed Power Plasma Sciences Conference (IEEE, 2007), p. 979]. First, Abel inversion of time-gated, self-emission x-ray images from a wire array implosion is studied. Second, we present an approach for unfolding neutron time-of-flight measurements from a deuterium gas puff z pinch to recover information about emission time history and energy distribution. Through these examples, we discuss how noise in the measured data limits the practical resolution of the inversion, and how the method handles discontinuities in the source function and artifacts in the projected image. We add to the method a propagation of errors calculation for estimating uncertainties in the inverted solution.« less

  13. Basis set expansion for inverse problems in plasma diagnostic analysis

    NASA Astrophysics Data System (ADS)

    Jones, B.; Ruiz, C. L.

    2013-07-01

    A basis set expansion method [V. Dribinski, A. Ossadtchi, V. A. Mandelshtam, and H. Reisler, Rev. Sci. Instrum. 73, 2634 (2002)], 10.1063/1.1482156 is applied to recover physical information about plasma radiation sources from instrument data, which has been forward transformed due to the nature of the measurement technique. This method provides a general approach for inverse problems, and we discuss two specific examples relevant to diagnosing fast z pinches on the 20-25 MA Z machine [M. E. Savage, L. F. Bennett, D. E. Bliss, W. T. Clark, R. S. Coats, J. M. Elizondo, K. R. LeChien, H. C. Harjes, J. M. Lehr, J. E. Maenchen, D. H. McDaniel, M. F. Pasik, T. D. Pointon, A. C. Owen, D. B. Seidel, D. L. Smith, B. S. Stoltzfus, K. W. Struve, W. A. Stygar, L. K. Warne, J. R. Woodworth, C. W. Mendel, K. R. Prestwich, R. W. Shoup, D. L. Johnson, J. P. Corley, K. C. Hodge, T. C. Wagoner, and P. E. Wakeland, in Proceedings of the Pulsed Power Plasma Sciences Conference (IEEE, 2007), p. 979]. First, Abel inversion of time-gated, self-emission x-ray images from a wire array implosion is studied. Second, we present an approach for unfolding neutron time-of-flight measurements from a deuterium gas puff z pinch to recover information about emission time history and energy distribution. Through these examples, we discuss how noise in the measured data limits the practical resolution of the inversion, and how the method handles discontinuities in the source function and artifacts in the projected image. We add to the method a propagation of errors calculation for estimating uncertainties in the inverted solution.

  14. Complete basis set extrapolations for low-lying triplet electronic states of acetylene and vinylidene

    SciTech Connect

    Sherrill, C. David; Byrd, Edward F. C.; Head-Gordon, Martin

    2000-07-22

    A recent study by Ahmed, Peterka, and Suits [J. Chem. Phys. 110, 4248 (1999)] has presented the first experimentally derived estimate of the singlet-triplet gap in the simplest alkyne, acetylene. Their value, T{sub 0}(a(tilde sign) {sup 3}B{sub 2})=28 900 cm{sup -1}, does not agree with previous theoretical predictions using the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] method and a triple-{zeta} plus double polarization plus f-function basis set (TZ2P f ), which yields 30 500{+-}1000 cm{sup -1}. This discrepancy has prompted us to investigate possible deficiencies in this usually-accurate theoretical approach. Employing extrapolations to the complete basis set limit alongmore » with corrections for full connected triple excitations, core correlation, and even relativistic effects, we obtain a value of 30 900 cm-1 (estimated uncertainty {+-}230 cm-1), demonstrating that the experimental value is underestimated. To assist in the interpretation of anticipated future experiments, we also present highly accurate excitation energies for the other three low-lying triplet states of acetylene, a(tilde sign) {sup 3}B{sub u}(33 570{+-}230 cm{sup -1}), b(tilde sign) {sup 3}A{sub u}(36 040{+-}260 cm{sup -1}), and b(tilde sign) {sup 3}A{sub 2}(38 380{+-}260 cm{sup -1}), and the three lowest-lying states of vinylidene, X(tilde sign) {sup 1}A{sub 1}(15 150{+-}230 cm{sup -1}), a(tilde sign) {sup 3}B{sub 2}(31 870{+-}230 cm{sup -1}), and b(tilde sign) {sup 3}A{sub 2}(36 840{+-}350 cm{sup -1}). Finally, we assess the ability of density functional theory (DFT) and the Gaussian-3 method to match our benchmark results for adiabatic excitation energies of C{sub 2}H{sub 2}. (c) 2000 American Institute of Physics.« less

  15. Basis set and electron correlation effects on the polarizability and second hyperpolarizability of model open-shell π-conjugated systems

    NASA Astrophysics Data System (ADS)

    Champagne, Benoı̂t; Botek, Edith; Nakano, Masayoshi; Nitta, Tomoshige; Yamaguchi, Kizashi

    2005-03-01

    The basis set and electron correlation effects on the static polarizability (α) and second hyperpolarizability (γ) are investigated ab initio for two model open-shell π-conjugated systems, the C5H7 radical and the C6H8 radical cation in their doublet state. Basis set investigations evidence that the linear and nonlinear responses of the radical cation necessitate the use of a less extended basis set than its neutral analog. Indeed, double-zeta-type basis sets supplemented by a set of d polarization functions but no diffuse functions already provide accurate (hyper)polarizabilities for C6H8 whereas diffuse functions are compulsory for C5H7, in particular, p diffuse functions. In addition to the 6-31G*+pd basis set, basis sets resulting from removing not necessary diffuse functions from the augmented correlation consistent polarized valence double zeta basis set have been shown to provide (hyper)polarizability values of similar quality as more extended basis sets such as augmented correlation consistent polarized valence triple zeta and doubly augmented correlation consistent polarized valence double zeta. Using the selected atomic basis sets, the (hyper)polarizabilities of these two model compounds are calculated at different levels of approximation in order to assess the impact of including electron correlation. As a function of the method of calculation antiparallel and parallel variations have been demonstrated for α and γ of the two model compounds, respectively. For the polarizability, the unrestricted Hartree-Fock and unrestricted second-order Møller-Plesset methods bracket the reference value obtained at the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples level whereas the projected unrestricted second-order Møller-Plesset results are in much closer agreement with the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples values than the projected unrestricted Hartree

  16. Evaluation of Density Functionals and Basis Sets for Carbohydrates

    USDA-ARS?s Scientific Manuscript database

    Correlated ab initio wave function calculations using MP2/aug-cc-pVTZ model chemistry have been performed for three test sets of gas phase saccharide conformations to provide reference values for their relative energies. The test sets consist of 15 conformers of alpha and beta-D-allopyranose, 15 of ...

  17. Small Atomic Orbital Basis Set First‐Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources

    PubMed Central

    Sure, Rebecca; Brandenburg, Jan Gerit

    2015-01-01

    Abstract In quantum chemical computations the combination of Hartree–Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double‐zeta quality is still widely used, for example, in the popular B3LYP/6‐31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean‐field methods. PMID:27308221

  18. Optimized auxiliary basis sets for density fitted post-Hartree-Fock calculations of lanthanide containing molecules

    NASA Astrophysics Data System (ADS)

    Chmela, Jiří; Harding, Michael E.

    2018-06-01

    Optimised auxiliary basis sets for lanthanide atoms (Ce to Lu) for four basis sets of the Karlsruhe error-balanced segmented contracted def2 - series (SVP, TZVP, TZVPP and QZVPP) are reported. These auxiliary basis sets enable the use of the resolution-of-the-identity (RI) approximation in post Hartree-Fock methods - as for example, second-order perturbation theory (MP2) and coupled cluster (CC) theory. The auxiliary basis sets are tested on an enlarged set of about a hundred molecules where the test criterion is the size of the RI error in MP2 calculations. Our tests also show that the same auxiliary basis sets can be used together with different effective core potentials. With these auxiliary basis set calculations of MP2 and CC quality can now be performed efficiently on medium-sized molecules containing lanthanides.

  19. Ab initio calculation of reaction energies. III. Basis set dependence of relative energies on the FH2 and H2CO potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Frisch, Michael J.; Binkley, J. Stephen; Schaefer, Henry F., III

    1984-08-01

    The relative energies of the stationary points on the FH2 and H2CO nuclear potential energy surfaces relevant to the hydrogen atom abstraction, H2 elimination and 1,2-hydrogen shift reactions have been examined using fourth-order Møller-Plesset perturbation theory and a variety of basis sets. The theoretical absolute zero activation energy for the F+H2→FH+H reaction is in better agreement with experiment than previous theoretical studies, and part of the disagreement between earlier theoretical calculations and experiment is found to result from the use of assumed rather than calculated zero-point vibrational energies. The fourth-order reaction energy for the elimination of hydrogen from formaldehyde is within 2 kcal mol-1 of the experimental value using the largest basis set considered. The qualitative features of the H2CO surface are unchanged by expansion of the basis set beyond the polarized triple-zeta level, but diffuse functions and several sets of polarization functions are found to be necessary for quantitative accuracy in predicted reaction and activation energies. Basis sets and levels of perturbation theory which represent good compromises between computational efficiency and accuracy are recommended.

  20. Ab Initio Density Fitting: Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions.

    PubMed

    Boström, Jonas; Aquilante, Francesco; Pedersen, Thomas Bondo; Lindh, Roland

    2009-06-09

    The accuracy of auxiliary basis sets derived by Cholesky decompositions of the electron repulsion integrals is assessed in a series of benchmarks on total ground state energies and dipole moments of a large test set of molecules. The test set includes molecules composed of atoms from the first three rows of the periodic table as well as transition metals. The accuracy of the auxiliary basis sets are tested for the 6-31G**, correlation consistent, and atomic natural orbital basis sets at the Hartree-Fock, density functional theory, and second-order Møller-Plesset levels of theory. By decreasing the decomposition threshold, a hierarchy of auxiliary basis sets is obtained with accuracies ranging from that of standard auxiliary basis sets to that of conventional integral treatments.

  1. On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer

    NASA Astrophysics Data System (ADS)

    Miliordos, Evangelos; Xantheas, Sotiris S.

    2015-03-01

    We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for De = - 16.1 ± 0.1 kcal/mol and for D0 = - 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of -14.22 ± 0.12 kcal/mol.

  2. Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures

    NASA Astrophysics Data System (ADS)

    Papior, Nick R.; Calogero, Gaetano; Brandbyge, Mads

    2018-06-01

    We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C60). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

  3. Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures.

    PubMed

    Papior, Nick R; Calogero, Gaetano; Brandbyge, Mads

    2018-06-27

    We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C 60 ). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

  4. Calculating Interaction Energies Using First Principle Theories: Consideration of Basis Set Superposition Error and Fragment Relaxation

    ERIC Educational Resources Information Center

    Bowen, J. Philip; Sorensen, Jennifer B.; Kirschner, Karl N.

    2007-01-01

    The analysis explains the basis set superposition error (BSSE) and fragment relaxation involved in calculating the interaction energies using various first principle theories. Interacting the correlated fragment and increasing the size of the basis set can help in decreasing the BSSE to a great extent.

  5. A Comparison of the Behavior of Functional/Basis Set Combinations for Hydrogen-Bonding in the Water Dimer with Emphasis on Basis Set Superposition Error

    PubMed Central

    Plumley, Joshua A.; Dannenberg, J. J.

    2011-01-01

    We evaluate the performance of nine functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-DFT molecular orbital calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise corrected PES. The calculated ΔE's with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, due to error compensation, the smaller basis sets gave the best results (in comparison to experimental and high level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. Since many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: 1) D95(d,p) with B3LYP, B97D, M06 or MPWB1k; 2) 6-311G(d,p) with B3LYP; 3) D95++(d,p) with B3LYP, B97D or MPWB1K; 4)6-311++G(d,p) with B3LYP or B97D; and 5) aug-cc-pVDZ with M05-2X, M06-2X or X3LYP. PMID:21328398

  6. A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error.

    PubMed

    Plumley, Joshua A; Dannenberg, J J

    2011-06-01

    We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP. Copyright © 2011 Wiley Periodicals, Inc.

  7. Derivation of a formula for the resonance integral for a nonorthogonal basis set

    PubMed Central

    Yim, Yung-Chang; Eyring, Henry

    1981-01-01

    In a self-consistent field calculation, a formula for the off-diagonal matrix elements of the core Hamiltonian is derived for a nonorthogonal basis set by a polyatomic approach. A set of parameters is then introduced for the repulsion integral formula of Mataga-Nishimoto to fit the experimental data. The matrix elements computed for the nonorthogonal basis set in the π-electron approximation are transformed to those for an orthogonal basis set by the Löwdin symmetrical orthogonalization. PMID:16593009

  8. Systematically convergent basis sets for transition metals. I. All-electron correlation consistent basis sets for the 3d elements Sc-Zn

    NASA Astrophysics Data System (ADS)

    Balabanov, Nikolai B.; Peterson, Kirk A.

    2005-08-01

    Sequences of basis sets that systematically converge towards the complete basis set (CBS) limit have been developed for the first-row transition metal elements Sc-Zn. Two families of basis sets, nonrelativistic and Douglas-Kroll-Hess (-DK) relativistic, are presented that range in quality from triple-ζ to quintuple-ζ. Separate sets are developed for the description of valence (3d4s) electron correlation (cc-pVnZ and cc-pVnZ-DK; n =T,Q, 5) and valence plus outer-core (3s3p3d4s) correlation (cc-pwCVnZ and cc-pwCVnZ-DK; n =T,Q, 5), as well as these sets augmented by additional diffuse functions for the description of negative ions and weak interactions (aug-cc-pVnZ and aug-cc-pVnZ-DK). Extensive benchmark calculations at the coupled cluster level of theory are presented for atomic excitation energies, ionization potentials, and electron affinities, as well as molecular calculations on selected hydrides (TiH, MnH, CuH) and other diatomics (TiF, Cu2). In addition to observing systematic convergence towards the CBS limits, both 3s3p electron correlation and scalar relativity are calculated to strongly impact many of the atomic and molecular properties investigated for these first-row transition metal species.

  9. Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory

    NASA Technical Reports Server (NTRS)

    Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.

    1990-01-01

    New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.

  10. Perturbation corrections to Koopmans' theorem. V - A study with large basis sets

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

    The vertical ionization potentials of N2, F2 and H2O were calculated by perturbation corrections to Koopmans' theorem using six different basis sets. The largest set used includes several sets of polarization functions. Comparison is made with measured values and with results of computations using Green's functions.

  11. Quantum Dynamics with Short-Time Trajectories and Minimal Adaptive Basis Sets.

    PubMed

    Saller, Maximilian A C; Habershon, Scott

    2017-07-11

    Methods for solving the time-dependent Schrödinger equation via basis set expansion of the wave function can generally be categorized as having either static (time-independent) or dynamic (time-dependent) basis functions. We have recently introduced an alternative simulation approach which represents a middle road between these two extremes, employing dynamic (classical-like) trajectories to create a static basis set of Gaussian wavepackets in regions of phase-space relevant to future propagation of the wave function [J. Chem. Theory Comput., 11, 8 (2015)]. Here, we propose and test a modification of our methodology which aims to reduce the size of basis sets generated in our original scheme. In particular, we employ short-time classical trajectories to continuously generate new basis functions for short-time quantum propagation of the wave function; to avoid the continued growth of the basis set describing the time-dependent wave function, we employ Matching Pursuit to periodically minimize the number of basis functions required to accurately describe the wave function. Overall, this approach generates a basis set which is adapted to evolution of the wave function while also being as small as possible. In applications to challenging benchmark problems, namely a 4-dimensional model of photoexcited pyrazine and three different double-well tunnelling problems, we find that our new scheme enables accurate wave function propagation with basis sets which are around an order-of-magnitude smaller than our original trajectory-guided basis set methodology, highlighting the benefits of adaptive strategies for wave function propagation.

  12. Combination of large and small basis sets in electronic structure calculations on large systems

    NASA Astrophysics Data System (ADS)

    Røeggen, Inge; Gao, Bin

    2018-04-01

    Two basis sets—a large and a small one—are associated with each nucleus of the system. Each atom has its own separate one-electron basis comprising the large basis set of the atom in question and the small basis sets for the partner atoms in the complex. The perturbed atoms in molecules and solids model is at core of the approach since it allows for the definition of perturbed atoms in a system. It is argued that this basis set approach should be particularly useful for periodic systems. Test calculations are performed on one-dimensional arrays of H and Li atoms. The ground-state energy per atom in the linear H array is determined versus bond length.

  13. Extrapolating MP2 and CCSD explicitly correlated correlation energies to the complete basis set limit with first and second row correlation consistent basis sets

    NASA Astrophysics Data System (ADS)

    Hill, J. Grant; Peterson, Kirk A.; Knizia, Gerald; Werner, Hans-Joachim

    2009-11-01

    Accurate extrapolation to the complete basis set (CBS) limit of valence correlation energies calculated with explicitly correlated MP2-F12 and CCSD(T)-F12b methods have been investigated using a Schwenke-style approach for molecules containing both first and second row atoms. Extrapolation coefficients that are optimal for molecular systems containing first row elements differ from those optimized for second row analogs, hence values optimized for a combined set of first and second row systems are also presented. The new coefficients are shown to produce excellent results in both Schwenke-style and equivalent power-law-based two-point CBS extrapolations, with the MP2-F12/cc-pV(D,T)Z-F12 extrapolations producing an average error of just 0.17 mEh with a maximum error of 0.49 for a collection of 23 small molecules. The use of larger basis sets, i.e., cc-pV(T,Q)Z-F12 and aug-cc-pV(Q,5)Z, in extrapolations of the MP2-F12 correlation energy leads to average errors that are smaller than the degree of confidence in the reference data (˜0.1 mEh). The latter were obtained through use of very large basis sets in MP2-F12 calculations on small molecules containing both first and second row elements. CBS limits obtained from optimized coefficients for conventional MP2 are only comparable to the accuracy of the MP2-F12/cc-pV(D,T)Z-F12 extrapolation when the aug-cc-pV(5+d)Z and aug-cc-pV(6+d)Z basis sets are used. The CCSD(T)-F12b correlation energy is extrapolated as two distinct parts: CCSD-F12b and (T). While the CCSD-F12b extrapolations with smaller basis sets are statistically less accurate than those of the MP2-F12 correlation energies, this is presumably due to the slower basis set convergence of the CCSD-F12b method compared to MP2-F12. The use of larger basis sets in the CCSD-F12b extrapolations produces correlation energies with accuracies exceeding the confidence in the reference data (also obtained in large basis set F12 calculations). It is demonstrated that the use

  14. On basis set superposition error corrected stabilization energies for large n-body clusters.

    PubMed

    Walczak, Katarzyna; Friedrich, Joachim; Dolg, Michael

    2011-10-07

    In this contribution, we propose an approximate basis set superposition error (BSSE) correction scheme for the site-site function counterpoise and for the Valiron-Mayer function counterpoise correction of second order to account for the basis set superposition error in clusters with a large number of subunits. The accuracy of the proposed scheme has been investigated for a water cluster series at the CCSD(T), CCSD, MP2, and self-consistent field levels of theory using Dunning's correlation consistent basis sets. The BSSE corrected stabilization energies for a series of water clusters are presented. A study regarding the possible savings with respect to computational resources has been carried out as well as a monitoring of the basis set dependence of the approximate BSSE corrections. © 2011 American Institute of Physics

  15. Near Hartree-Fock quality GTO basis sets for the second-row atoms

    NASA Technical Reports Server (NTRS)

    Partridge, Harry

    1987-01-01

    Energy optimized, near Hartree-Fock quality Gaussian basis sets ranging in size from (17s12p) to (20s15p) are presented for the ground states of the second-row atoms for Na(2P), Na(+), Na(-), Mg(3P), P(-), S(-), and Cl(-). In addition, optimized supplementary functions are given for the ground state basis sets to describe the negative ions, and the excited Na(2P) and Mg(3P) atomic states. The ratios of successive orbital exponents describing the inner part of the 1s and 2p orbitals are found to be nearly independent of both nuclear charge and basis set size. This provides a method of obtaining good starting estimates for other basis set optimizations.

  16. Basis set limit and systematic errors in local-orbital based all-electron DFT

    NASA Astrophysics Data System (ADS)

    Blum, Volker; Behler, Jörg; Gehrke, Ralf; Reuter, Karsten; Scheffler, Matthias

    2006-03-01

    With the advent of efficient integration schemes,^1,2 numeric atom-centered orbitals (NAO's) are an attractive basis choice in practical density functional theory (DFT) calculations of nanostructured systems (surfaces, clusters, molecules). Though all-electron, the efficiency of practical implementations promises to be on par with the best plane-wave pseudopotential codes, while having a noticeably higher accuracy if required: Minimal-sized effective tight-binding like calculations and chemically accurate all-electron calculations are both possible within the same framework; non-periodic and periodic systems can be treated on equal footing; and the localized nature of the basis allows in principle for O(N)-like scaling. However, converging an observable with respect to the basis set is less straightforward than with competing systematic basis choices (e.g., plane waves). We here investigate the basis set limit of optimized NAO basis sets in all-electron calculations, using as examples small molecules and clusters (N2, Cu2, Cu4, Cu10). meV-level total energy convergence is possible using <=50 basis functions per atom in all cases. We also find a clear correlation between the errors which arise from underconverged basis sets, and the system geometry (interatomic distance). ^1 B. Delley, J. Chem. Phys. 92, 508 (1990), ^2 J.M. Soler et al., J. Phys.: Condens. Matter 14, 2745 (2002).

  17. A novel Gaussian-Sinc mixed basis set for electronic structure calculations

    SciTech Connect

    Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.

    2015-08-14

    A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definablemore » and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H{sub 2}, O{sub 2}, and N{sub 2}, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.« less

  18. Relativistic well-tempered Gaussian basis sets for helium through mercury

    SciTech Connect

    Okada, S.; Matsuoka, O.

    1989-10-01

    Exponent parameters of the nonrelativistically optimized well-tempered Gaussian basis sets of Huzinaga and Klobukowski have been employed for Dirac--Fock--Roothaan calculations without their reoptimization. For light atoms He (atomic number {ital Z}=2)--Rh ({ital Z}=45), the number of exponent parameters used has been the same as the nonrelativistic basis sets and for heavier atoms Pd ({ital Z}=46)--Hg({ital Z}=80), two 2{ital p} (and three 3{ital d}) Gaussian basis functions have been augmented. The scheme of kinetic energy balance and the uniformly charged sphere model of atomic nuclei have been adopted. The qualities of the calculated basis sets are close to the Dirac--Fock limit.

  19. zeta 1 and zeta 2 Reticuli and the existence of the zeta Herculis group

    NASA Astrophysics Data System (ADS)

    del Peloso, E. F.; da Silva, L.; Porto de Mello, G. F.

    2000-06-01

    We report the detailed analysis of the solar type stars zeta 1 and zeta 2 Reticuli. We obtained accurate effective temperatures (T_eff = 5746 +/- 27 K and 5859 +/- 27 K respectively) and surface gravities (log g = 4.54 +/- 0.02 and 4.46 +/- 0.01 respectively). Both stars are slightly metal deficient ([Fe/H] = -0.22 +/- 0.05) and their element abundance patterns are compatible with one another and with the Sun. The hypothesis, suggested by previous detailed analyses, that these stars could be helium rich relative to the Sun, was investigated. The stars were found to have a normal, solar helium abundance. We analysed the stars' membership of the zeta Herculis stellar kinematic group (SKG). Some probable members have nearly the same galactic orbital parameters, chemical composition and evolutionary states, which confirm the existence of a metal deficient SKG. Since we determined that zeta Herculis does not belong to this group, we propose it be renamed zeta Reticuli SKG. Based on observations collected at the European Southern Observatory, La Silla, Chile, and at the Observatório do Pico dos Dias, operated by the Laboratório Nacional de Astrofísica, CNPq, Brazil.

  20. Near Hartree-Fock quality GTO basis sets for the first- and third-row atoms

    NASA Technical Reports Server (NTRS)

    Partridge, Harry

    1989-01-01

    Energy-optimized Gaussian-type-orbital (GTO) basis sets of accuracy approaching that of numerical Hartree-Fock computations are compiled for the elements of the first and third rows of the periodic table. The methods employed in calculating the sets are explained; the applicability of the sets to electronic-structure calculations is discussed; and the results are presented in tables and briefly characterized.

  1. Narrowing the error in electron correlation calculations by basis set re-hierarchization and use of the unified singlet and triplet electron-pair extrapolation scheme: Application to a test set of 106 systems

    SciTech Connect

    Varandas, A. J. C., E-mail: varandas@uc.pt; Departamento de Física, Universidade Federal do Espírito Santo, 29075-910 Vitória; Pansini, F. N. N.

    2014-12-14

    A method previously suggested to calculate the correlation energy at the complete one-electron basis set limit by reassignment of the basis hierarchical numbers and use of the unified singlet- and triplet-pair extrapolation scheme is applied to a test set of 106 systems, some with up to 48 electrons. The approach is utilized to obtain extrapolated correlation energies from raw values calculated with second-order Møller-Plesset perturbation theory and the coupled-cluster singles and doubles excitations method, some of the latter also with the perturbative triples corrections. The calculated correlation energies have also been used to predict atomization energies within an additive scheme.more » Good agreement is obtained with the best available estimates even when the (d, t) pair of hierarchical numbers is utilized to perform the extrapolations. This conceivably justifies that there is no strong reason to exclude double-zeta energies in extrapolations, especially if the basis is calibrated to comply with the theoretical model.« less

  2. Approximations to complete basis set-extrapolated, highly correlated non-covalent interaction energies.

    PubMed

    Mackie, Iain D; DiLabio, Gino A

    2011-10-07

    The first-principles calculation of non-covalent (particularly dispersion) interactions between molecules is a considerable challenge. In this work we studied the binding energies for ten small non-covalently bonded dimers with several combinations of correlation methods (MP2, coupled-cluster single double, coupled-cluster single double (triple) (CCSD(T))), correlation-consistent basis sets (aug-cc-pVXZ, X = D, T, Q), two-point complete basis set energy extrapolations, and counterpoise corrections. For this work, complete basis set results were estimated from averaged counterpoise and non-counterpoise-corrected CCSD(T) binding energies obtained from extrapolations with aug-cc-pVQZ and aug-cc-pVTZ basis sets. It is demonstrated that, in almost all cases, binding energies converge more rapidly to the basis set limit by averaging the counterpoise and non-counterpoise corrected values than by using either counterpoise or non-counterpoise methods alone. Examination of the effect of basis set size and electron correlation shows that the triples contribution to the CCSD(T) binding energies is fairly constant with the basis set size, with a slight underestimation with CCSD(T)∕aug-cc-pVDZ compared to the value at the (estimated) complete basis set limit, and that contributions to the binding energies obtained by MP2 generally overestimate the analogous CCSD(T) contributions. Taking these factors together, we conclude that the binding energies for non-covalently bonded systems can be accurately determined using a composite method that combines CCSD(T)∕aug-cc-pVDZ with energy corrections obtained using basis set extrapolated MP2 (utilizing aug-cc-pVQZ and aug-cc-pVTZ basis sets), if all of the components are obtained by averaging the counterpoise and non-counterpoise energies. With such an approach, binding energies for the set of ten dimers are predicted with a mean absolute deviation of 0.02 kcal/mol, a maximum absolute deviation of 0.05 kcal/mol, and a mean percent

  3. Accurate and balanced anisotropic Gaussian type orbital basis sets for atoms in strong magnetic fields

    NASA Astrophysics Data System (ADS)

    Zhu, Wuming; Trickey, S. B.

    2017-12-01

    In high magnetic field calculations, anisotropic Gaussian type orbital (AGTO) basis functions are capable of reconciling the competing demands of the spherically symmetric Coulombic interaction and cylindrical magnetic (B field) confinement. However, the best available a priori procedure for composing highly accurate AGTO sets for atoms in a strong B field [W. Zhu et al., Phys. Rev. A 90, 022504 (2014)] yields very large basis sets. Their size is problematical for use in any calculation with unfavorable computational cost scaling. Here we provide an alternative constructive procedure. It is based upon analysis of the underlying physics of atoms in B fields that allow identification of several principles for the construction of AGTO basis sets. Aided by numerical optimization and parameter fitting, followed by fine tuning of fitting parameters, we devise formulae for generating accurate AGTO basis sets in an arbitrary B field. For the hydrogen iso-electronic sequence, a set depends on B field strength, nuclear charge, and orbital quantum numbers. For multi-electron systems, the basis set formulae also include adjustment to account for orbital occupations. Tests of the new basis sets for atoms H through C (1 ≤ Z ≤ 6) and ions Li+, Be+, and B+, in a wide B field range (0 ≤ B ≤ 2000 a.u.), show an accuracy better than a few μhartree for single-electron systems and a few hundredths to a few mHs for multi-electron atoms. The relative errors are similar for different atoms and ions in a large B field range, from a few to a couple of tens of millionths, thereby confirming rather uniform accuracy across the nuclear charge Z and B field strength values. Residual basis set errors are two to three orders of magnitude smaller than the electronic correlation energies in multi-electron atoms, a signal of the usefulness of the new AGTO basis sets in correlated wavefunction or density functional calculations for atomic and molecular systems in an external strong B field.

  4. Accurate and balanced anisotropic Gaussian type orbital basis sets for atoms in strong magnetic fields.

    PubMed

    Zhu, Wuming; Trickey, S B

    2017-12-28

    In high magnetic field calculations, anisotropic Gaussian type orbital (AGTO) basis functions are capable of reconciling the competing demands of the spherically symmetric Coulombic interaction and cylindrical magnetic (B field) confinement. However, the best available a priori procedure for composing highly accurate AGTO sets for atoms in a strong B field [W. Zhu et al., Phys. Rev. A 90, 022504 (2014)] yields very large basis sets. Their size is problematical for use in any calculation with unfavorable computational cost scaling. Here we provide an alternative constructive procedure. It is based upon analysis of the underlying physics of atoms in B fields that allow identification of several principles for the construction of AGTO basis sets. Aided by numerical optimization and parameter fitting, followed by fine tuning of fitting parameters, we devise formulae for generating accurate AGTO basis sets in an arbitrary B field. For the hydrogen iso-electronic sequence, a set depends on B field strength, nuclear charge, and orbital quantum numbers. For multi-electron systems, the basis set formulae also include adjustment to account for orbital occupations. Tests of the new basis sets for atoms H through C (1 ≤ Z ≤ 6) and ions Li + , Be + , and B + , in a wide B field range (0 ≤ B ≤ 2000 a.u.), show an accuracy better than a few μhartree for single-electron systems and a few hundredths to a few mHs for multi-electron atoms. The relative errors are similar for different atoms and ions in a large B field range, from a few to a couple of tens of millionths, thereby confirming rather uniform accuracy across the nuclear charge Z and B field strength values. Residual basis set errors are two to three orders of magnitude smaller than the electronic correlation energies in multi-electron atoms, a signal of the usefulness of the new AGTO basis sets in correlated wavefunction or density functional calculations for atomic and molecular systems in an external strong B

  5. On the basis set convergence of electron–electron entanglement measures: helium-like systems

    PubMed Central

    Hofer, Thomas S.

    2013-01-01

    A systematic investigation of three different electron–electron entanglement measures, namely the von Neumann, the linear and the occupation number entropy at full configuration interaction level has been performed for the four helium-like systems hydride, helium, Li+ and Be2+ using a large number of different basis sets. The convergence behavior of the resulting energies and entropies revealed that the latter do in general not show the expected strictly monotonic increase upon increase of the one–electron basis. Overall, the three different entanglement measures show good agreement among each other, the largest deviations being observed for small basis sets. The data clearly demonstrates that it is important to consider the nature of the chemical system when investigating entanglement phenomena in the framework of Gaussian type basis sets: while in case of hydride the use of augmentation functions is crucial, the application of core functions greatly improves the accuracy in case of cationic systems such as Li+ and Be2+. In addition, numerical derivatives of the entanglement measures with respect to the nucleic charge have been determined, which proved to be a very sensitive probe of the convergence leading to qualitatively wrong results (i.e., the wrong sign) if too small basis sets are used. PMID:24790952

  6. On the basis set convergence of electron-electron entanglement measures: helium-like systems.

    PubMed

    Hofer, Thomas S

    2013-01-01

    A systematic investigation of three different electron-electron entanglement measures, namely the von Neumann, the linear and the occupation number entropy at full configuration interaction level has been performed for the four helium-like systems hydride, helium, Li(+) and Be(2+) using a large number of different basis sets. The convergence behavior of the resulting energies and entropies revealed that the latter do in general not show the expected strictly monotonic increase upon increase of the one-electron basis. Overall, the three different entanglement measures show good agreement among each other, the largest deviations being observed for small basis sets. The data clearly demonstrates that it is important to consider the nature of the chemical system when investigating entanglement phenomena in the framework of Gaussian type basis sets: while in case of hydride the use of augmentation functions is crucial, the application of core functions greatly improves the accuracy in case of cationic systems such as Li(+) and Be(2+). In addition, numerical derivatives of the entanglement measures with respect to the nucleic charge have been determined, which proved to be a very sensitive probe of the convergence leading to qualitatively wrong results (i.e., the wrong sign) if too small basis sets are used.

  7. Relativistic well-tempered Gaussian basis sets for helium through mercury. Breit interaction included

    SciTech Connect

    Okada, S.; Shinada, M.; Matsuoka, O.

    1990-10-01

    A systematic calculation of new relativistic Gaussian basis sets is reported. The new basis sets are similar to the previously reported ones (J. Chem. Phys. {bold 91}, 4193 (1989)), but, in the calculation, the Breit interaction has been explicitly included besides the Dirac--Coulomb Hamiltonian. They have been adopted for the calculation of the self-consistent field effect on the Breit interaction energies and are expected to be useful for the studies on higher-order effects such as the electron correlations and other quantum electrodynamical effects.

  8. Asymptotic behavior and interpretation of virtual states: The effects of confinement and of basis sets

    NASA Astrophysics Data System (ADS)

    Boffi, Nicholas M.; Jain, Manish; Natan, Amir

    2016-02-01

    A real-space high order finite difference method is used to analyze the effect of spherical domain size on the Hartree-Fock (and density functional theory) virtual eigenstates. We show the domain size dependence of both positive and negative virtual eigenvalues of the Hartree-Fock equations for small molecules. We demonstrate that positive states behave like a particle in spherical well and show how they approach zero. For the negative eigenstates, we show that large domains are needed to get the correct eigenvalues. We compare our results to those of Gaussian basis sets and draw some conclusions for real-space, basis-sets, and plane-waves calculations.

  9. Use of an auxiliary basis set to describe the polarization in the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Fedorov, Dmitri G.; Kitaura, Kazuo

    2014-03-01

    We developed a dual basis approach within the fragment molecular orbital formalism enabling efficient and accurate use of large basis sets. The method was tested on water clusters and polypeptides and applied to perform geometry optimization of chignolin (PDB: 1UAO) in solution at the level of DFT/6-31++G∗∗, obtaining a structure in agreement with experiment (RMSD of 0.4526 Å). The polarization in polypeptides is discussed with a comparison of the α-helix and β-strand.

  10. Polyatomic molecular Dirac-Hartree-Fock calculations with Gaussian basis sets

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Faegri, Knut, Jr.; Taylor, Peter R.

    1990-01-01

    Numerical methods have been used successfully in atomic Dirac-Hartree-Fock (DHF) calculations for many years. Some DHF calculations using numerical methods have been done on diatomic molecules, but while these serve a useful purpose for calibration, the computational effort in extending this approach to polyatomic molecules is prohibitive. An alternative more in line with traditional quantum chemistry is to use an analytical basis set expansion of the wave function. This approach fell into disrepute in the early 1980's due to problems with variational collapse and intruder states, but has recently been put on firm theoretical foundations. In particular, the problems of variational collapse are well understood, and prescriptions for avoiding the most serious failures have been developed. Consequently, it is now possible to develop reliable molecular programs using basis set methods. This paper describes such a program and reports results of test calculations to demonstrate the convergence and stability of the method.

  11. First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets.

    PubMed

    Demichelis, Raffaella; Bruno, Marco; Massaro, Francesco R; Prencipe, Mauro; De La Pierre, Marco; Nestola, Fabrizio

    2015-07-15

    The seven main crystal surfaces of forsterite (Mg2 SiO4 ) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor s of the dispersion formulation. An estimation for the surface energy is provided through adopting C6 coefficients that are more suitable than the standard ones to describe O-O interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface. © 2015 Wiley Periodicals, Inc.

  12. Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C

    NASA Astrophysics Data System (ADS)

    Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

    2017-06-01

    With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which—when stripped of BSSE—is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals—such as B97M-V—to recover large-basis results at a fraction of the cost.

  13. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

    SciTech Connect

    Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe

    2016-07-28

    Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set producesmore » <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.« less

  14. Geminal embedding scheme for optimal atomic basis set construction in correlated calculations

    SciTech Connect

    Sorella, S., E-mail: sorella@sissa.it; Devaux, N.; Dagrada, M., E-mail: mario.dagrada@impmc.upmc.fr

    2015-12-28

    We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wavemore » function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.« less

  15. Accuracy of Lagrange-sinc functions as a basis set for electronic structure calculations of atoms and molecules

    SciTech Connect

    Choi, Sunghwan; Hong, Kwangwoo; Kim, Jaewook

    2015-03-07

    We developed a self-consistent field program based on Kohn-Sham density functional theory using Lagrange-sinc functions as a basis set and examined its numerical accuracy for atoms and molecules through comparison with the results of Gaussian basis sets. The result of the Kohn-Sham inversion formula from the Lagrange-sinc basis set manifests that the pseudopotential method is essential for cost-effective calculations. The Lagrange-sinc basis set shows faster convergence of the kinetic and correlation energies of benzene as its size increases than the finite difference method does, though both share the same uniform grid. Using a scaling factor smaller than or equal tomore » 0.226 bohr and pseudopotentials with nonlinear core correction, its accuracy for the atomization energies of the G2-1 set is comparable to all-electron complete basis set limits (mean absolute deviation ≤1 kcal/mol). The same basis set also shows small mean absolute deviations in the ionization energies, electron affinities, and static polarizabilities of atoms in the G2-1 set. In particular, the Lagrange-sinc basis set shows high accuracy with rapid convergence in describing density or orbital changes by an external electric field. Moreover, the Lagrange-sinc basis set can readily improve its accuracy toward a complete basis set limit by simply decreasing the scaling factor regardless of systems.« less

  16. Time Domain Propagation of Quantum and Classical Systems using a Wavelet Basis Set Method

    NASA Astrophysics Data System (ADS)

    Lombardini, Richard; Nowara, Ewa; Johnson, Bruce

    2015-03-01

    The use of an orthogonal wavelet basis set (Optimized Maximum-N Generalized Coiflets) to effectively model physical systems in the time domain, in particular the electromagnetic (EM) pulse and quantum mechanical (QM) wavefunction, is examined in this work. Although past research has demonstrated the benefits of wavelet basis sets to handle computationally expensive problems due to their multiresolution properties, the overlapping supports of neighboring wavelet basis functions poses problems when dealing with boundary conditions, especially with material interfaces in the EM case. Specifically, this talk addresses this issue using the idea of derivative matching creating fictitious grid points (T.A. Driscoll and B. Fornberg), but replaces the latter element with fictitious wavelet projections in conjunction with wavelet reconstruction filters. Two-dimensional (2D) systems are analyzed, EM pulse incident on silver cylinders and the QM electron wave packet circling the proton in a hydrogen atom system (reduced to 2D), and the new wavelet method is compared to the popular finite-difference time-domain technique.

  17. Spectral properties of minimal-basis-set orbitals: Implications for molecular electronic continuum states

    NASA Astrophysics Data System (ADS)

    Langhoff, P. W.; Winstead, C. L.

    Early studies of the electronically excited states of molecules by John A. Pople and coworkers employing ab initio single-excitation configuration interaction (SECI) calculations helped to simulate related applications of these methods to the partial-channel photoionization cross sections of polyatomic molecules. The Gaussian representations of molecular orbitals adopted by Pople and coworkers can describe SECI continuum states when sufficiently large basis sets are employed. Minimal-basis virtual Fock orbitals stabilized in the continuous portions of such SECI spectra are generally associated with strong photoionization resonances. The spectral attributes of these resonance orbitals are illustrated here by revisiting previously reported experimental and theoretical studies of molecular formaldehyde (H2CO) in combination with recently calculated continuum orbital amplitudes.

  18. Zeta potential in ceramic industry

    NASA Technical Reports Server (NTRS)

    Lecuit, M.

    1984-01-01

    Deflocculation, electrical conductivity and zeta potential (ZP) are studied for the addition of 0 to 10000 ppm Na2SiO3 deflocculator to slips obtained from three argillaceous materials (kaolin d'Arvor, ball clay Hyplas 64, and/or Granger Clay No. 10). The quantity of Na2SO3 required to deflocculate a slip is independent of the density but differes for each clay. The ZP is directly related to the density of the slip. The higher the ZP the more stable a slip is; the value of the ZP of a mixture does not follow a simple law but the electrical resistance of a mixture does follow a simple additive law. The ZP appears to have linear relation with the specific surface of the argillaceous material.

  19. Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods.

    PubMed

    Gaspari, Roberto; Rapallo, Arnaldo

    2008-06-28

    In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum

  20. Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology.

    PubMed

    Galas, David J; Sakhanenko, Nikita A; Skupin, Alexander; Ignac, Tomasz

    2014-02-01

    Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity," we use an information theory approach to formulate general measures of systems complexity. We examine the properties of multivariable dependency starting with the concept of interaction information. We then present a new measure for unbiased detection of multivariable dependency, "differential interaction information." This quantity for two variables reduces to the pairwise "set complexity" previously proposed as a context-dependent measure of information in biological systems. We generalize it here to an arbitrary number of variables. Critical limiting properties of the "differential interaction information" are key to the generalization. This measure extends previous ideas about biological information and provides a more sophisticated basis for the study of complexity. The properties of "differential interaction information" also suggest new approaches to data analysis. Given a data set of system measurements, differential interaction information can provide a measure of collective dependence, which can be represented in hypergraphs describing complex system interaction patterns. We investigate this kind of analysis using simulated data sets. The conjoining of a generalized set complexity measure, multivariable dependency analysis, and hypergraphs is our central result. While our focus is on complex biological systems, our results are applicable to any complex system.

  1. Many-body calculations of molecular electric polarizabilities in asymptotically complete basis sets

    NASA Astrophysics Data System (ADS)

    Monten, Ruben; Hajgató, Balázs; Deleuze, Michael S.

    2011-10-01

    The static dipole polarizabilities of Ne, CO, N2, F2, HF, H2O, HCN, and C2H2 (acetylene) have been determined close to the Full-CI limit along with an asymptotically complete basis set (CBS), according to the principles of a Focal Point Analysis. For this purpose the results of Finite Field calculations up to the level of Coupled Cluster theory including Single, Double, Triple, Quadruple and perturbative Pentuple excitations [CCSDTQ(P)] were used, in conjunction with suited extrapolations of energies obtained using augmented and doubly-augmented Dunning's correlation consistent polarized valence basis sets of improving quality. The polarizability characteristics of C2H4 (ethylene) and C2H6 (ethane) have been determined on the same grounds at the CCSDTQ level in the CBS limit. Comparison is made with results obtained using lower levels in electronic correlation, or taking into account the relaxation of the molecular structure due to an adiabatic polarization process. Vibrational corrections to electronic polarizabilities have been empirically estimated according to Born-Oppenheimer Molecular Dynamical simulations employing Density Functional Theory. Confrontation with experiment ultimately indicates relative accuracies of the order of 1 to 2%.

  2. Polarization functions for the modified m6-31G basis sets for atoms Ga through Kr.

    PubMed

    Mitin, Alexander V

    2013-09-05

    The 2df polarization functions for the modified m6-31G basis sets of the third-row atoms Ga through Kr (Int J Quantum Chem, 2007, 107, 3028; Int J. Quantum Chem, 2009, 109, 1158) are proposed. The performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets were examined in molecular calculations carried out by the density functional theory (DFT) method with B3LYP hybrid functional, Møller-Plesset perturbation theory of the second order (MP2), quadratic configuration interaction method with single and double substitutions and were compared with those for the known 6-31G basis sets as well as with the other similar 641 and 6-311G basis sets with and without polarization functions. Obtained results have shown that the performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets are better in comparison with the performances of the known 6-31G, 6-31G(d,p) and 6-31G(2df,p) basis sets. These improvements are mainly reached due to better approximations of different electrons belonging to the different atomic shells in the modified basis sets. Applicability of the modified basis sets in thermochemical calculations is also discussed. © 2013 Wiley Periodicals, Inc.

  3. Influence of basis-set size on the X Σ 1 /2 +2 , A Π 1 /2 2 , A Π 3 /2 2 , and B Σ 1 /2 +2 potential-energy curves, A Π 3 /2 2 vibrational energies, and D1 and D2 line shapes of Rb+He

    NASA Astrophysics Data System (ADS)

    Blank, L. Aaron; Sharma, Amit R.; Weeks, David E.

    2018-03-01

    The X Σ 1 /2 +2 , A Π 1 /2 2 , A Π 3 /2 2 , and B2Σ1/2 + potential-energy curves for Rb+He are computed at the spin-orbit multireference configuration interaction level of theory using a hierarchy of Gaussian basis sets at the double-zeta (DZ), triple-zeta (TZ), and quadruple-zeta (QZ) levels of valence quality. Counterpoise and Davidson-Silver corrections are employed to remove basis-set superposition error and ameliorate size-consistency error. An extrapolation is performed to obtain a final set of potential-energy curves in the complete basis-set (CBS) limit. This yields four sets of systematically improved X Σ 1 /2 +2 , A Π 1 /2 2 , A Π 3 /2 2 , and B2Σ1/2 + potential-energy curves that are used to compute the A Π 3 /2 2 bound vibrational energies, the position of the D2 blue satellite peak, and the D1 and D2 pressure broadening and shifting coefficients, at the DZ, TZ, QZ, and CBS levels. Results are compared with previous calculations and experimental observation.

  4. 42 CFR 415.170 - Conditions for payment on a fee schedule basis for physician services in a teaching setting.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE... BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND RESIDENTS IN CERTAIN SETTINGS Physician Services in Teaching Settings § 415.170 Conditions for payment on a fee schedule basis...

  5. Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism

    NASA Astrophysics Data System (ADS)

    Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; Nicholson, D. M.; Johnson, Duane D.

    2014-11-01

    The Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an efficient site-centered, electronic-structure technique for addressing an assembly of N scatterers. Wave functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number Lmax=(l,mmax), while scattering matrices, which determine spectral properties, are truncated at Lt r=(l,mt r) where phase shifts δl >ltr are negligible. Historically, Lmax is set equal to Lt r, which is correct for large enough Lmax but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for Lmax>Lt r with δl >ltr set to zero [X.-G. Zhang and W. H. Butler, Phys. Rev. B 46, 7433 (1992), 10.1103/PhysRevB.46.7433]. We present a numerically efficient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R3 process with rank N (ltr+1 ) 2 ] and includes higher-L contributions via linear algebra [R2 process with rank N (lmax+1) 2 ]. The augmented-KKR approach yields properly normalized wave functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe, and L 1 0 CoPt and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus Lmax for a given Lt r.

  6. Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism

    DOE PAGES

    Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; ...

    2014-11-04

    Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an ecient sitecentered, electronic-structure technique for addressing an assembly of N scatterers. Wave-functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number L max = (l,m) max, while scattering matrices, which determine spectral properties, are truncated at L tr = (l,m) tr where phase shifts δl>l tr are negligible. Historically, L max is set equal to L tr, which is correct for large enough L max but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for L maxmore » > L tr with δl>l tr set to zero [Zhang and Butler, Phys. Rev. B 46, 7433]. We present a numerically ecient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R 3 process with rank N(l tr + 1) 2] and includes higher-L contributions via linear algebra [R 2 process with rank N(l max +1) 2]. Augmented-KKR approach yields properly normalized wave-functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe and L1 0 CoPt, and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus L max for a given L tr.« less

  7. Zeta potential control for electrophoresis cells

    NASA Technical Reports Server (NTRS)

    Fogal, G. L.

    1973-01-01

    Zeta potential arises from fact that ions tend to be adsorbed on surface of cell walls. This potential interfaces with electric field sensed by migrating particles and degrades resolution of separation. By regulating sign and magnitude of applied potential induced charge can be used to increase or decrease effective wall zeta potential.

  8. Dopaminergic basis for deficits in working memory but not attentional set-shifting in Parkinson's disease.

    PubMed

    Lewis, Simon J G; Slabosz, Aleksandra; Robbins, Trevor W; Barker, Roger A; Owen, Adrian M

    2005-01-01

    Although Parkinson's disease is a common neurodegenerative disorder characterised by its motoric symptoms, there is an increasing recognition of accompanying impairments in cognition that have a profound impact on the quality of life of these patients. These deficits predominantly affect executive function and impairments of working memory have been frequently reported. However, the underlying neurochemical and pathological basis for these deficits are not well understood. In this study, 20 patients were tested 'on' and 'off' levodopa (L-dopa) medication on a task that allowed different aspects of working memory function such as maintenance, retrieval and manipulation to be tested within the same general paradigm as well as on an unrelated test of attentional set-shifting, which is known to be sensitive to deficits in early Parkinson's disease. Compared to healthy volunteers, PD patients were impaired at manipulation more than maintenance or retrieval of information within working memory. The patients were also impaired at the attentional set-shifting task. However, whereas L-dopa ameliorated the working memory deficit in manipulation (improving both accuracy and cognitive response time), it had no effect on the attentional set-shifting impairment. These results confirm that working memory deficits in PD are both psychologically specific and related to dopamine depletion. It is anticipated that greater understanding of these mechanisms will lead to future therapeutic improvements.

  9. Velocity-gauge real-time TDDFT within a numerical atomic orbital basis set

    DOE PAGES

    Pemmaraju, C. D.; Vila, F. D.; Kas, J. J.; ...

    2018-02-07

    The interaction of laser fields with solid-state systems can be modeled efficiently within the velocity-gauge formalism of real-time time dependent density functional theory (RT-TDDFT). In this article, we discuss the implementation of the velocity-gauge RT-TDDFT equations for electron dynamics within a linear combination of atomic orbitals (LCAO) basis set framework. Numerical results obtained from our LCAO implementation, for the electronic response of periodic systems to both weak and intense laser fields, are compared to those obtained from established real-space grid and Full-Potential Linearized Augmented Planewave approaches. As a result, potential applications of the LCAO based scheme in the context ofmore » extreme ultra-violet and soft X-ray spectroscopies involving core-electronic excitations are discussed.« less

  10. Velocity-gauge real-time TDDFT within a numerical atomic orbital basis set

    SciTech Connect

    Pemmaraju, C. D.; Vila, F. D.; Kas, J. J.

    The interaction of laser fields with solid-state systems can be modeled efficiently within the velocity-gauge formalism of real-time time dependent density functional theory (RT-TDDFT). In this article, we discuss the implementation of the velocity-gauge RT-TDDFT equations for electron dynamics within a linear combination of atomic orbitals (LCAO) basis set framework. Numerical results obtained from our LCAO implementation, for the electronic response of periodic systems to both weak and intense laser fields, are compared to those obtained from established real-space grid and Full-Potential Linearized Augmented Planewave approaches. As a result, potential applications of the LCAO based scheme in the context ofmore » extreme ultra-violet and soft X-ray spectroscopies involving core-electronic excitations are discussed.« less

  11. Velocity-gauge real-time TDDFT within a numerical atomic orbital basis set

    NASA Astrophysics Data System (ADS)

    Pemmaraju, C. D.; Vila, F. D.; Kas, J. J.; Sato, S. A.; Rehr, J. J.; Yabana, K.; Prendergast, David

    2018-05-01

    The interaction of laser fields with solid-state systems can be modeled efficiently within the velocity-gauge formalism of real-time time dependent density functional theory (RT-TDDFT). In this article, we discuss the implementation of the velocity-gauge RT-TDDFT equations for electron dynamics within a linear combination of atomic orbitals (LCAO) basis set framework. Numerical results obtained from our LCAO implementation, for the electronic response of periodic systems to both weak and intense laser fields, are compared to those obtained from established real-space grid and Full-Potential Linearized Augmented Planewave approaches. Potential applications of the LCAO based scheme in the context of extreme ultra-violet and soft X-ray spectroscopies involving core-electronic excitations are discussed.

  12. Dynamic sensitivity analysis of long running landslide models through basis set expansion and meta-modelling

    NASA Astrophysics Data System (ADS)

    Rohmer, Jeremy

    2016-04-01

    Predicting the temporal evolution of landslides is typically supported by numerical modelling. Dynamic sensitivity analysis aims at assessing the influence of the landslide properties on the time-dependent predictions (e.g., time series of landslide displacements). Yet two major difficulties arise: 1. Global sensitivity analysis require running the landslide model a high number of times (> 1000), which may become impracticable when the landslide model has a high computation time cost (> several hours); 2. Landslide model outputs are not scalar, but function of time, i.e. they are n-dimensional vectors with n usually ranging from 100 to 1000. In this article, I explore the use of a basis set expansion, such as principal component analysis, to reduce the output dimensionality to a few components, each of them being interpreted as a dominant mode of variation in the overall structure of the temporal evolution. The computationally intensive calculation of the Sobol' indices for each of these components are then achieved through meta-modelling, i.e. by replacing the landslide model by a "costless-to-evaluate" approximation (e.g., a projection pursuit regression model). The methodology combining "basis set expansion - meta-model - Sobol' indices" is then applied to the La Frasse landslide to investigate the dynamic sensitivity analysis of the surface horizontal displacements to the slip surface properties during the pore pressure changes. I show how to extract information on the sensitivity of each main modes of temporal behaviour using a limited number (a few tens) of long running simulations. In particular, I identify the parameters, which trigger the occurrence of a turning point marking a shift between a regime of low values of landslide displacements and one of high values.

  13. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

    SciTech Connect

    Hsu, Po Jen; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw; Rapallo, Arnaldo

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible syntheticmore » polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed

  14. Rocket spectroscopy of zeta Orionis.

    NASA Technical Reports Server (NTRS)

    Smith, A. M.

    1972-01-01

    Analysis of a spectrum of zeta Ori extending from 922 to 1453 A with approximately 0.8 A resolution recorded at rocket altitudes. All lines used in existing models of stellar atmospheres appear in the recorded spectrum with the exception of those masked by telluric N2 or strong P Cygni-type profiles and by an O V line at 1371.29 A. Fifteen multiplets of subordinate lines have been reliably identified, indicating an approximate range of excitation from 0 to 50 eV. Transitions in C III (1176 A), N III (991 A), N V (1239, 1243 A), O VI (1032, 1038 A), Si IV (1394, 1403 A), S IV (1063, 1074 A), and S VI (933, 944 A) have been observed as P Cygni-type profiles presumably arising in a circumstellar envelope. The degree of ionization, transitions present, and mean radial velocities are all consistent with viewing the envelope as a hot (about 100,000 K), rarefied plasma in which collisional ionization is important. Interstellar lines in C I (1277, 1280 A), C II (1036, 1334 A), N I (1134-1135 A), N I (1200-1201 A), N II (1084-1086 A), O I (1302, 1305 A), Si II (1190, 1193 A), Si II (1260 A), and Si II (1304 A) have been definitely identified. Other transitions in Ar II, S I, C I, and Fe II are tentatively identified. The equivalent width of the L alpha line is found to be 10.4 plus or minus 1.6 A, corresponding to a columnar density of 2.0 plus or minus 0.7 x 10 to the 20th per cu cm.

  15. Updating the OMERACT filter: core areas as a basis for defining core outcome sets.

    PubMed

    Kirwan, John R; Boers, Maarten; Hewlett, Sarah; Beaton, Dorcas; Bingham, Clifton O; Choy, Ernest; Conaghan, Philip G; D'Agostino, Maria-Antonietta; Dougados, Maxime; Furst, Daniel E; Guillemin, Francis; Gossec, Laure; van der Heijde, Désirée M; Kloppenburg, Margreet; Kvien, Tore K; Landewé, Robert B M; Mackie, Sarah L; Matteson, Eric L; Mease, Philip J; Merkel, Peter A; Ostergaard, Mikkel; Saketkoo, Lesley Ann; Simon, Lee; Singh, Jasvinder A; Strand, Vibeke; Tugwell, Peter

    2014-05-01

    The Outcome Measures in Rheumatology (OMERACT) Filter provides guidelines for the development and validation of outcome measures for use in clinical research. The "Truth" section of the OMERACT Filter presupposes an explicit framework for identifying the relevant core outcomes that are universal to all studies of the effects of intervention effects. There is no published outline for instrument choice or development that is aimed at measuring outcome, was derived from broad consensus over its underlying philosophy, or includes a structured and documented critique. Therefore, a new proposal for defining core areas of measurement ("Filter 2.0 Core Areas of Measurement") was presented at OMERACT 11 to explore areas of consensus and to consider whether already endorsed core outcome sets fit into this newly proposed framework. Discussion groups critically reviewed the extent to which case studies of current OMERACT Working Groups complied with or negated the proposed framework, whether these observations had a more general application, and what issues remained to be resolved. Although there was broad acceptance of the framework in general, several important areas of construction, presentation, and clarity of the framework were questioned. The discussion groups and subsequent feedback highlighted 20 such issues. These issues will require resolution to reach consensus on accepting the proposed Filter 2.0 framework of Core Areas as the basis for the selection of Core Outcome Domains and hence appropriate Core Outcome Sets for clinical trials.

  16. Kinetic balance and variational bounds failure in the solution of the Dirac equation in a finite Gaussian basis set

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Faegri, Knut, Jr.

    1990-01-01

    The paper investigates bounds failure in calculations using Gaussian basis sets for the solution of the one-electron Dirac equation for the 2p1/2 state of Hg(79+). It is shown that bounds failure indicates inadequacies in the basis set, both in terms of the exponent range and the number of functions. It is also shown that overrepresentation of the small component space may lead to unphysical results. It is concluded that it is important to use matched large and small component basis sets with an adequate size and exponent range.

  17. Chromospheric Structure and Wind Acceleration in Zeta Aur Stars

    NASA Technical Reports Server (NTRS)

    Bennett, Philip D.

    2001-01-01

    This NASA grant supported an analysis of the variability of the wind of the supergiant primary star (K4 Ib) in the eclipsing binary Zeta Aurigae (Zeta Aur). In the ultraviolet, the main-sequence companion star (B5 V) dominates the observed flux, and therefore serves as a convenient probe of the cool supergiant's wind. This study utilized the extensive set of (100+) ultraviolet spectroscopic observations obtained with the International Ultraviolet Explorer (IUE) satellite over its operational lifetime of 1978-1995. Although the resolution of IUE is limited (about 25 km/s), it is adequate to resolve variability in the wind features in Zeta Aur's ultraviolet spectrum, which are blueshifted 70 km/s from line center. Our analysis used the tau-v technique of Cardelli and Savage, which makes full use of the available line profile information. We find that the wind column densities vary by up to an order of magnitude over time. These results are being written up for submission to the Astrophysical Journal as the third paper of a series on the chromosphere and wind of Zeta Aurigae. The first two papers report on the construction of mean chromosphere and wind models respectively, based on HST/GHRS observations and funded by STScI. The third paper - this research - reports on variability of the Zeta Aur wind as determined from our analysis of the long IUE time series. This paper will be completed within the next three months; the delay in publication was to allow the completion of Papers 1 and 2, which logically precede the present work. Therefore, an additional no-cost extension was requested in order to ensure budgeted funds remain available for publication of this work. Unfortunately, this request was denied, and so I am forced to write this final report before publication of Paper 3. Regardless, this paper will be submitted for publication within the next three months.

  18. Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets

    SciTech Connect

    Holden, Zachary C.; Richard, Ryan M.; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu

    2013-12-28

    An implementation of Ewald summation for use in mixed quantum mechanics/molecular mechanics (QM/MM) calculations is presented, which builds upon previous work by others that was limited to semi-empirical electronic structure for the QM region. Unlike previous work, our implementation describes the wave function's periodic images using “ChElPG” atomic charges, which are determined by fitting to the QM electrostatic potential evaluated on a real-space grid. This implementation is stable even for large Gaussian basis sets with diffuse exponents, and is thus appropriate when the QM region is described by a correlated wave function. Derivatives of the ChElPG charges with respect tomore » the QM density matrix are a potentially serious bottleneck in this approach, so we introduce a ChElPG algorithm based on atom-centered Lebedev grids. The ChElPG charges thus obtained exhibit good rotational invariance even for sparse grids, enabling significant cost savings. Detailed analysis of the optimal choice of user-selected Ewald parameters, as well as timing breakdowns, is presented.« less

  19. Rank-order-selective neurons form a temporal basis set for the generation of motor sequences.

    PubMed

    Salinas, Emilio

    2009-04-08

    Many behaviors are composed of a series of elementary motor actions that must occur in a specific order, but the neuronal mechanisms by which such motor sequences are generated are poorly understood. In particular, if a sequence consists of a few motor actions, a primate can learn to replicate it from memory after practicing it for just a few trials. How do the motor and premotor areas of the brain assemble motor sequences so fast? The network model presented here reveals part of the solution to this problem. The model is based on experiments showing that, during the performance of motor sequences, some cortical neurons are always activated at specific times, regardless of which motor action is being executed. In the model, a population of such rank-order-selective (ROS) cells drives a layer of downstream motor neurons so that these generate specific movements at different times in different sequences. A key ingredient of the model is that the amplitude of the ROS responses must be modulated by sequence identity. Because of this modulation, which is consistent with experimental reports, the network is able not only to produce multiple sequences accurately but also to learn a new sequence with minimal changes in connectivity. The ROS neurons modulated by sequence identity thus serve as a basis set for constructing arbitrary sequences of motor responses downstream. The underlying mechanism is analogous to the mechanism described in parietal areas for generating coordinate transformations in the spatial domain.

  20. RANK-ORDER-SELECTIVE NEURONS FORM A TEMPORAL BASIS SET FOR THE GENERATION OF MOTOR SEQUENCES

    PubMed Central

    Salinas, Emilio

    2009-01-01

    Many behaviors are composed of a series of elementary motor actions that must occur in a specific order, but the neuronal mechanisms by which such motor sequences are generated are poorly understood. In particular, if a sequence consists of a few motor actions, a primate can learn to replicate it from memory after practicing it for just a few trials. How do the motor and premotor areas of the brain assemble motor sequences so fast? The network model presented here reveals part of the solution to this problem. The model is based on experiments showing that, during the performance of motor sequences, some cortical neurons are always activated at specific times, regardless of which motor action is being executed. In the model, a population of such rank-order-selective (ROS) cells drives a layer of downstream motor neurons so that these generate specific movements at different times in different sequences. A key ingredient of the model is that the amplitude of the ROS responses must be modulated by sequence identity. Because of this modulation, which is consistent with experimental reports, the network is able not only to produce multiple sequences accurately but also to learn a new sequence with minimal changes in connectivity. The ROS neurons modulated by sequence identity thus serve as a basis set for constructing arbitrary sequences of motor responses downstream. The underlying mechanism is analogous to the mechanism described in parietal areas for generating coordinate transformations in the spatial domain. PMID:19357265

  1. Numerical Aspects of Atomic Physics: Helium Basis Sets and Matrix Diagonalization

    NASA Astrophysics Data System (ADS)

    Jentschura, Ulrich; Noble, Jonathan

    2014-03-01

    We present a matrix diagonalization algorithm for complex symmetric matrices, which can be used in order to determine the resonance energies of auto-ionizing states of comparatively simple quantum many-body systems such as helium. The algorithm is based in multi-precision arithmetic and proceeds via a tridiagonalization of the complex symmetric (not necessarily Hermitian) input matrix using generalized Householder transformations. Example calculations involving so-called PT-symmetric quantum systems lead to reference values which pertain to the imaginary cubic perturbation (the imaginary cubic anharmonic oscillator). We then proceed to novel basis sets for the helium atom and present results for Bethe logarithms in hydrogen and helium, obtained using the enhanced numerical techniques. Some intricacies of ``canned'' algorithms such as those used in LAPACK will be discussed. Our algorithm, for complex symmetric matrices such as those describing cubic resonances after complex scaling, is faster than LAPACK's built-in routines, for specific classes of input matrices. It also offer flexibility in terms of the calculation of the so-called implicit shift, which is used in order to ``pivot'' the system toward the convergence to diagonal form. We conclude with a wider overview.

  2. Communication: Density functional theory embedding with the orthogonality constrained basis set expansion procedure

    NASA Astrophysics Data System (ADS)

    Culpitt, Tanner; Brorsen, Kurt R.; Hammes-Schiffer, Sharon

    2017-06-01

    Density functional theory (DFT) embedding approaches have generated considerable interest in the field of computational chemistry because they enable calculations on larger systems by treating subsystems at different levels of theory. To circumvent the calculation of the non-additive kinetic potential, various projector methods have been developed to ensure the orthogonality of molecular orbitals between subsystems. Herein the orthogonality constrained basis set expansion (OCBSE) procedure is implemented to enforce this subsystem orbital orthogonality without requiring a level shifting parameter. This scheme is a simple alternative to existing parameter-free projector-based schemes, such as the Huzinaga equation. The main advantage of the OCBSE procedure is that excellent convergence behavior is attained for DFT-in-DFT embedding without freezing any of the subsystem densities. For the three chemical systems studied, the level of accuracy is comparable to or higher than that obtained with the Huzinaga scheme with frozen subsystem densities. Allowing both the high-level and low-level DFT densities to respond to each other during DFT-in-DFT embedding calculations provides more flexibility and renders this approach more generally applicable to chemical systems. It could also be useful for future extensions to embedding approaches combining wavefunction theories and DFT.

  3. On the effects of basis set truncation and electron correlation in conformers of 2-hydroxy-acetamide

    NASA Astrophysics Data System (ADS)

    Szarecka, A.; Day, G.; Grout, P. J.; Wilson, S.

    Ab initio quantum chemical calculations have been used to study the differences in energy between two gas phase conformers of the 2-hydroxy-acetamide molecule that possess intramolecular hydrogen bonding. In particular, rotation around the central C-C bond has been considered as a factor determining the structure of the hydrogen bond and stabilization of the conformer. Energy calculations include full geometiy optimization using both the restricted matrix Hartree-Fock model and second-order many-body perturbation theory with a number of commonly used basis sets. The basis sets employed ranged from the minimal STO-3G set to [`]split-valence' sets up to 6-31 G. The effects of polarization functions were also studied. The results display a strong basis set dependence.

  4. The Scientific Basis of Uncertainty Factors Used in Setting Occupational Exposure Limits.

    PubMed

    Dankovic, D A; Naumann, B D; Maier, A; Dourson, M L; Levy, L S

    2015-01-01

    The uncertainty factor concept is integrated into health risk assessments for all aspects of public health practice, including by most organizations that derive occupational exposure limits. The use of uncertainty factors is predicated on the assumption that a sufficient reduction in exposure from those at the boundary for the onset of adverse effects will yield a safe exposure level for at least the great majority of the exposed population, including vulnerable subgroups. There are differences in the application of the uncertainty factor approach among groups that conduct occupational assessments; however, there are common areas of uncertainty which are considered by all or nearly all occupational exposure limit-setting organizations. Five key uncertainties that are often examined include interspecies variability in response when extrapolating from animal studies to humans, response variability in humans, uncertainty in estimating a no-effect level from a dose where effects were observed, extrapolation from shorter duration studies to a full life-time exposure, and other insufficiencies in the overall health effects database indicating that the most sensitive adverse effect may not have been evaluated. In addition, a modifying factor is used by some organizations to account for other remaining uncertainties-typically related to exposure scenarios or accounting for the interplay among the five areas noted above. Consideration of uncertainties in occupational exposure limit derivation is a systematic process whereby the factors applied are not arbitrary, although they are mathematically imprecise. As the scientific basis for uncertainty factor application has improved, default uncertainty factors are now used only in the absence of chemical-specific data, and the trend is to replace them with chemical-specific adjustment factors whenever possible. The increased application of scientific data in the development of uncertainty factors for individual chemicals also has

  5. Characterizing and Understanding the Remarkably Slow Basis Set Convergence of Several Minnesota Density Functionals for Intermolecular Interaction Energies

    SciTech Connect

    Mardirossian, Narbe; Head-Gordon, Martin

    2013-08-22

    For a set of eight equilibrium intermolecular complexes, it is discovered in this paper that the basis set limit (BSL) cannot be reached by aug-cc-pV5Z for three of the Minnesota density functionals: M06-L, M06-HF, and M11-L. In addition, the M06 and M11 functionals exhibit substantial, but less severe, difficulties in reaching the BSL. By using successively finer grids, it is demonstrated that this issue is not related to the numerical integration of the exchange-correlation functional. In addition, it is shown that the difficulty in reaching the BSL is not a direct consequence of the structure of the augmented functions inmore » Dunning’s basis sets, since modified augmentation yields similar results. By using a very large custom basis set, the BSL appears to be reached for the HF dimer for all of the functionals. As a result, it is concluded that the difficulties faced by several of the Minnesota density functionals are related to an interplay between the form of these functionals and the structure of standard basis sets. It is speculated that the difficulty in reaching the basis set limit is related to the magnitude of the inhomogeneity correction factor (ICF) of the exchange functional. A simple modification of the M06-L exchange functional that systematically reduces the basis set superposition error (BSSE) for the HF dimer in the aug-cc-pVQZ basis set is presented, further supporting the speculation that the difficulty in reaching the BSL is caused by the magnitude of the exchange functional ICF. In conclusion, the BSSE is plotted with respect to the internuclear distance of the neon dimer for two of the examined functionals.« less

  6. Atomic Cholesky decompositions: a route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency.

    PubMed

    Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

    2009-04-21

    Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

  7. Atomic Cholesky decompositions: A route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency

    NASA Astrophysics Data System (ADS)

    Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

    2009-04-01

    Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

  8. Expressing clinical data sets with openEHR archetypes: a solid basis for ubiquitous computing.

    PubMed

    Garde, Sebastian; Hovenga, Evelyn; Buck, Jasmin; Knaup, Petra

    2007-12-01

    The purpose of this paper is to analyse the feasibility and usefulness of expressing clinical data sets (CDSs) as openEHR archetypes. For this, we present an approach to transform CDS into archetypes, and outline typical problems with CDS and analyse whether some of these problems can be overcome by the use of archetypes. Literature review and analysis of a selection of existing Australian, German, other European and international CDSs; transfer of a CDS for Paediatric Oncology into openEHR archetypes; implementation of CDSs in application systems. To explore the feasibility of expressing CDS as archetypes an approach to transform existing CDSs into archetypes is presented in this paper. In case of the Paediatric Oncology CDS (which consists of 260 data items) this lead to the definition of 48 openEHR archetypes. To analyse the usefulness of expressing CDS as archetypes, we identified nine problems with CDS that currently remain unsolved without a common model underpinning the CDS. Typical problems include incompatible basic data types and overlapping and incompatible definitions of clinical content. A solution to most of these problems based on openEHR archetypes is motivated. With regard to integrity constraints, further research is required. While openEHR cannot overcome all barriers to Ubiquitous Computing, it can provide the common basis for ubiquitous presence of meaningful and computer-processable knowledge and information, which we believe is a basic requirement for Ubiquitous Computing. Expressing CDSs as openEHR archetypes is feasible and advantageous as it fosters semantic interoperability, supports ubiquitous computing, and helps to develop archetypes that are arguably of better quality than the original CDS.

  9. Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors

    SciTech Connect

    Kamiya, Muneaki; Hirata, So; Valiev, Marat

    2008-02-19

    Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly-interacting molecular clusters [Hirata et al. Mol. Phys. 103, 2255 (2005)] have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine–water clusters with an excellent result for an initial performance assessment. Our original method included up to two- or three-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the dipole–dipole approximation. In this work, the dipole moments are replaced by atom-centered point charges determined so that they reproduce the electrostatic potentials of themore » cluster subunits as closely as possible and also self-consistently with one another in the cluster environment. They have been shown to lead to dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits like zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSE) known to plague direct evaluation of weak interactions have been eliminated by com-bining the Valiron–Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method in an economical fashion (quadratic scaling n2 with respect to the number of subunits n when n is small and linear scaling when n is large). A new variant of VMFC has also been proposed in which three-body and all higher-order Coulomb effects on BSSE are estimated approximately. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results of conventional electron correlation calculations within 0.1 kcal/mol. The proposed method is significantly more accurate and also efficient than conventional correlation methods uncorrected of BSSE.« less

  10. On the Use of a Mixed Gaussian/Finite-Element Basis Set for the Calculation of Rydberg States

    NASA Technical Reports Server (NTRS)

    Thuemmel, Helmar T.; Langhoff, Stephen (Technical Monitor)

    1996-01-01

    Configuration-interaction studies are reported for the Rydberg states of the helium atom using mixed Gaussian/finite-element (GTO/FE) one particle basis sets. Standard Gaussian valence basis sets are employed, like those, used extensively in quantum chemistry calculations. It is shown that the term values for high-lying Rydberg states of the helium atom can be obtained accurately (within 1 cm -1), even for a small GTO set, by augmenting the n-particle space with configurations, where orthonormalized interpolation polynomials are singly occupied.

  11. Auxiliary basis sets for density-fitting second-order Møller-Plesset perturbation theory: weighted core-valence correlation consistent basis sets for the 4d elements Y-Pd.

    PubMed

    Hill, J Grant

    2013-09-30

    Auxiliary basis sets (ABS) specifically matched to the cc-pwCVnZ-PP and aug-cc-pwCVnZ-PP orbital basis sets (OBS) have been developed and optimized for the 4d elements Y-Pd at the second-order Møller-Plesset perturbation theory level. Calculation of the core-valence electron correlation energies for small to medium sized transition metal complexes demonstrates that the error due to the use of these new sets in density fitting is three to four orders of magnitude smaller than that due to the OBS incompleteness, and hence is considered negligible. Utilizing the ABSs in the resolution-of-the-identity component of explicitly correlated calculations is also investigated, where it is shown that i-type functions are important to produce well-controlled errors in both integrals and correlation energy. Benchmarking at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations level indicates impressive convergence with respect to basis set size for the spectroscopic constants of 4d monofluorides; explicitly correlated double-ζ calculations produce results close to conventional quadruple-ζ, and triple-ζ is within chemical accuracy of the complete basis set limit. Copyright © 2013 Wiley Periodicals, Inc.

  12. The application of midbond basis sets in efficient and accurate ab initio calculations on electron-deficient systems

    NASA Astrophysics Data System (ADS)

    Choi, Chu Hwan

    2002-09-01

    Ab initio chemistry has shown great promise in reproducing experimental results and in its predictive power. The many complicated computational models and methods seem impenetrable to an inexperienced scientist, and the reliability of the results is not easily interpreted. The application of midbond orbitals is used to determine a general method for use in calculating weak intermolecular interactions, especially those involving electron-deficient systems. Using the criteria of consistency, flexibility, accuracy and efficiency we propose a supermolecular method of calculation using the full counterpoise (CP) method of Boys and Bernardi, coupled with Moller-Plesset (MP) perturbation theory as an efficient electron-correlative method. We also advocate the use of the highly efficient and reliable correlation-consistent polarized valence basis sets of Dunning. To these basis sets, we add a general set of midbond orbitals and demonstrate greatly enhanced efficiency in the calculation. The H2-H2 dimer is taken as a benchmark test case for our method, and details of the computation are elaborated. Our method reproduces with great accuracy the dissociation energies of other previous theoretical studies. The added efficiency of extending the basis sets with conventional means is compared with the performance of our midbond-extended basis sets. The improvement found with midbond functions is notably superior in every case tested. Finally, a novel application of midbond functions to the BH5 complex is presented. The system is an unusual van der Waals complex. The interaction potential curves are presented for several standard basis sets and midbond-enhanced basis sets, as well as for two popular, alternative correlation methods. We report that MP theory appears to be superior to coupled-cluster (CC) in speed, while it is more stable than B3LYP, a widely-used density functional theory (DFT). Application of our general method yields excellent results for the midbond basis sets

  13. Open-ended recursive calculation of single residues of response functions for perturbation-dependent basis sets.

    PubMed

    Friese, Daniel H; Ringholm, Magnus; Gao, Bin; Ruud, Kenneth

    2015-10-13

    We present theory, implementation, and applications of a recursive scheme for the calculation of single residues of response functions that can treat perturbations that affect the basis set. This scheme enables the calculation of nonlinear light absorption properties to arbitrary order for other perturbations than an electric field. We apply this scheme for the first treatment of two-photon circular dichroism (TPCD) using London orbitals at the Hartree-Fock level of theory. In general, TPCD calculations suffer from the problem of origin dependence, which has so far been solved by using the velocity gauge for the electric dipole operator. This work now enables comparison of results from London orbital and velocity gauge based TPCD calculations. We find that the results from the two approaches both exhibit strong basis set dependence but that they are very similar with respect to their basis set convergence.

  14. Møller-Plesset perturbation energies and distances for HeC(20) extrapolated to the complete basis set limit.

    PubMed

    Varandas, A J C

    2009-02-01

    The potential energy surface for the C(20)-He interaction is extrapolated for three representative cuts to the complete basis set limit using second-order Møller-Plesset perturbation calculations with correlation consistent basis sets up to the doubly augmented variety. The results both with and without counterpoise correction show consistency with each other, supporting that extrapolation without such a correction provides a reliable scheme to elude the basis-set-superposition error. Converged attributes are obtained for the C(20)-He interaction, which are used to predict the fullerene dimer ones. Time requirements show that the method can be drastically more economical than the counterpoise procedure and even competitive with Kohn-Sham density functional theory for the title system.

  15. 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 (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.

  16. Parallel Douglas-Kroll Energy and Gradients in NWChem. Estimating Scalar Relativistic Effects Using Douglas-Kroll Contracted Basis Sets.

    SciTech Connect

    De Jong, Wibe A.; Harrison, Robert J.; Dixon, David A.

    A parallel implementation of the spin-free one-electron Douglas-Kroll(-Hess) Hamiltonian (DKH) in NWChem is discussed. An efficient and accurate method to calculate DKH gradients is introduced. It is shown that the use of standard (non-relativistic) contracted basis set can produce erroneous results for elements beyond the first row elements. The generation of DKH contracted cc-pVXZ (X = D, T, Q, 5) basis sets for H, He, B - Ne, Al - Ar, and Ga - Br will be discussed.

  17. A minimization method on the basis of embedding the feasible set and the epigraph

    NASA Astrophysics Data System (ADS)

    Zabotin, I. Ya; Shulgina, O. N.; Yarullin, R. S.

    2016-11-01

    We propose a conditional minimization method of the convex nonsmooth function which belongs to the class of cutting-plane methods. During constructing iteration points a feasible set and an epigraph of the objective function are approximated by the polyhedral sets. In this connection, auxiliary problems of constructing iteration points are linear programming problems. In optimization process there is some opportunity of updating sets which approximate the epigraph. These updates are performed by periodically dropping of cutting planes which form embedding sets. Convergence of the proposed method is proved, some realizations of the method are discussed.

  18. Computational strategies for the Riemann zeta function

    NASA Astrophysics Data System (ADS)

    Borwein, Jonathan M.; Bradley, David M.; Crandall, Richard E.

    2000-09-01

    We provide a compendium of evaluation methods for the Riemann zeta function, presenting formulae ranging from historical attempts to recently found convergent series to curious oddities old and new. We concentrate primarily on practical computational issues, such issues depending on the domain of the argument, the desired speed of computation, and the incidence of what we call "value recycling".

  19. Accurate Gaussian basis sets for atomic and molecular calculations obtained from the generator coordinate method with polynomial discretization.

    PubMed

    Celeste, Ricardo; Maringolo, Milena P; Comar, Moacyr; Viana, Rommel B; Guimarães, Amanda R; Haiduke, Roberto L A; da Silva, Albérico B F

    2015-10-01

    Accurate Gaussian basis sets for atoms from H to Ba were obtained by means of the generator coordinate Hartree-Fock (GCHF) method based on a polynomial expansion to discretize the Griffin-Wheeler-Hartree-Fock equations (GWHF). The discretization of the GWHF equations in this procedure is based on a mesh of points not equally distributed in contrast with the original GCHF method. The results of atomic Hartree-Fock energies demonstrate the capability of these polynomial expansions in designing compact and accurate basis sets to be used in molecular calculations and the maximum error found when compared to numerical values is only 0.788 mHartree for indium. Some test calculations with the B3LYP exchange-correlation functional for N2, F2, CO, NO, HF, and HCN show that total energies within 1.0 to 2.4 mHartree compared to the cc-pV5Z basis sets are attained with our contracted bases with a much smaller number of polarization functions (2p1d and 2d1f for hydrogen and heavier atoms, respectively). Other molecular calculations performed here are also in very good accordance with experimental and cc-pV5Z results. The most important point to be mentioned here is that our generator coordinate basis sets required only a tiny fraction of the computational time when compared to B3LYP/cc-pV5Z calculations.

  20. Straightening the Hierarchical Staircase for Basis Set Extrapolations: A Low-Cost Approach to High-Accuracy Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Varandas, António J. C.

    2018-04-01

    Because the one-electron basis set limit is difficult to reach in correlated post-Hartree-Fock ab initio calculations, the low-cost route of using methods that extrapolate to the estimated basis set limit attracts immediate interest. The situation is somewhat more satisfactory at the Hartree-Fock level because numerical calculation of the energy is often affordable at nearly converged basis set levels. Still, extrapolation schemes for the Hartree-Fock energy are addressed here, although the focus is on the more slowly convergent and computationally demanding correlation energy. Because they are frequently based on the gold-standard coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)], correlated calculations are often affordable only with the smallest basis sets, and hence single-level extrapolations from one raw energy could attain maximum usefulness. This possibility is examined. Whenever possible, this review uses raw data from second-order Møller-Plesset perturbation theory, as well as CCSD, CCSD(T), and multireference configuration interaction methods. Inescapably, the emphasis is on work done by the author's research group. Certain issues in need of further research or review are pinpointed.

  1. Push it to the limit: Characterizing the convergence of common sequences of basis sets for intermolecular interactions as described by density functional theory

    NASA Astrophysics Data System (ADS)

    Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

    2016-05-01

    With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.

  2. Accelerating wavefunction in density-functional-theory embedding by truncating the active basis set

    NASA Astrophysics Data System (ADS)

    Bennie, Simon J.; Stella, Martina; Miller, Thomas F.; Manby, Frederick R.

    2015-07-01

    Methods where an accurate wavefunction is embedded in a density-functional description of the surrounding environment have recently been simplified through the use of a projection operator to ensure orthogonality of orbital subspaces. Projector embedding already offers significant performance gains over conventional post-Hartree-Fock methods by reducing the number of correlated occupied orbitals. However, in our first applications of the method, we used the atomic-orbital basis for the full system, even for the correlated wavefunction calculation in a small, active subsystem. Here, we further develop our method for truncating the atomic-orbital basis to include only functions within or close to the active subsystem. The number of atomic orbitals in a calculation on a fixed active subsystem becomes asymptotically independent of the size of the environment, producing the required O ( N 0 ) scaling of cost of the calculation in the active subsystem, and accuracy is controlled by a single parameter. The applicability of this approach is demonstrated for the embedded many-body expansion of binding energies of water hexamers and calculation of reaction barriers of SN2 substitution of fluorine by chlorine in α-fluoroalkanes.

  3. Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics

    NASA Astrophysics Data System (ADS)

    Lazariev, A.; Allouche, A.-R.; Aubert-Frécon, M.; Fauvelle, F.; Piotto, M.; Elbayed, K.; Namer, I.-J.; van Ormondt, D.; Graveron-Demilly, D.

    2011-11-01

    High-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) is playing an increasingly important role for diagnosis. This technique enables setting up metabolite profiles of ex vivo pathological and healthy tissue. The need to monitor diseases and pharmaceutical follow-up requires an automatic quantitation of HRMAS 1H signals. However, for several metabolites, the values of chemical shifts of proton groups may slightly differ according to the micro-environment in the tissue or cells, in particular to its pH. This hampers the accurate estimation of the metabolite concentrations mainly when using quantitation algorithms based on a metabolite basis set: the metabolite fingerprints are not correct anymore. In this work, we propose an accurate method coupling quantum mechanical simulations and quantitation algorithms to handle basis-set changes. The proposed algorithm automatically corrects mismatches between the signals of the simulated basis set and the signal under analysis by maximizing the normalized cross-correlation between the mentioned signals. Optimized chemical shift values of the metabolites are obtained. This method, QM-QUEST, provides more robust fitting while limiting user involvement and respects the correct fingerprints of metabolites. Its efficiency is demonstrated by accurately quantitating 33 signals from tissue samples of human brains with oligodendroglioma, obtained at 11.7 tesla. The corresponding chemical shift changes of several metabolites within the series are also analyzed.

  4. Efficient G0W0 using localized basis sets: a benchmark for molecules

    NASA Astrophysics Data System (ADS)

    Koval, Petr; Per Ljungberg, Mathias; Sanchez-Portal, Daniel

    Electronic structure calculations within Hedin's GW approximation are becoming increasingly accessible to the community. In particular, as it has been shown earlier and we confirm by calculations using our MBPT_LCAO package, the computational cost of the so-called G0W0 can be made comparable to the cost of a regular Hartree-Fock calculation. In this work, we study the performance of our new implementation of G0W0 to reproduce the ionization potentials of all 117 closed-shell molecules belonging to the G2/97 test set, using a pseudo-potential starting point provided by the popular density-functional package SIESTA. Moreover, the ionization potentials and electron affinities of a set of 24 acceptor molecules are compared to experiment and to reference all-electron calculations. PK: Guipuzcoa Fellow; PK,ML,DSP: Deutsche Forschungsgemeinschaft (SFB1083); PK,DSP: MINECO MAT2013-46593-C6-2-P.

  5. The prefabricated building risk decision research of DM technology on the basis of Rough Set

    NASA Astrophysics Data System (ADS)

    Guo, Z. L.; Zhang, W. B.; Ma, L. H.

    2017-08-01

    With the resources crises and more serious pollution, the green building has been strongly advocated by most countries and become a new building style in the construction field. Compared with traditional building, the prefabricated building has its own irreplaceable advantages but is influenced by many uncertainties. So far, a majority of scholars have been studying based on qualitative researches from all of the word. This paper profoundly expounds its significance about the prefabricated building. On the premise of the existing research methods, combined with rough set theory, this paper redefines the factors which affect the prefabricated building risk. Moreover, it quantifies risk factors and establish an expert knowledge base through assessing. And then reduced risk factors about the redundant attributes and attribute values, finally form the simplest decision rule. This simplest decision rule, which is based on the DM technology of rough set theory, provides prefabricated building with a controllable new decision-making method.

  6. Group entropies, correlation laws, and zeta functions.

    PubMed

    Tempesta, Piergiulio

    2011-08-01

    The notion of group entropy is proposed. It enables the unification and generaliztion of many different definitions of entropy known in the literature, such as those of Boltzmann-Gibbs, Tsallis, Abe, and Kaniadakis. Other entropic functionals are introduced, related to nontrivial correlation laws characterizing universality classes of systems out of equilibrium when the dynamics is weakly chaotic. The associated thermostatistics are discussed. The mathematical structure underlying our construction is that of formal group theory, which provides the general structure of the correlations among particles and dictates the associated entropic functionals. As an example of application, the role of group entropies in information theory is illustrated and generalizations of the Kullback-Leibler divergence are proposed. A new connection between statistical mechanics and zeta functions is established. In particular, Tsallis entropy is related to the classical Riemann zeta function.

  7. Kohn-Sham potentials from electron densities using a matrix representation within finite atomic orbital basis sets

    NASA Astrophysics Data System (ADS)

    Zhang, Xing; Carter, Emily A.

    2018-01-01

    We revisit the static response function-based Kohn-Sham (KS) inversion procedure for determining the KS effective potential that corresponds to a given target electron density within finite atomic orbital basis sets. Instead of expanding the potential in an auxiliary basis set, we directly update the potential in its matrix representation. Through numerical examples, we show that the reconstructed density rapidly converges to the target density. Preliminary results are presented to illustrate the possibility of obtaining a local potential in real space from the optimized potential in its matrix representation. We have further applied this matrix-based KS inversion approach to density functional embedding theory. A proof-of-concept study of a solvated proton transfer reaction demonstrates the method's promise.

  8. General contraction of Gaussian basis sets. Part 2: Atomic natural orbitals and the calculation of atomic and molecular properties

    NASA Technical Reports Server (NTRS)

    Almloef, Jan; Taylor, Peter R.

    1989-01-01

    A recently proposed scheme for using natural orbitals from atomic configuration interaction (CI) wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outmost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital (ANO) sets.

  9. Perturbation expansion theory corrected from basis set superposition error. I. Locally projected excited orbitals and single excitations.

    PubMed

    Nagata, Takeshi; Iwata, Suehiro

    2004-02-22

    The locally projected self-consistent field molecular orbital method for molecular interaction (LP SCF MI) is reformulated for multifragment systems. For the perturbation expansion, two types of the local excited orbitals are defined; one is fully local in the basis set on a fragment, and the other has to be partially delocalized to the basis sets on the other fragments. The perturbation expansion calculations only within single excitations (LP SE MP2) are tested for water dimer, hydrogen fluoride dimer, and colinear symmetric ArM+ Ar (M = Na and K). The calculated binding energies of LP SE MP2 are all close to the corresponding counterpoise corrected SCF binding energy. By adding the single excitations, the deficiency in LP SCF MI is thus removed. The results suggest that the exclusion of the charge-transfer effects in LP SCF MI might indeed be the cause of the underestimation for the binding energy. (c) 2004 American Institute of Physics.

  10. General contraction of Gaussian basis sets. II - Atomic natural orbitals and the calculation of atomic and molecular properties

    NASA Technical Reports Server (NTRS)

    Almlof, Jan; Taylor, Peter R.

    1990-01-01

    A recently proposed scheme for using natural orbitals from atomic configuration interaction wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outermost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital sets.

  11. Approaching the theoretical limit in periodic local MP2 calculations with atomic-orbital basis sets: the case of LiH.

    PubMed

    Usvyat, Denis; Civalleri, Bartolomeo; Maschio, Lorenzo; Dovesi, Roberto; Pisani, Cesare; Schütz, Martin

    2011-06-07

    The atomic orbital basis set limit is approached in periodic correlated calculations for solid LiH. The valence correlation energy is evaluated at the level of the local periodic second order Møller-Plesset perturbation theory (MP2), using basis sets of progressively increasing size, and also employing "bond"-centered basis functions in addition to the standard atom-centered ones. Extended basis sets, which contain linear dependencies, are processed only at the MP2 stage via a dual basis set scheme. The local approximation (domain) error has been consistently eliminated by expanding the orbital excitation domains. As a final result, it is demonstrated that the complete basis set limit can be reached for both HF and local MP2 periodic calculations, and a general scheme is outlined for the definition of high-quality atomic-orbital basis sets for solids. © 2011 American Institute of Physics

  12. Zeta Pegasi: An SPB Variable Star

    NASA Technical Reports Server (NTRS)

    Goebel, John H.

    2007-01-01

    Broadband photometric observations of the bright star Zeta Pegasi are presented that display brightness variability of 488.2 +/- 6.6 micromag (ppm) range with a period of 22.952 +/- 0.804 hr (f approx. equals 1.04566 c/d). The variation is monosinusoidal, so the star is recommended for membership in the class of small-amplitude Slowly Pulsating B-Stars (SPB) variables oscillating in a non-radial g-mode.

  13. Orthonormal vector polynomials in a unit circle, Part I: Basis set derived from gradients of Zernike polynomials.

    PubMed

    Zhao, Chunyu; Burge, James H

    2007-12-24

    Zernike polynomials provide a well known, orthogonal set of scalar functions over a circular domain, and are commonly used to represent wavefront phase or surface irregularity. A related set of orthogonal functions is given here which represent vector quantities, such as mapping distortion or wavefront gradient. These functions are generated from gradients of Zernike polynomials, made orthonormal using the Gram- Schmidt technique. This set provides a complete basis for representing vector fields that can be defined as a gradient of some scalar function. It is then efficient to transform from the coefficients of the vector functions to the scalar Zernike polynomials that represent the function whose gradient was fit. These new vector functions have immediate application for fitting data from a Shack-Hartmann wavefront sensor or for fitting mapping distortion for optical testing. A subsequent paper gives an additional set of vector functions consisting only of rotational terms with zero divergence. The two sets together provide a complete basis that can represent all vector distributions in a circular domain.

  14. Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: application to SSSH.

    PubMed

    Kolmann, Stephen J; Jordan, Meredith J T

    2010-02-07

    One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol(-1) at the CCSD(T)/6-31G* level of theory, has a 4 kJ mol(-1) dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol(-1) lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol(-1) lower in energy at the CCSD(T)/6-31G* level of theory. Ideally, for sub-kJ mol(-1) thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

  15. Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: Application to SSSH

    NASA Astrophysics Data System (ADS)

    Kolmann, Stephen J.; Jordan, Meredith J. T.

    2010-02-01

    One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol-1 at the CCSD(T)/6-31G∗ level of theory, has a 4 kJ mol-1 dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol-1 lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol-1 lower in energy at the CCSD(T)/6-31G∗ level of theory. Ideally, for sub-kJ mol-1 thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

  16. XZP + 1d and XZP + 1d-DKH basis sets for second-row elements: application to CCSD(T) zero-point vibrational energy and atomization energy calculations.

    PubMed

    Campos, Cesar T; Jorge, Francisco E; Alves, Júlia M A

    2012-09-01

    Recently, segmented all-electron contracted double, triple, quadruple, quintuple, and sextuple zeta valence plus polarization function (XZP, X = D, T, Q, 5, and 6) basis sets for the elements from H to Ar were constructed for use in conjunction with nonrelativistic and Douglas-Kroll-Hess Hamiltonians. In this work, in order to obtain a better description of some molecular properties, the XZP sets for the second-row elements were augmented with high-exponent d "inner polarization functions," which were optimized in the molecular environment at the second-order Møller-Plesset level. At the coupled cluster level of theory, the inclusion of tight d functions for these elements was found to be essential to improve the agreement between theoretical and experimental zero-point vibrational energies (ZPVEs) and atomization energies. For all of the molecules studied, the ZPVE errors were always smaller than 0.5 %. The atomization energies were also improved by applying corrections due to core/valence correlation and atomic spin-orbit effects. This led to estimates for the atomization energies of various compounds in the gaseous phase. The largest error (1.2 kcal mol(-1)) was found for SiH(4).

  17. Kinetic energy classification and smoothing for compact B-spline basis sets in quantum Monte Carlo

    DOE PAGES

    Krogel, Jaron T.; Reboredo, Fernando A.

    2018-01-25

    Quantum Monte Carlo calculations of defect properties of transition metal oxides have become feasible in recent years due to increases in computing power. As the system size has grown, availability of on-node memory has become a limiting factor. Saving memory while minimizing computational cost is now a priority. The main growth in memory demand stems from the B-spline representation of the single particle orbitals, especially for heavier elements such as transition metals where semi-core states are present. Despite the associated memory costs, splines are computationally efficient. In this paper, we explore alternatives to reduce the memory usage of splined orbitalsmore » without significantly affecting numerical fidelity or computational efficiency. We make use of the kinetic energy operator to both classify and smooth the occupied set of orbitals prior to splining. By using a partitioning scheme based on the per-orbital kinetic energy distributions, we show that memory savings of about 50% is possible for select transition metal oxide systems. Finally, for production supercells of practical interest, our scheme incurs a performance penalty of less than 5%.« less

  18. Kinetic energy classification and smoothing for compact B-spline basis sets in quantum Monte Carlo

    SciTech Connect

    Krogel, Jaron T.; Reboredo, Fernando A.

    Quantum Monte Carlo calculations of defect properties of transition metal oxides have become feasible in recent years due to increases in computing power. As the system size has grown, availability of on-node memory has become a limiting factor. Saving memory while minimizing computational cost is now a priority. The main growth in memory demand stems from the B-spline representation of the single particle orbitals, especially for heavier elements such as transition metals where semi-core states are present. Despite the associated memory costs, splines are computationally efficient. In this paper, we explore alternatives to reduce the memory usage of splined orbitalsmore » without significantly affecting numerical fidelity or computational efficiency. We make use of the kinetic energy operator to both classify and smooth the occupied set of orbitals prior to splining. By using a partitioning scheme based on the per-orbital kinetic energy distributions, we show that memory savings of about 50% is possible for select transition metal oxide systems. Finally, for production supercells of practical interest, our scheme incurs a performance penalty of less than 5%.« less

  19. [The BASYS observation system for the analysis of aggressive behavior in classroom-settings].

    PubMed

    Wettstein, Alexander

    2012-01-01

    Educational or therapeutic measures of aggressive student behavior are often based on the judgments of teachers. However, empirical studies show that the objectivity of these judgments is generally low. In order to assess aggressive behavior in classroom settings, we developed a context-sensitive observational system. The observation system exists in a version for teachers in action as well as a version for the uninvolved observer. The teacher version allows categorizing aggressive behavior while teaching. The aim is to differentiate the perception and the judgments of teachers, so that the judgments can serve as trustable diagnostic information. The version for an independent observer, in addition, contains categories to collect information about the context in which aggressions take place. The behavior observation system was tested in four field-studies in regular and special classes. The empirical results show that, after training, teachers were able to make objective observations, and that aggressive behavior depends to a large extent on situational factors. The system allows identification of problematic people-environment relationships and the derivation of intervention measures.

  20. Kinetic energy classification and smoothing for compact B-spline basis sets in quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Krogel, Jaron T.; Reboredo, Fernando A.

    2018-01-01

    Quantum Monte Carlo calculations of defect properties of transition metal oxides have become feasible in recent years due to increases in computing power. As the system size has grown, availability of on-node memory has become a limiting factor. Saving memory while minimizing computational cost is now a priority. The main growth in memory demand stems from the B-spline representation of the single particle orbitals, especially for heavier elements such as transition metals where semi-core states are present. Despite the associated memory costs, splines are computationally efficient. In this work, we explore alternatives to reduce the memory usage of splined orbitals without significantly affecting numerical fidelity or computational efficiency. We make use of the kinetic energy operator to both classify and smooth the occupied set of orbitals prior to splining. By using a partitioning scheme based on the per-orbital kinetic energy distributions, we show that memory savings of about 50% is possible for select transition metal oxide systems. For production supercells of practical interest, our scheme incurs a performance penalty of less than 5%.

  1. Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT.

    PubMed

    Götz, Andreas W; Kollmar, Christian; Hess, Bernd A

    2005-09-01

    We present a systematic procedure for the optimization of the expansion basis for the limited expansion of diatomic overlap density functional theory (LEDO-DFT) and report on optimized auxiliary orbitals for the Ahlrichs split valence plus polarization basis set (SVP) for the elements H, Li--F, and Na--Cl. A new method to deal with near-linear dependences in the LEDO expansion basis is introduced, which greatly reduces the computational effort of LEDO-DFT calculations. Numerical results for a test set of small molecules demonstrate the accuracy of electronic energies, structural parameters, dipole moments, and harmonic frequencies. For larger molecular systems the numerical errors introduced by the LEDO approximation can lead to an uncontrollable behavior of the self-consistent field (SCF) process. A projection technique suggested by Löwdin is presented in the framework of LEDO-DFT, which guarantees for SCF convergence. Numerical results on some critical test molecules suggest the general applicability of the auxiliary orbitals presented in combination with this projection technique. Timing results indicate that LEDO-DFT is competitive with conventional density fitting methods. (c) 2005 Wiley Periodicals, Inc.

  2. Zeta functions on tori using contour integration

    NASA Astrophysics Data System (ADS)

    Elizalde, Emilio; Kirsten, Klaus; Robles, Nicolas; Williams, Floyd

    2015-12-01

    A new, seemingly useful presentation of zeta functions on complex tori is derived by using contour integration. It is shown to agree with the one obtained by using the Chowla-Selberg series formula, for which an alternative proof is thereby given. In addition, a new proof of the functional determinant on the torus results, which does not use the Kronecker first limit formula nor the functional equation of the non-holomorphic Eisenstein series. As a bonus, several identities involving the Dedekind eta function are obtained as well.

  3. GRANULATION IN THE PHOTOSPHERE OF {zeta} CYGNI

    SciTech Connect

    Gray, David F., E-mail: dfgray@uwo.ca

    2012-05-15

    A series of 35 high-resolution spectra are used to measure the third-signature plot of the G8 III star, {zeta} Cygni, which shows convective velocities only 8% larger than the Sun. Bisector mapping yields a flux deficit, a measure of granulation contrast, typical of other giants. The observations also give radial velocities with errors {approx}30 m s{sup -1} and allow the orbit to be refined. Velocity excursions relative to the smooth orbital motion, possibly from the granulation, have values exceeding 200 m s{sup -1}. Temperature variations were looked for using line-depth ratios, but none were found.

  4. A quantum molecular similarity analysis of changes in molecular electron density caused by basis set flotation and electric field application

    NASA Astrophysics Data System (ADS)

    Simon, Sílvia; Duran, Miquel

    1997-08-01

    Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.

  5. Structural basis for inhibition of the histone chaperone activity of SET/TAF-Iβ by cytochrome c

    PubMed Central

    González-Arzola, Katiuska; Díaz-Moreno, Irene; Cano-González, Ana; Díaz-Quintana, Antonio; Velázquez-Campoy, Adrián; Moreno-Beltrán, Blas; López-Rivas, Abelardo; De la Rosa, Miguel A.

    2015-01-01

    Chromatin is pivotal for regulation of the DNA damage process insofar as it influences access to DNA and serves as a DNA repair docking site. Recent works identify histone chaperones as key regulators of damaged chromatin’s transcriptional activity. However, understanding how chaperones are modulated during DNA damage response is still challenging. This study reveals that the histone chaperone SET/TAF-Iβ interacts with cytochrome c following DNA damage. Specifically, cytochrome c is shown to be translocated into cell nuclei upon induction of DNA damage, but not upon stimulation of the death receptor or stress-induced pathways. Cytochrome c was found to competitively hinder binding of SET/TAF-Iβ to core histones, thereby locking its histone-binding domains and inhibiting its nucleosome assembly activity. In addition, we have used NMR spectroscopy, calorimetry, mutagenesis, and molecular docking to provide an insight into the structural features of the formation of the complex between cytochrome c and SET/TAF-Iβ. Overall, these findings establish a framework for understanding the molecular basis of cytochrome c-mediated blocking of SET/TAF-Iβ, which subsequently may facilitate the development of new drugs to silence the oncogenic effect of SET/TAF-Iβ’s histone chaperone activity. PMID:26216969

  6. Structural basis for inhibition of the histone chaperone activity of SET/TAF-Iβ by cytochrome c.

    PubMed

    González-Arzola, Katiuska; Díaz-Moreno, Irene; Cano-González, Ana; Díaz-Quintana, Antonio; Velázquez-Campoy, Adrián; Moreno-Beltrán, Blas; López-Rivas, Abelardo; De la Rosa, Miguel A

    2015-08-11

    Chromatin is pivotal for regulation of the DNA damage process insofar as it influences access to DNA and serves as a DNA repair docking site. Recent works identify histone chaperones as key regulators of damaged chromatin's transcriptional activity. However, understanding how chaperones are modulated during DNA damage response is still challenging. This study reveals that the histone chaperone SET/TAF-Iβ interacts with cytochrome c following DNA damage. Specifically, cytochrome c is shown to be translocated into cell nuclei upon induction of DNA damage, but not upon stimulation of the death receptor or stress-induced pathways. Cytochrome c was found to competitively hinder binding of SET/TAF-Iβ to core histones, thereby locking its histone-binding domains and inhibiting its nucleosome assembly activity. In addition, we have used NMR spectroscopy, calorimetry, mutagenesis, and molecular docking to provide an insight into the structural features of the formation of the complex between cytochrome c and SET/TAF-Iβ. Overall, these findings establish a framework for understanding the molecular basis of cytochrome c-mediated blocking of SET/TAF-Iβ, which subsequently may facilitate the development of new drugs to silence the oncogenic effect of SET/TAF-Iβ's histone chaperone activity.

  7. An expanded calibration study of the explicitly correlated CCSD(T)-F12b method using large basis set standard CCSD(T) atomization energies.

    PubMed

    Feller, David; Peterson, Kirk A

    2013-08-28

    The effectiveness of the recently developed, explicitly correlated coupled cluster method CCSD(T)-F12b is examined in terms of its ability to reproduce atomization energies derived from complete basis set extrapolations of standard CCSD(T). Most of the standard method findings were obtained with aug-cc-pV7Z or aug-cc-pV8Z basis sets. For a few homonuclear diatomic molecules it was possible to push the basis set to the aug-cc-pV9Z level. F12b calculations were performed with the cc-pVnZ-F12 (n = D, T, Q) basis set sequence and were also extrapolated to the basis set limit using a Schwenke-style, parameterized formula. A systematic bias was observed in the F12b method with the (VTZ-F12/VQZ-F12) basis set combination. This bias resulted in the underestimation of reference values associated with small molecules (valence correlation energies <0.5 E(h)) and an even larger overestimation of atomization energies for bigger systems. Consequently, caution should be exercised in the use of F12b for high accuracy studies. Root mean square and mean absolute deviation error metrics for this basis set combination were comparable to complete basis set values obtained with standard CCSD(T) and the aug-cc-pVDZ through aug-cc-pVQZ basis set sequence. However, the mean signed deviation was an order of magnitude larger. Problems partially due to basis set superposition error were identified with second row compounds which resulted in a weak performance for the smaller VDZ-F12/VTZ-F12 combination of basis sets.

  8. Rotationally excited HD toward Zeta Ophiuchi

    NASA Technical Reports Server (NTRS)

    Wright, E. L.; Morton, D. C.

    1979-01-01

    Copernicus satellite measurements of HD in J-double prime = 1 and J-double prime = 0 toward Zeta Oph are reported. The ratio of the number densities of HD in the J = 0 and J = 1 states is determined to be 0.15 + or - 0.02 at the 1-sigma level. A value of approximately 24 x 10 to the -17th erg/cu cm per A at 1000 A is obtained for the UV energy density at the Zeta Oph cloud, and the mechanisms for excitation of HD are examined. A tight upper limit is derived for the abundance of HCl, which has been predicted to be present due to the interaction of ionized chlorine with neutral hydrogen. A calculation is performed which indicates that the cloud is 28 pc from the star. It is shown that the two-component cloud model of Black and Dalgarno (1977) with densities of 500 and 2500 H nuclei per cu cm for the outer regions and core, respectively, is in excellent agreement with the observations.

  9. The interacting correlated fragments model for weak interactions, basis set superposition error, and the helium dimer potential

    NASA Astrophysics Data System (ADS)

    Liu, B.; McLean, A. D.

    1989-08-01

    We report the LM-2 helium dimer interaction potential, from helium separations of 1.6 Å to dissociation, obtained by careful convergence studies with respect to configuration space, through a sequence of interacting correlated fragment (ICF) wave functions, and with respect to the primitive Slater-type basis used for orbital expansion. Parameters of the LM-2 potential are re=2.969 Å, rm=2.642 Å, and De=10.94 K, in near complete agreement with those of the best experimental potential of Aziz, McCourt, and Wong [Mol. Phys. 61, 1487 (1987)], which are re=2.963 Å, rm=2.637 Å, and De=10.95 K. The computationally estimated accuracy of each point on the potential is given; at re it is 0.03 K. Extrapolation procedures used to produce the LM-2 potential make use of the orbital basis inconsistency (OBI) and configuration base inconsistency (CBI) adjustments to separated fragment energies when computing the interaction energy. These components of basis set superposition error (BSSE) are given a full discussion.

  10. Performance of local orbital basis sets in the self-consistent Sternheimer method for dielectric matrices of extended systems

    NASA Astrophysics Data System (ADS)

    Hübener, H.; Pérez-Osorio, M. A.; Ordejón, P.; Giustino, F.

    2012-09-01

    We present a systematic study of the performance of numerical pseudo-atomic orbital basis sets in the calculation of dielectric matrices of extended systems using the self-consistent Sternheimer approach of [F. Giustino et al., Phys. Rev. B 81, 115105 (2010)]. In order to cover a range of systems, from more insulating to more metallic character, we discuss results for the three semiconductors diamond, silicon, and germanium. Dielectric matrices of silicon and diamond calculated using our method fall within 1% of reference planewaves calculations, demonstrating that this method is promising. We find that polarization orbitals are critical for achieving good agreement with planewaves calculations, and that only a few additional ζ's are required for obtaining converged results, provided the split norm is properly optimized. Our present work establishes the validity of local orbital basis sets and the self-consistent Sternheimer approach for the calculation of dielectric matrices in extended systems, and prepares the ground for future studies of electronic excitations using these methods.

  11. Relativistic Prolapse-Free Gaussian Basis Sets of Quadruple-ζ Quality: (aug-)RPF-4Z. III. The f-Block Elements.

    PubMed

    Teodoro, Tiago Quevedo; Visscher, Lucas; da Silva, Albérico Borges Ferreira; Haiduke, Roberto Luiz Andrade

    2017-03-14

    The f-block elements are addressed in this third part of a series of prolapse-free basis sets of quadruple-ζ quality (RPF-4Z). Relativistic adapted Gaussian basis sets (RAGBSs) are used as primitive sets of functions while correlating/polarization (C/P) functions are chosen by analyzing energy lowerings upon basis set increments in Dirac-Coulomb multireference configuration interaction calculations with single and double excitations of the valence spinors. These function exponents are obtained by applying the RAGBS parameters in a polynomial expression. Moreover, through the choice of C/P characteristic exponents from functions of lower angular momentum spaces, a reduction in the computational demand is attained in relativistic calculations based on the kinetic balance condition. The present study thus complements the RPF-4Z sets for the whole periodic table (Z ≤ 118). The sets are available as Supporting Information and can also be found at http://basis-sets.iqsc.usp.br .

  12. Need for reaction coordinates to ensure a complete basis set in an adiabatic representation of ion-atom collisions

    NASA Astrophysics Data System (ADS)

    Rabli, Djamal; McCarroll, Ronald

    2018-02-01

    This review surveys the different theoretical approaches, used to describe inelastic and rearrangement processes in collisions involving atoms and ions. For a range of energies from a few meV up to about 1 keV, the adiabatic representation is expected to be valid and under these conditions, inelastic and rearrangement processes take place via a network of avoided crossings of the potential energy curves of the collision system. In general, such avoided crossings are finite in number. The non-adiabatic coupling, due to the breakdown of the Born-Oppenheimer separation of the electronic and nuclear variables, depends on the ratio of the electron mass to the nuclear mass terms in the total Hamiltonian. By limiting terms in the total Hamiltonian correct to first order in the electron to nuclear mass ratio, a system of reaction coordinates is found which allows for a correct description of both inelastic channels. The connection between the use of reaction coordinates in the quantum description and the electron translation factors of the impact parameter approach is established. A major result is that only when reaction coordinates are used, is it possible to introduce the notion of a minimal basis set. Such a set must include all avoided crossings including both radial coupling and long range Coriolis coupling. But, only when reactive coordinates are used, can such a basis set be considered as complete. In particular when the centre of nuclear mass is used as centre of coordinates, rather than the correct reaction coordinates, it is shown that erroneous results are obtained. A few results to illustrate this important point are presented: one concerning a simple two-state Landau-Zener type avoided crossing, the other concerning a network of multiple crossings in a typical electron capture process involving a highly charged ion with a neutral atom.

  13. Application of the zeta potential for stationary phase characterization in ion chromatography.

    PubMed

    Buszewski, Bogusław; Jaćkowska, Magdalena; Bocian, Szymon; Dziubakiewicz, Ewelina

    2013-01-01

    Two series of homemade stationary bonded phases for ion chromatography were investigated according to their zeta potential. One set of dendrimer anion exchanger was synthesized on the polymer support whereas the second material was prepared on the silica gel. The zeta potential data in water environment as well as buffered water solution were obtained. The influence of the length of anion-exchanger chains, the type of the support of the modified surface, and charge distribution on these data was investigated. Additionally, the zeta potential was correlated with retention factor of inorganic ions to describe their influence on the retention mechanism in ion chromatography. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. On small values of the Riemann zeta-function at Gram points

    SciTech Connect

    Korolev, M A

    In this paper, we prove the existence of a large set of Gram points t{sub n} such that the values ζ(0.5+it{sub n}) are 'anomalously' close to zero. A lower bound for the negative 'discrete' moment of the Riemann zeta-function on the critical line is also given. Bibliography: 13 titles.

  15. Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit.

    PubMed

    Lemke, Kono H

    2017-06-21

    This study presents results for the binding energy and geometry of the H 2 S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of D e , E ZPE , D o , and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of D e are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance r SS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H 2 S dimer geometry and binding energy. As regards the structure of (H 2 S) 2 , MPn, CCSD, and CCSD(T) level values of r SS , obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy D e are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies D e with E ZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields D o = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide

  16. Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit

    NASA Astrophysics Data System (ADS)

    Lemke, Kono H.

    2017-06-01

    This study presents results for the binding energy and geometry of the H2S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of De, EZPE, Do, and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of De are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance rSS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H2S dimer geometry and binding energy. As regards the structure of (H2S)2, MPn, CCSD, and CCSD(T) level values of rSS, obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy De are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies De with EZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields Do = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.

  17. Zeta potential orientation dependence of sapphire substrates.

    PubMed

    Kershner, Ryan J; Bullard, Joseph W; Cima, Michael J

    2004-05-11

    The zeta potential of planar sapphire substrates for three different crystallographic orientations was measured by a streaming potential technique in the presence of KCl and (CH3)4NCl electrolytes. The streaming potential was measured for large single crystalline C-plane (0001), A-plane (1120), and R-plane (1102) wafers over a full pH range at three or more ionic strengths ranging from 1 to 100 mM. The roughness of the epi-polished wafers was verified using atomic force microscopy to be on the order of atomic scale, and X-ray photoelectron spectroscopy (XPS) was used to ensure that the samples were free of silica and other contaminants. The results reveal a shift in the isoelectric point (iep) of the three samples by as much as two pH units, with the R-plane surface exhibiting the most acidic behavior and the C-plane samples having the highest iep. The iep at all ionic strengths was tightly centered around a single pH for each wafer. These values of iep are substantially different from the range of pH 8-10 consistently reported in the literature for alpha-Al2O3 particles. Particle zeta potential measurements were performed on a model powder using phase analysis light scattering, and the iep was confirmed to occur at pH 8. Modified Auger parameters (MAP) were calculated from XPS spectra of a monolayer of iridium metal deposited on the sapphire by electron beam deposition. A shift in MAP consistent with the observed differences in iep of the surfaces confirms the effect of surface structure on the transfer of charge between the Ir and sapphire, hence accounting for the changes in acidity as a function of crystallographic orientation.

  18. Real-Space Density Functional Theory on Graphical Processing Units: Computational Approach and Comparison to Gaussian Basis Set Methods.

    PubMed

    Andrade, Xavier; Aspuru-Guzik, Alán

    2013-10-08

    We discuss the application of graphical processing units (GPUs) to accelerate real-space density functional theory (DFT) calculations. To make our implementation efficient, we have developed a scheme to expose the data parallelism available in the DFT approach; this is applied to the different procedures required for a real-space DFT calculation. We present results for current-generation GPUs from AMD and Nvidia, which show that our scheme, implemented in the free code Octopus, can reach a sustained performance of up to 90 GFlops for a single GPU, representing a significant speed-up when compared to the CPU version of the code. Moreover, for some systems, our implementation can outperform a GPU Gaussian basis set code, showing that the real-space approach is a competitive alternative for DFT simulations on GPUs.

  19. Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

    NASA Astrophysics Data System (ADS)

    Lee, Hee-Seung; Tuckerman, Mark E.

    2007-04-01

    Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

  20. Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit.

    PubMed

    Lee, Hee-Seung; Tuckerman, Mark E

    2007-04-28

    Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

  1. 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.

  2. An Alternate Set of Basis Functions for the Electromagnetic Solution of Arbitrarily-Shaped, Three-Dimensional, Closed, Conducting Bodies Using Method of Moments

    NASA Technical Reports Server (NTRS)

    Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

    2008-01-01

    In this work, we present an alternate set of basis functions, each defined over a pair of planar triangular patches, for the method of moments solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped, closed, conducting surfaces. The present basis functions are point-wise orthogonal to the pulse basis functions previously defined. The prime motivation to develop the present set of basis functions is to utilize them for the electromagnetic solution of dielectric bodies using a surface integral equation formulation which involves both electric and magnetic cur- rents. However, in the present work, only the conducting body solution is presented and compared with other data.

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

    PubMed

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

    2011-12-09

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

  4. Zeta Ophiuchi -- Runaway Star Plowing through Space Dust

    NASA Image and Video Library

    2011-01-24

    The blue star near the center of this image is Zeta Ophiuchi. Zeta Ophiuchi is actually a very massive, hot, bright blue star plowing its way through a large cloud of interstellar dust and gas in this image from NASA Wide-field Infrared Survey Explorer.

  5. Hyperpolarizability of H 2O revisited: accurate estimate of the basis set limit and the size of electron correlation effects

    NASA Astrophysics Data System (ADS)

    Maroulis, George

    1998-06-01

    A large (18s 13p 8d 5f / 12s 7p 3d 2f) basis set consisting of 256 uncontracted gaussian-type functions is expected to yield values near the Hartree-Fock limit for the static hyperpolarizability of H 2O: βzxx=-9.40, βzyy=-1.35, βzzz=-7.71 and β¯=-11.07 for βαβγ ( e3a03Eh-2) and γxxxx=569, γyyyy=1422, γzzzz=907, γxxyy=338, γyyzz=389, γzzxx=287 and γ¯=985 for γαβγδ ( e4a04Eh-3) at the experimental equilibrium geometry (with z as the C 2 axis, molecule on the xz plane). The respective electron correlation corrections obtained with the single, double and perturbatively linked triple excitations coupled-cluster method and a [9s 6p 6d 3f / 6s 4p 2d 1f] basis set are βzxx=-0.45, βzyy=-4.19, βzzz=-6.09, β¯=-6.44 and γxxxx=267, γyyyy=1228, γzzzz=574, γxxyy=295, γyyzz=322, γzzxx=152, γ¯=721 . For the static limit we propose β¯=-17.5±0.3 e3a03Eh-2 and γ¯=(171±6)×10 1e4a04Eh-3, in near agreement with the experimental findings of β¯=-19.2±0.9 e3a03Eh-2 and γ¯=1800±150 e4a04Eh-3 deduced from EFISH measurements at 1064 nm by Kaatz et al. [P. Kaatz, E.A. Donley, D.P. Shelton, J. Chem. Phys. 108 (1998) 849].

  6. Correlation consistent valence basis sets for use with the Stuttgart-Dresden-Bonn relativistic effective core potentials: The atoms Ga-Kr and In-Xe

    NASA Astrophysics Data System (ADS)

    Martin, Jan M. L.; Sundermann, Andreas

    2001-02-01

    We propose large-core correlation-consistent (cc) pseudopotential basis sets for the heavy p-block elements Ga-Kr and In-Xe. The basis sets are of cc-pVTZ and cc-pVQZ quality, and have been optimized for use with the large-core (valence-electrons only) Stuttgart-Dresden-Bonn (SDB) relativistic pseudopotentials. Validation calculations on a variety of third-row and fourth-row diatomics suggest them to be comparable in quality to the all-electron cc-pVTZ and cc-pVQZ basis sets for lighter elements. Especially the SDB-cc-pVQZ basis set in conjunction with a core polarization potential (CPP) yields excellent agreement with experiment for compounds of the later heavy p-block elements. For accurate calculations on Ga (and, to a lesser extent, Ge) compounds, explicit treatment of 13 valence electrons appears to be desirable, while it seems inevitable for In compounds. For Ga and Ge, we propose correlation consistent basis sets extended for (3d) correlation. For accurate calculations on organometallic complexes of interest to homogenous catalysis, we recommend a combination of the standard cc-pVTZ basis set for first- and second-row elements, the presently derived SDB-cc-pVTZ basis set for heavier p-block elements, and for transition metals, the small-core [6s5p3d] Stuttgart-Dresden basis set-relativistic effective core potential combination supplemented by (2f1g) functions with exponents given in the Appendix to the present paper.

  7. Design of cognitive engine for cognitive radio based on the rough sets and radial basis function neural network

    NASA Astrophysics Data System (ADS)

    Yang, Yanchao; Jiang, Hong; Liu, Congbin; Lan, Zhongli

    2013-03-01

    Cognitive radio (CR) is an intelligent wireless communication system which can dynamically adjust the parameters to improve system performance depending on the environmental change and quality of service. The core technology for CR is the design of cognitive engine, which introduces reasoning and learning methods in the field of artificial intelligence, to achieve the perception, adaptation and learning capability. Considering the dynamical wireless environment and demands, this paper proposes a design of cognitive engine based on the rough sets (RS) and radial basis function neural network (RBF_NN). The method uses experienced knowledge and environment information processed by RS module to train the RBF_NN, and then the learning model is used to reconfigure communication parameters to allocate resources rationally and improve system performance. After training learning model, the performance is evaluated according to two benchmark functions. The simulation results demonstrate the effectiveness of the model and the proposed cognitive engine can effectively achieve the goal of learning and reconfiguration in cognitive radio.

  8. Geometric Energy Derivatives at the Complete Basis Set Limit: Application to the Equilibrium Structure and Molecular Force Field of Formaldehyde.

    PubMed

    Morgan, W James; Matthews, Devin A; Ringholm, Magnus; Agarwal, Jay; Gong, Justin Z; Ruud, Kenneth; Allen, Wesley D; Stanton, John F; Schaefer, Henry F

    2018-03-13

    Geometric energy derivatives which rely on core-corrected focal-point energies extrapolated to the complete basis set (CBS) limit of coupled cluster theory with iterative and noniterative quadruple excitations, CCSDTQ and CCSDT(Q), are used as elements of molecular gradients and, in the case of CCSDT(Q), expansion coefficients of an anharmonic force field. These gradients are used to determine the CCSDTQ/CBS and CCSDT(Q)/CBS equilibrium structure of the S 0 ground state of H 2 CO where excellent agreement is observed with previous work and experimentally derived results. A fourth-order expansion about this CCSDT(Q)/CBS reference geometry using the same level of theory produces an exceptional level of agreement to spectroscopically observed vibrational band origins with a MAE of 0.57 cm -1 . Second-order vibrational perturbation theory (VPT2) and variational discrete variable representation (DVR) results are contrasted and discussed. Vibration-rotation, anharmonicity, and centrifugal distortion constants from the VPT2 analysis are reported and compared to previous work. Additionally, an initial application of a sum-over-states fourth-order vibrational perturbation theory (VPT4) formalism is employed herein, utilizing quintic and sextic derivatives obtained with a recursive algorithmic approach for response theory.

  9. Molecular origins of the zeta potential

    DOE PAGES

    Predota, Milan; Machesky, Michael L.; Wesolowski, David J.

    2016-09-19

    The zeta potential (ZP) is an oft-reported measure of the macroscopic charge state of solid surfaces and colloidal particles in contact with solvents. However, the origin of this readily measurable parameter has remained divorced from the molecular-level processes governing the underlying electrokinetic phenomena, which limits its usefulness. Here, we connect the macroscopic measure to the microscopic realm through nonequilibrium molecular dynamics simulations of electroosmotic flow between parallel slabs of the hydroxylated (110) rutile (TiO 2) surface. These simulations provided streaming mobilities, which were converted to ZP via the commonly used Helmholtz-Smoluchowski equation. A range of rutile surface charge densities (0.1more » to –0.4 C/m 2), corresponding to pH values between about 2.8 and 9.4, in RbCl, NaCl, and SrCl 2 aqueous solutions, were modeled and compared to experimental ZPs for TiO 2 particle suspensions. Simulated ZPs qualitatively agree with experiment and show that “anomalous” ZP values and inequalities between the point of zero charge derived from electrokinetic versus pH titration measurements both arise from differing co- and counterion sorption affinities. We show that at the molecular level the ZP arises from the delicate interplay of spatially varying dynamics, structure, and electrostatics in a narrow interfacial region within about 15 Å of the surface, even in dilute salt solutions. This contrasts fundamentally with continuum descriptions of such interfaces, which predict the ZP response region to be inversely related to ionic strength. In reality the properties of this interfacial region are dominated by relatively immobile and structured water. Furthermore, viscosity values are substantially greater than in the bulk, and electrostatic potential profiles are oscillatory in nature.« less

  10. Influence of the Dukhin and Reynolds numbers on the apparent zeta potential of granular porous media.

    PubMed

    Crespy, A; Bolève, A; Revil, A

    2007-01-01

    The Helmholtz-Smoluchowski (HS) equation is widely used to determine the apparent zeta potential of porous materials using the streaming potential method. We present a model able to correct this apparent zeta potential of granular media of the influence of the Dukhin and Reynolds numbers. The Dukhin number represents the ratio between the surface conductivity (mainly occurring in the Stern layer) and the pore water conductivity. The Reynolds number represents the ratio between inertial and viscous forces in the Navier-Stokes equation. We show here that the HS equation can lead to serious errors if it is used to predict the dependence of zeta potential on flow in the inertial laminar flow regime without taking into account these corrections. For indifferent 1:1 electrolytes (such as sodium chloride), we derived two simple scaling laws for the dependence of the streaming potential coupling coefficient (or the apparent zeta potential) on the Dukhin and Reynolds numbers. Our model is compared with a new set of experimental data obtained on glass bead packs saturated with NaCl solutions at different salinities and pH. We find fairly good agreement between the model and these experimental data.

  11. Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

    SciTech Connect

    Zhang, Gaigong; Lin, Lin, E-mail: linlin@math.berkeley.edu; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

    Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

  12. Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

    DOE PAGES

    Zhang, Gaigong; Lin, Lin; Hu, Wei; ...

    2017-01-27

    Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

  13. Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

    SciTech Connect

    Zhang, Gaigong; Lin, Lin; Hu, Wei

    Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

  14. Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

    2017-04-01

    Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

  15. On what basis are medical cost-effectiveness thresholds set? Clashing opinions and an absence of data: a systematic review.

    PubMed

    Cameron, David; Ubels, Jasper; Norström, Fredrik

    2018-01-01

    The amount a government should be willing to invest in adopting new medical treatments has long been under debate. With many countries using formal cost-effectiveness (C/E) thresholds when examining potential new treatments and ever-growing medical costs, accurately setting the level of a C/E threshold can be essential for an efficient healthcare system. The aim of this systematic review is to describe the prominent approaches to setting a C/E threshold, compile available national-level C/E threshold data and willingness-to-pay (WTP) data, and to discern whether associations exist between these values, gross domestic product (GDP) and health-adjusted life expectancy (HALE). This review further examines current obstacles faced with the presently available data. A systematic review was performed to collect articles which have studied national C/E thresholds and willingness-to-pay (WTP) per quality-adjusted life year (QALY) in the general population. Associations between GDP, HALE, WTP, and C/E thresholds were analyzed with correlations. Seventeen countries were identified from nine unique sources to have formal C/E thresholds within our inclusion criteria. Thirteen countries from nine sources were identified to have WTP per QALY data within our inclusion criteria. Two possible associations were identified: C/E thresholds with HALE (quadratic correlation of 0.63), and C/E thresholds with GDP per capita (polynomial correlation of 0.84). However, these results are based on few observations and therefore firm conclusions cannot be made. Most national C/E thresholds identified in our review fall within the WHO's recommended range of one-to-three times GDP per capita. However, the quality and quantity of data available regarding national average WTP per QALY, opportunity costs, and C/E thresholds is poor in comparison to the importance of adequate investment in healthcare. There exists an obvious risk that countries might either over- or underinvest in healthcare if they

  16. On what basis are medical cost-effectiveness thresholds set? Clashing opinions and an absence of data: a systematic review

    PubMed Central

    Cameron, David; Ubels, Jasper; Norström, Fredrik

    2018-01-01

    ABSTRACT Background: The amount a government should be willing to invest in adopting new medical treatments has long been under debate. With many countries using formal cost-effectiveness (C/E) thresholds when examining potential new treatments and ever-growing medical costs, accurately setting the level of a C/E threshold can be essential for an efficient healthcare system. Objectives: The aim of this systematic review is to describe the prominent approaches to setting a C/E threshold, compile available national-level C/E threshold data and willingness-to-pay (WTP) data, and to discern whether associations exist between these values, gross domestic product (GDP) and health-adjusted life expectancy (HALE). This review further examines current obstacles faced with the presently available data. Methods: A systematic review was performed to collect articles which have studied national C/E thresholds and willingness-to-pay (WTP) per quality-adjusted life year (QALY) in the general population. Associations between GDP, HALE, WTP, and C/E thresholds were analyzed with correlations. Results: Seventeen countries were identified from nine unique sources to have formal C/E thresholds within our inclusion criteria. Thirteen countries from nine sources were identified to have WTP per QALY data within our inclusion criteria. Two possible associations were identified: C/E thresholds with HALE (quadratic correlation of 0.63), and C/E thresholds with GDP per capita (polynomial correlation of 0.84). However, these results are based on few observations and therefore firm conclusions cannot be made. Conclusions: Most national C/E thresholds identified in our review fall within the WHO’s recommended range of one-to-three times GDP per capita. However, the quality and quantity of data available regarding national average WTP per QALY, opportunity costs, and C/E thresholds is poor in comparison to the importance of adequate investment in healthcare. There exists an obvious risk that

  17. Midbond basis functions for weakly bound complexes

    NASA Astrophysics Data System (ADS)

    Shaw, Robert A.; Hill, J. Grant

    2018-06-01

    Weakly bound systems present a difficult problem for conventional atom-centred basis sets due to large separations, necessitating the use of large, computationally expensive bases. This can be remedied by placing a small number of functions in the region between molecules in the complex. We present compact sets of optimised midbond functions for a range of complexes involving noble gases, alkali metals and small molecules for use in high accuracy coupled -cluster calculations, along with a more robust procedure for their optimisation. It is shown that excellent results are possible with double-zeta quality orbital basis sets when a few midbond functions are added, improving both the interaction energy and the equilibrium bond lengths of a series of noble gas dimers by 47% and 8%, respectively. When used in conjunction with explicitly correlated methods, near complete basis set limit accuracy is readily achievable at a fraction of the cost that using a large basis would entail. General purpose auxiliary sets are developed to allow explicitly correlated midbond function studies to be carried out, making it feasible to perform very high accuracy calculations on weakly bound complexes.

  18. Performance assessment of density functional methods with Gaussian and Slater basis sets using 7σ orbital momentum distributions of N2O

    NASA Astrophysics Data System (ADS)

    Wang, Feng; Pang, Wenning; Duffy, Patrick

    2012-12-01

    Performance of a number of commonly used density functional methods in chemistry (B3LYP, Bhandh, BP86, PW91, VWN, LB94, PBe0, SAOP and X3LYP and the Hartree-Fock (HF) method) has been assessed using orbital momentum distributions of the 7σ orbital of nitrous oxide (NNO), which models electron behaviour in a chemically significant region. The density functional methods are combined with a number of Gaussian basis sets (Pople's 6-31G*, 6-311G**, DGauss TZVP and Dunning's aug-cc-pVTZ as well as even-tempered Slater basis sets, namely, et-DZPp, et-QZ3P, et-QZ+5P and et-pVQZ). Orbital momentum distributions of the 7σ orbital in the ground electronic state of NNO, which are obtained from a Fourier transform into momentum space from single point electronic calculations employing the above models, are compared with experimental measurement of the same orbital from electron momentum spectroscopy (EMS). The present study reveals information on performance of (a) the density functional methods, (b) Gaussian and Slater basis sets, (c) combinations of the density functional methods and basis sets, that is, the models, (d) orbital momentum distributions, rather than a group of specific molecular properties and (e) the entire region of chemical significance of the orbital. It is found that discrepancies of this orbital between the measured and the calculated occur in the small momentum region (i.e. large r region). In general, Slater basis sets achieve better overall performance than the Gaussian basis sets. Performance of the Gaussian basis sets varies noticeably when combining with different Vxc functionals, but Dunning's augcc-pVTZ basis set achieves the best performance for the momentum distributions of this orbital. The overall performance of the B3LYP and BP86 models is similar to newer models such as X3LYP and SAOP. The present study also demonstrates that the combinations of the density functional methods and the basis sets indeed make a difference in the quality of the

  19. Characterising Biomass Burning Aerosol in WRF-Chem using the Volatility Basis Set, with Evaluation against SAMBBA Flight Data

    NASA Astrophysics Data System (ADS)

    Lowe, D.; Topping, D. O.; Archer-Nicholls, S.; Darbyshire, E.; Morgan, W.; Liu, D.; Allan, J. D.; Coe, H.; McFiggans, G.

    2015-12-01

    The burning of forests in the Amazonia region is a globally significant source of carbonaceous aerosol, containing both absorbing and scattering components [1]. In addition biomass burning aerosol (BBA) are also efficient cloud condensation nuclei (CCN), modifying cloud properties and influencing atmospheric circulation and precipitation tendencies [2]. The impacts of BBA are highly dependent on their size distribution and composition. A bottom-up emissions inventory, the Brazilian Biomass Burning Emissions Model (3BEM) [3], utilising satellite products to generate daily fire emission maps is used. Injection of flaming emissions within the atmospheric column is simulated using both a sub-grid plume-rise parameterisation [4], and simpler schemes, within the Weather Research and Forecasting Model with Chemistry (WRF-Chem, v3.4.1) [5]. Aerosol dynamics are simulated using the sectional MOSAIC scheme [6], incorporating a volatility basis set (VBS) treatment of organic aerosol [7]. For this work we have modified the 9-bin VBS to use the biomass burning specific scheme developed by May et al. [8]. The model has been run for September 2012 over South America (at a 25km resolution). We will present model results evaluating the modelled aerosol vertical distribution, size distribution, and composition against measurements taken by the FAAM BAe-146 research aircraft during the SAMBBA campaign. The main focus will be on investigating the factors controlling the vertical gradient of the organic mass to black carbon ratio of the measured aerosol. This work is supported by the Nature Environment Research Council (NERC) as part of the SAMBBA project under grant NE/J010073/1. [1] D. G. Streets et al., 2004, J. Geophys. Res., 109, D24212. [2] M. O. Andreae et al., 2004, Science, 303, 1337-1342. [3] K. Longo et al., 2010, Atmos. Chem. Phys., 10, 5,785-5,795. [4] S. Freitas et al., 2007, Atmos. Chem. Phys., 7, 3,385-3,398. [5] S. Archer-Nicholls et al., 2015, Geosci. Model Dev., 8

  20. Exact solution for the hydrogen atom confined by a dielectric continuum and the correct basis set to study many-electron atoms under similar confinements

    NASA Astrophysics Data System (ADS)

    Martínez-Sánchez, Michael-Adán; Aquino, Norberto; Vargas, Rubicelia; Garza, Jorge

    2017-12-01

    The Schrödinger equation associated to the hydrogen atom confined by a dielectric continuum is solved exactly and suggests the appropriate basis set to be used when an atom is immersed in a dielectric continuum. Exact results show that this kind of confinement spread the electron density, which is confirmed through the Shannon entropy. The basis set suggested by the exact results is similar to Slater type orbitals and it was applied on two-electron atoms, where the H- ion ejects one electron for moderate confinements for distances much larger than those commonly used to generate cavities in solvent models.

  1. Investigating the clinical potential for 14-3-3 zeta protein to serve as a biomarker for epithelial ovarian cancer

    PubMed Central

    2013-01-01

    Objective Recently, 14-3-3 zeta protein was identified as a potential serum biomarker of epithelial ovarian cancer (EOC). The goal of this study was to investigate the clinical potential of 14-3-3 zeta protein for monitoring EOC progression compared with CA-125 and HE4. Design Prospective follow-up study. Setting University of Pecs Medical Center Department of Obstetrics and Gynecology/Oncology (Pecs, Hungary). Population Thirteen EOC patients with advanced stage (FIGO IIb-IIIc) epithelial ovarian cancer that underwent radical surgery and received six consecutive cycles of first line chemotherapy (paclitaxel, carboplatin) in 21-day intervals. Methods Pre- and post-chemotherapy computed tomography (CT) scans were performed. Serum levels of CA-125, HE4, and 14-3-3 zeta protein were detected by enzyme-linked immunosorbent assay (ELISA) and quantitative electrochemiluminescence assay (ECLIA). Main outcome measures Serum levels of CA-125, HE4, and 14-3-3 zeta protein, as well as lesion size according to pre- and post-chemotherapy CT scans. Results Serum levels of CA-125 and HE4 were found to significantly decrease following chemotherapy, and this was consistent with the decrease in lesion size detected post-chemotherapy. In contrast, 14-3-3 zeta protein levels did not significantly differ in healthy postmenopausal patients versus EOC patients. Conclusions Determination of CA-125 and HE4 serum levels for the determination of the risk of ovarian malignancy algorithm (ROMA) represents a useful tool for the prediction of chemotherapy efficacy for EOC patients. However, levels of 14-3-3 zeta protein were not found to vary significantly as a consequence of treatment. Therefore we question if 14-3-3 zeta protein is a reliable biomarker, which correlates with the clinical behavior of EOC. PMID:24238270

  2. Red blood cell membrane viscoelasticity, agglutination and zeta potential measurements with double optical tweezers

    NASA Astrophysics Data System (ADS)

    Fontes, Adriana; Fernandes, Heloise P.; Barjas-Castro, Maria L.; de Thomaz, André A.; de Ysasa Pozzo, Liliana; Barbosa, Luiz C.; Cesar, Carlos L.

    2006-02-01

    The red blood cell (RBC) viscoelastic membrane contains proteins and glycolproteins embedded in, or attached, to a fluid lipid bilayer and are negatively charged, which creates a repulsive electric (zeta) potential between the cells and prevents their aggregation in the blood stream. There are techniques, however, to decrease the zeta potential to allow cell agglutination which are the basis of most of the tests of antigen-antibody interactions in blood banks. This report shows the use of a double optical tweezers to measure RBC membrane viscosity, agglutination and zeta potential. In our technique one of the optical tweezers trap a silica bead that binds strongly to a RBC at the end of a RBCs rouleaux and, at the same time, acts as a pico-Newton force transducer, after calibration through its displacement from the equilibrium position. The other optical tweezers trap the RBC at the other end. To measure the membrane viscosity the optical force is measured as a function of the velocity between the RBCs. To measure the adhesion the tweezers are slowly displaced apart until the RBCs disagglutination happens. The RBC zeta potential is measured in two complimentary ways, by the force on the silica bead attached to a single RBC in response to an applied electric field, and the conventional way, by the measurement of terminal velocity of the RBC after released from the optical trap. These two measurements provide information about the RBC charges and, also, electrolytic solution properties. We believe this can improve the methods of diagnosis in blood banks.

  3. Novel Method for Finding [zeta](2[rho]) from a Product of Sines

    ERIC Educational Resources Information Center

    Osler, Thomas J.

    2006-01-01

    Euler gave a simple method for showing that [zeta](2)=1/1[superscript 2] + 1/2[superscript 2] + 1/3[superscript 2] + ... = [pi][superscript 2]/6. He generalized his method so as to find [zeta](4), [zeta](6), [zeta](8),.... His computations became increasingly more complex as the arguments increased. In this note we show a different generalization…

  4. Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks.

    PubMed

    Saravanan, Chandra; Shao, Yihan; Baer, Roi; Ross, Philip N; Head-Gordon, Martin

    2003-04-15

    A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 618-622, 2003

  5. The possibility of evaluating turbo-set bearing misalignment defects on the basis of bearing trajectory features

    NASA Astrophysics Data System (ADS)

    Rybczyński, Józef

    2011-02-01

    This paper presents the results of computer simulation of bearing misalignment defects in a power turbogenerator. This malfunction is typical for great multi-rotor and multi-bearing rotating machines and very common in power turbo-sets. Necessary calculations were carried out by the computer code system MESWIR, developed and used at the IFFM in Gdansk for calculating dynamics of rotors supported on oil bearings. The results are presented in the form of a set of journal and bush trajectories of all turbo-set bearings. Our analysis focuses on the vibrational effects of displacing the two most vulnerable machine bearings in horizontal and vertical directions by the maximum acceptable range calculated with regard to bearing vibration criterion. This assumption required preliminary assessment of the maximum values for the permissible bearing dislocations. We show the relations between the attributes of the particular bearing trajectories and the bearing displacements in relation to their base design position. The shape and dimensions of bearing trajectories are interpreted based on the theory of hydrodynamic lubrication of oil bearings. It was shown that the relative journal trajectories and absolute bush trajectories carry much important information about the dynamic state of the machine, indicating also the way in which bearings are loaded. Therefore, trajectories can be a source of information about the position and direction of bearing misalignments. This article indicates the potential of using trajectory patterns for diagnosing misalignment defects in rotating machines and suggests including sets of trajectory patterns to the knowledge base of a machine diagnostic system.

  6. Carbon-Hydrogen Bond Activation in Hydridotris(pyrazolyl)borate Platinum(IV) Complexes:  Comparison of Density Functionals, Basis Sets, and Bonding Patterns.

    PubMed

    Vastine, Benjamin Alan; Webster, Charles Edwin; Hall, Michael B

    2007-11-01

    The reaction mechanism for the cycle beginning with the reductive elimination (RE) of methane from κ(3)-TpPt(IV)(CH3)2H (1) (Tp = hydridotris(pyrazolyl)borate) and subsequent oxidative addition (OA) of benzene to form finally κ(3)-TpPt(IV)(Ph)2H (19) was investigated by density functional theory (DFT). Two mechanistic steps are of particular interest, namely the barrier to C-H coupling (barrier 1 - Ba1) and the barrier to methane release (barrier 2 - Ba2). For 31 density functionals, the calculated values for Ba1 and Ba2 were benchmarked against the experimentally reported values of 26 (Ba1) and 35 (Ba2) kcal·mol(-1), respectively. Specifically, the values for Ba1 and Ba2, calculated at the B3LYP/double-ζ plus polarization level of theory, are 24.6 and 34.3 kcal·mol(-1), respectively. Overall, the best performing functional was BPW91 where the mae associated with the calculated values of the two barriers is 0.68 kcal·mol(-1). The calculated B3LYP values of Ba1 ranged between 20 and 26 kcal·mol(-1) for 12 effective core potential basis sets for platinum and 29 all-electron basis sets for the first row elements. Polarization functions for the first row elements were important for accurate values, but the addition of diffuse functions to non-hydrogen (+) and hydrogen atoms (++) had little effect on the calculated values. Basis set saturation was achieved with APNO basis sets utilized for first-row atoms. Bader's "Atoms in Molecules" was used to analyze the electron density of several complexes, and the electron density at the Pt-Nax bond critical point (trans to the active site for C-H coupling) varied over a wider range than any of the other Pt-N bonds.

  7. Investigating the time-dependent zeta potential of wood surfaces.

    PubMed

    Muff, Livius F; Luxbacher, Thomas; Burgert, Ingo; Michen, Benjamin

    2018-05-15

    This work reports on streaming potential measurements through natural capillaries in wood and investigates the cause of a time-dependent zeta potential measured during the equilibration of wood cell-walls with an electrolyte solution. For the biomaterial, this equilibration phase takes several hours, which is much longer than for many other materials that have been characterized by electrokinetic measurements. During this equilibration phase the zeta potential magnitude is decaying due to two parallel mechanisms: (i) the swelling of the cell-wall which causes a dimensional change reducing the charge density at the capillary interface; (ii) the transport of ions from the electrolyte solution into the permeable cell-wall which alters the electrical potential at the interface by internal charge compensation. The obtained results demonstrate the importance of equilibration kinetics for an accurate determination of the zeta potential, especially for materials that interact strongly with the measurement electrolyte. Moreover, the change in zeta potential with time can be correlated with the bulk swelling of wood if the effect of electrolyte ion diffusion is excluded. This study shows the potential of streaming potential measurements of wood, and possibly of other hygroscopic and nanoporous materials, to reveal kinetic information about their interaction with liquids, such as swelling and ion uptake. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Third-Order Incremental Dual-Basis Set Zero-Buffer Approach: An Accurate and Efficient Way To Obtain CCSD and CCSD(T) Energies.

    PubMed

    Zhang, Jun; Dolg, Michael

    2013-07-09

    An efficient way to obtain accurate CCSD and CCSD(T) energies for large systems, i.e., the third-order incremental dual-basis set zero-buffer approach (inc3-db-B0), has been developed and tested. This approach combines the powerful incremental scheme with the dual-basis set method, and along with the new proposed K-means clustering (KM) method and zero-buffer (B0) approximation, can obtain very accurate absolute and relative energies efficiently. We tested the approach for 10 systems of different chemical nature, i.e., intermolecular interactions including hydrogen bonding, dispersion interaction, and halogen bonding; an intramolecular rearrangement reaction; aliphatic and conjugated hydrocarbon chains; three compact covalent molecules; and a water cluster. The results show that the errors for relative energies are <1.94 kJ/mol (or 0.46 kcal/mol), for absolute energies of <0.0026 hartree. By parallelization, our approach can be applied to molecules of more than 30 atoms and more than 100 correlated electrons with high-quality basis set such as cc-pVDZ or cc-pVTZ, saving computational cost by a factor of more than 10-20, compared to traditional implementation. The physical reasons of the success of the inc3-db-B0 approach are also analyzed.

  9. The convergence of complete active space self-consistent-field configuration interaction including all single and double excitation energies to the complete basis set limit

    NASA Astrophysics Data System (ADS)

    Petersson, George A.; Malick, David K.; Frisch, Michael J.; Braunstein, Matthew

    2006-07-01

    Examination of the convergence of full valence complete active space self-consistent-field configuration interaction including all single and double excitation (CASSCF-CISD) energies with expansion of the one-electron basis set reveals a pattern very similar to the convergence of single determinant energies. Calculations on the lowest four singlet states and the lowest four triplet states of N2 with the sequence of n-tuple-ζ augmented polarized (nZaP) basis sets (n =2, 3, 4, 5, and 6) are used to establish the complete basis set limits. Full configuration-interaction (CI) and core electron contributions must be included for very accurate potential energy surfaces. However, a simple extrapolation scheme that has no adjustable parameters and requires nothing more demanding than CAS(10e -,8orb)-CISD/3ZaP calculations gives the Re, ωe, ωeXe, Te, and De for these eight states with rms errors of 0.0006Å, 4.43cm-1, 0.35cm-1, 0.063eV, and 0.018eV, respectively.

  10. Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

    NASA Astrophysics Data System (ADS)

    Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.

    2012-10-01

    We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.

  11. Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: dispersion, induction, and basis set superposition error.

    PubMed

    Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T; Dannenberg, J J

    2012-10-07

    We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states.

  12. Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

    PubMed Central

    Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.

    2012-01-01

    We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states. PMID:23039587

  13. Scanning tunneling microscopy image simulation of the rutile (110) TiO2 surface with hybrid functionals and the localized basis set approach

    NASA Astrophysics Data System (ADS)

    Di Valentin, Cristiana

    2007-10-01

    In this work we present a simplified procedure to use hybrid functionals and localized atomic basis sets to simulate scanning tunneling microscopy (STM) images of stoichiometric, reduced and hydroxylated rutile (110) TiO2 surface. For the two defective systems it is necessary to introduce some exact Hartree-Fock exchange in the exchange functional in order to correctly describe the details of the electronic structure. Results are compared to the standard density functional theory and planewave basis set approach. Both methods have advantages and drawbacks that are analyzed in detail. In particular, for the localized basis set approach, it is necessary to introduce a number of Gaussian function in the vacuum region above the surface in order to correctly describe the exponential decay of the integrated local density of states from the surface. In the planewave periodic approach, a thick vacuum region is required to achieve correct results. Simulated STM images are obtained for both the reduced and hydroxylated surface which nicely compare with experimental findings. A direct comparison of the two defects as displayed in the simulated STM images indicates that the OH groups should appear brighter than oxygen vacancies in perfect agreement with the experimental STM data.

  14. Slater-type geminals in explicitly-correlated perturbation theory: application to n-alkanols and analysis of errors and basis-set requirements.

    PubMed

    Höfener, Sebastian; Bischoff, Florian A; Glöss, Andreas; Klopper, Wim

    2008-06-21

    In the recent years, Slater-type geminals (STGs) have been used with great success to expand the first-order wave function in an explicitly-correlated perturbation theory. The present work reports on this theory's implementation in the framework of the Turbomole suite of programs. A formalism is presented for evaluating all of the necessary molecular two-electron integrals by means of the Obara-Saika recurrence relations, which can be applied when the STG is expressed as a linear combination of a small number (n) of Gaussians (STG-nG geminal basis). In the Turbomole implementation of the theory, density fitting is employed and a complementary auxiliary basis set (CABS) is used for the resolution-of-the-identity (RI) approximation of explicitly-correlated theory. By virtue of this RI approximation, the calculation of molecular three- and four-electron integrals is avoided. An approximation is invoked to avoid the two-electron integrals over the commutator between the operators of kinetic energy and the STG. This approximation consists of computing commutators between matrices in place of operators. Integrals over commutators between operators would have occurred if the theory had been formulated and implemented as proposed originally. The new implementation in Turbomole was tested by performing a series of calculations on rotational conformers of the alkanols n-propanol through n-pentanol. Basis-set requirements concerning the orbital basis, the auxiliary basis set for density fitting and the CABS were investigated. Furthermore, various (constrained) optimizations of the amplitudes of the explicitly-correlated double excitations were studied. These amplitudes can be optimized in orbital-variant and orbital-invariant manners, or they can be kept fixed at the values governed by the rational generator approach, that is, by the electron cusp conditions. Electron-correlation effects beyond the level of second-order perturbation theory were accounted for by conventional

  15. A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

    NASA Astrophysics Data System (ADS)

    Kruse, Holger; Grimme, Stefan

    2012-04-01

    A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model

  16. Scaled Quantum Mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model

    NASA Astrophysics Data System (ADS)

    Legler, C. R.; Brown, N. R.; Dunbar, R. A.; Harness, M. D.; Nguyen, K.; Oyewole, O.; Collier, W. B.

    2015-06-01

    The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.

  17. Application of ab initio many-body perturbation theory with Gaussian basis sets to the singlet and triplet excitations of organic molecules

    NASA Astrophysics Data System (ADS)

    Hamed, Samia; Rangel, Tonatiuh; Bruneval, Fabien; Neaton, Jeffrey B.

    Quantitative understanding of charged and neutral excitations of organic molecules is critical in diverse areas of study that include astrophysics and the development of energy technologies that are clean and efficient. The recent use of local basis sets with ab initio many-body perturbation theory in the GW approximation and the Bethe-Saltpeter equation approach (BSE), methods traditionally applied to periodic condensed phases with a plane-wave basis, has opened the door to detailed study of such excitations for molecules, as well as accurate numerical benchmarks. Here, through a series of systematic benchmarks with a Gaussian basis, we report on the extent to which the predictive power and utility of this approach depend critically on interdependent underlying approximations and choices for molecules, including the mean-field starting point (eg optimally-tuned range separated hybrids, pure DFT functionals, and untuned hybrids), the GW scheme, and the Tamm Dancoff approximation. We demonstrate the effects of these choices in the context of Thiels' set while drawing analogies to linear-response time-dependent DFT and making comparisons to best theoretical estimates from higher-order wavefunction-based theories.

  18. Evolution in time of an N-atom system. I. A physical basis set for the projection of the master equation

    NASA Astrophysics Data System (ADS)

    Freedhoff, Helen

    2004-01-01

    We study an aggregate of N identical two-level atoms (TLA’s) coupled by the retarded interatomic interaction, using the Lehmberg-Agarwal master equation. First, we calculate the entangled eigenstates of the system; then, we use these eigenstates as a basis set for the projection of the master equation. We demonstrate that in this basis the equations of motion for the level populations, as well as the expressions for the emission and absorption spectra, assume a simple mathematical structure and allow for a transparent physical interpretation. To illustrate the use of the general theory in emission processes, we study an isosceles triangle of atoms, and present in the long wavelength limit the (cascade) emission spectrum for a hexagon of atoms fully excited at t=0. To illustrate its use for absorption processes, we tabulate (in the same limit) the biexciton absorption frequencies, linewidths, and relative intensities for polygons consisting of N=2,…,9 TLA’s.

  19. Relating zeta functions of discrete and quantum graphs

    NASA Astrophysics Data System (ADS)

    Harrison, Jonathan; Weyand, Tracy

    2018-02-01

    We write the spectral zeta function of the Laplace operator on an equilateral metric graph in terms of the spectral zeta function of the normalized Laplace operator on the corresponding discrete graph. To do this, we apply a relation between the spectrum of the Laplacian on a discrete graph and that of the Laplacian on an equilateral metric graph. As a by-product, we determine how the multiplicity of eigenvalues of the quantum graph, that are also in the spectrum of the graph with Dirichlet conditions at the vertices, depends on the graph geometry. Finally we apply the result to calculate the vacuum energy and spectral determinant of a complete bipartite graph and compare our results with those for a star graph, a graph in which all vertices are connected to a central vertex by a single edge.

  20. Effects of image charges, interfacial charge discreteness, and surface roughness on the zeta potential of spherical electric double layers.

    PubMed

    Gan, Zecheng; Xing, Xiangjun; Xu, Zhenli

    2012-07-21

    We investigate the effects of image charges, interfacial charge discreteness, and surface roughness on spherical electric double layer structures in electrolyte solutions with divalent counterions in the setting of the primitive model. By using Monte Carlo simulations and the image charge method, the zeta potential profile and the integrated charge distribution function are computed for varying surface charge strengths and salt concentrations. Systematic comparisons were carried out between three distinct models for interfacial charges: (1) SURF1 with uniform surface charges, (2) SURF2 with discrete point charges on the interface, and (3) SURF3 with discrete interfacial charges and finite excluded volume. By comparing the integrated charge distribution function and the zeta potential profile, we argue that the potential at the distance of one ion diameter from the macroion surface is a suitable location to define the zeta potential. In SURF2 model, we find that image charge effects strongly enhance charge inversion for monovalent interfacial charges, and strongly suppress charge inversion for multivalent interfacial charges. For SURF3, the image charge effect becomes much smaller. Finally, with image charges in action, we find that excluded volumes (in SURF3) suppress charge inversion for monovalent interfacial charges and enhance charge inversion for multivalent interfacial charges. Overall, our results demonstrate that all these aspects, i.e., image charges, interfacial charge discreteness, their excluding volumes, have significant impacts on zeta potentials of electric double layers.

  1. Systematization, condensed description, and prediction of sets of anion exchange extraction constants on the basis of their statistical treatment by computer

    SciTech Connect

    Mezhov, E.A.; Reimarov, G.A.; Rubisov, V.N.

    1987-05-01

    On the basis of a statistical treatment of the entire set of published data on anion exchange extraction constants, the authors have refined and expanded the scale of the hydration parameters for the anions ..delta..G/sub hydr/ (the effective free energies of hydration for the anions). The authors have estimated the parameters ..delta..G for 93 anions and the coefficients % for 94 series of extraction systems, which are distinguished within each series only by the nature of the exchanging anions. The series are distinguished from one another by the nature of the cation extraction agent and the diluent.

  2. An accurate and efficient computational protocol for obtaining the complete basis set limits of the binding energies of water clusters at the MP2 and CCSD(T) levels of theory: Application to (H₂O) m, m=2-6, 8, 11, 16 and 17

    SciTech Connect

    Miliordos, Evangelos; Xantheas, Sotiris S.

    2015-06-21

    We report MP2 and CCSD(T) binding energies with basis sets up to pentuple zeta quality for the m = 2-6, 8 clusters. Or best CCSD(T)/CBS estimates are -4.99 kcal/mol (dimer), -15.77 kcal/mol (trimer), -27.39 kcal/mol (tetramer), -35.9 ± 0.3 kcal/mol (pentamer), -46.2 ± 0.3 kcal/mol (prism hexamer), -45.9 ± 0.3 kcal/mol (cage hexamer), -45.4 ± 0.3 kcal/mol (book hexamer), -44.3 ± 0.3 kcal/mol (ring hexamer), -73.0 ± 0.5 kcal/mol (D 2d octamer) and -72.9 ± 0.5 kcal/mol (S4 octamer). We have found that the percentage of both the uncorrected (dimer) and BSSE-corrected (dimer CP e) binding energies recovered with respectmore » to the CBS limit falls into a narrow range for each basis set for all clusters and in addition this range was found to decrease upon increasing the basis set. Relatively accurate estimates (within < 0.5%) of the CBS limits can be obtained when using the “ 2/3, 1/3” (for the AVDZ set) or the “½ , ½” (for the AVTZ, AVQZ and AV5Z sets) mixing ratio between dimer e and dimer CPe. Based on those findings we propose an accurate and efficient computational protocol that can be used to estimate accurate binding energies of clusters at the MP2 (for up to 100 molecules) and CCSD(T) (for up to 30 molecules) levels of theory. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multi program national laboratory operated for DOE by Battelle. This research also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. AC02-05CH11231.« less

  3. Surface electrochemical properties of red mud (bauxite residue): zeta potential and surface charge density.

    PubMed

    Liu, Yanju; Naidu, Ravendra; Ming, Hui

    2013-03-15

    The surface electrochemical properties of red mud (bauxite residue) from different alumina refineries in Australia and China were studied by electrophoresis and measuring surface charge density obtained from acid/base potentiometric titrations. The electrophoretic properties were measured from zeta potentials obtained in the presence of 0.01 and 0.001 M KNO(3) over a wide pH range (3.5-10) by titration. The isoelectric point (IEP) values were found to vary from 6.35 to 8.70 for the red mud samples. Further investigation into the surface charge density of one sample (RRM) by acid/base potentiometric titration showed similar results for pH(PZC) with pH(IEP) obtained from electrokinetic measurements. The pH(IEP) determined from zeta potential measurements can be used as a characteristic property of red mud. The minerals contained in red mud contributed to the different values of pH(IEP) of samples obtained from different refineries. Different relationships of pH(IEP) with Al/Fe and Al/Si ratios (molar basis) were also found for different red mud samples. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. The interstellar line spectra of zeta Ophiuchi and zeta Persei and their relation to the short wavelength microwave background radiation. Ph.D. Thesis - N. Y. Univ.

    NASA Technical Reports Server (NTRS)

    Bortolot, V. J., Jr.

    1972-01-01

    Thirty-one high dispersion Coude spectrograms of zeta Ophiuchi and seven of zeta Persei were numerically synthesized to produce high resolution, low noise spectra in the interval 3650 A to 4350 that yield data on atomic and molecular absorption in well-defined regions of the interstellar medium. The detection threshold is improved by as much as a factor 5 over single plates. Several interstellar lines were discovered in the zeta Oph - 15km/sec cloud and the zeta Per + 13 km/sec cloud.

  5. Molecular Properties by Quantum Monte Carlo: An Investigation on the Role of the Wave Function Ansatz and the Basis Set in the Water Molecule

    PubMed Central

    Zen, Andrea; Luo, Ye; Sorella, Sandro; Guidoni, Leonardo

    2014-01-01

    Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely, the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Through a systematic study, we provide a useful guide to the choice of the wave function, the pseudopotential, and the basis set for QMC calculations. We also introduce a new method for the computation of forces with finite variance on open systems and a new strategy for the definition of the atomic orbitals involved in the Jastrow-Antisymmetrised Geminal power wave function, in order to drastically reduce the number of variational parameters. This scheme significantly improves the efficiency of QMC energy minimization in case of large basis sets. PMID:24526929

  6. The 6-31B(d) basis set and the BMC-QCISD and BMC-CCSD multicoefficient correlation methods.

    PubMed

    Lynch, Benjamin J; Zhao, Yan; Truhlar, Donald G

    2005-03-03

    Three new multicoefficient correlation methods (MCCMs) called BMC-QCISD, BMC-CCSD, and BMC-CCSD-C are optimized against 274 data that include atomization energies, electron affinities, ionization potentials, and reaction barrier heights. A new basis set called 6-31B(d) is developed and used as part of the new methods. BMC-QCISD has mean unsigned errors in calculating atomization energies per bond and barrier heights of 0.49 and 0.80 kcal/mol, respectively. BMC-CCSD has mean unsigned errors of 0.42 and 0.71 kcal/mol for the same two quantities. BMC-CCSD-C is an equally effective variant of BMC-CCSD that employs Cartesian rather than spherical harmonic basis sets. The mean unsigned error of BMC-CCSD or BMC-CCSD-C for atomization energies, barrier heights, ionization potentials, and electron affinities is 22% lower than G3SX(MP2) at an order of magnitude less cost for gradients for molecules with 9-13 atoms, and it scales better (N6 vs N,7 where N is the number of atoms) when the size of the molecule is increased.

  7. Accurate potential energy surface for the 1(2)A' state of NH(2): scaling of external correlation versus extrapolation to the complete basis set limit.

    PubMed

    Li, Y Q; Varandas, A J C

    2010-09-16

    An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system which is suitable for dynamics and kinetics studies of the reactions of N(2D) + H2(X1Sigmag+) NH(a1Delta) + H(2S) and their isotopomeric variants. It is obtained by fitting ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set, after slightly correcting semiempirically the dynamical correlation using the double many-body expansion-scaled external correlation method. The function so obtained is compared in detail with a potential energy surface of the same family obtained by extrapolating the calculated raw energies to the complete basis set limit. The topographical features of the novel global potential energy surface are examined in detail and found to be in general good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. The novel function has been built so as to become degenerate at linear geometries with the ground-state potential energy surface of A'' symmetry reported by our group, where both form a Renner-Teller pair.

  8. Sea ice in the Baltic Sea - revisiting BASIS ice, a~historical data set covering the period 1960/1961-1978/1979

    NASA Astrophysics Data System (ADS)

    Löptien, U.; Dietze, H.

    2014-06-01

    The Baltic Sea is a seasonally ice-covered, marginal sea, situated in central northern Europe. It is an essential waterway connecting highly industrialised countries. Because ship traffic is intermittently hindered by sea ice, the local weather services have been monitoring sea ice conditions for decades. In the present study we revisit a historical monitoring data set, covering the winters 1960/1961. This data set, dubbed Data Bank for Baltic Sea Ice and Sea Surface Temperatures (BASIS) ice, is based on hand-drawn maps that were collected and then digitised 1981 in a joint project of the Finnish Institute of Marine Research (today Finish Meteorological Institute (FMI)) and the Swedish Meteorological and Hydrological Institute (SMHI). BASIS ice was designed for storage on punch cards and all ice information is encoded by five digits. This makes the data hard to access. Here we present a post-processed product based on the original five-digit code. Specifically, we convert to standard ice quantities (including information on ice types), which we distribute in the current and free Network Common Data Format (NetCDF). Our post-processed data set will help to assess numerical ice models and provide easy-to-access unique historical reference material for sea ice in the Baltic Sea. In addition we provide statistics showcasing the data quality. The website www.baltic-ocean.org hosts the post-prossed data and the conversion code. The data are also archived at the Data Publisher for Earth & Environmental Science PANGEA (doi:10.1594/PANGEA.832353).

  9. Sea ice in the Baltic Sea - revisiting BASIS ice, a historical data set covering the period 1960/1961-1978/1979

    NASA Astrophysics Data System (ADS)

    Löptien, U.; Dietze, H.

    2014-12-01

    The Baltic Sea is a seasonally ice-covered, marginal sea in central northern Europe. It is an essential waterway connecting highly industrialised countries. Because ship traffic is intermittently hindered by sea ice, the local weather services have been monitoring sea ice conditions for decades. In the present study we revisit a historical monitoring data set, covering the winters 1960/1961 to 1978/1979. This data set, dubbed Data Bank for Baltic Sea Ice and Sea Surface Temperatures (BASIS) ice, is based on hand-drawn maps that were collected and then digitised in 1981 in a joint project of the Finnish Institute of Marine Research (today the Finnish Meteorological Institute (FMI)) and the Swedish Meteorological and Hydrological Institute (SMHI). BASIS ice was designed for storage on punch cards and all ice information is encoded by five digits. This makes the data hard to access. Here we present a post-processed product based on the original five-digit code. Specifically, we convert to standard ice quantities (including information on ice types), which we distribute in the current and free Network Common Data Format (NetCDF). Our post-processed data set will help to assess numerical ice models and provide easy-to-access unique historical reference material for sea ice in the Baltic Sea. In addition we provide statistics showcasing the data quality. The website http://www.baltic-ocean.org hosts the post-processed data and the conversion code. The data are also archived at the Data Publisher for Earth & Environmental Science, PANGAEA (doi:10.1594/PANGAEA.832353).

  10. Activation-induced proteolysis of cytoplasmic domain of zeta in T cell receptors and Fc receptors.

    PubMed

    Taupin, J L; Anderson, P

    1994-12-01

    The CD3-T cell receptor (TCR) complex on T cells and the Fc gamma receptor type III (Fc gamma RIII)-zeta-gamma complex on natural killer cells are functionally analogous activation receptors that associate with a family of disulfide-linked dimers composed of the related subunits zeta and gamma. Immunochemical analysis of receptor complexes separated on two-dimensional diagonal gels allowed the identification of a previously uncharacterized zeta-p14 heterodimer. zeta-p14 is a component of both CD3-TCR and Fc gamma RIII-zeta-gamma. Peptide mapping analysis shows that p14 is structurally related to zeta, suggesting that it is either: (i) derived from zeta proteolytically or (ii) the product of an alternatively spliced mRNA. The observation that COS cells transformed with a cDNA encoding zeta express zeta-p14 supports the former possibility. The expression of CD3-TCR complexes including zeta-p14 increases following activation with phorbol 12-myristate 13-acetate or concanavalin A, suggesting that proteolysis of zeta may contribute to receptor modulation or desensitization.

  11. Detection of boron, cobalt, and other weak interstellar lines toward Zeta Ophiuchi

    NASA Technical Reports Server (NTRS)

    Federman, S. R.; Sheffer, Y.; Lambert, D. L.; Gilliland, R. L.

    1993-01-01

    Numerous weak lines from interstellar atomic species toward Zeta Ophiuchi were observed with the Goddard High-Resolution Spectrograph. Of particular note are the first interstellar detection of cobalt and the detection of boron in this sight line. These measurements provide estimates for the amount of depletion for the two elements. Boron, a volatile, and cobalt, a refractory element, display the depletion pattern found by Savage et al. (1992). The abundance of phosphorus in the H II region associated with the star was obtained from a detection of P III. Additional weak lines from S I, C I, Ni II, and Cu II were detected for the first time; these lines provide the basis for refinements in oscillator strength and column density. Analysis of the neutral sulfur data indicates that the atomic gas is more widely distributed than the molecular material in the main component.

  12. Local zeta factors and geometries under Spec Z

    NASA Astrophysics Data System (ADS)

    Manin, Yu I.

    2016-08-01

    The first part of this note shows that the odd-period polynomial of each Hecke cusp eigenform for the full modular group produces via the Rodriguez-Villegas transform ([1]) a polynomial satisfying the functional equation of zeta type and having non-trivial zeros only in the middle line of its critical strip. The second part discusses the Chebyshev lambda-structure of the polynomial ring as Borger's descent data to \\mathbf{F}_1 and suggests its role in a possible relation of the Γ\\mathbf{R}-factor to 'real geometry over \\mathbf{F}_1' (cf. [2]).

  13. On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit

    NASA Astrophysics Data System (ADS)

    Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

    2007-11-01

    The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Møller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.

  14. On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: benchmarks approaching the complete basis set limit.

    PubMed

    Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

    2007-11-14

    The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Moller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.

  15. Evaluation of the vibration-rotation-tunneling dynamics at the basis set superposition error corrected global minimum geometry of the ammonia dimer

    NASA Astrophysics Data System (ADS)

    Muguet, Francis F.; Robinson, G. Wilse; Bassez-Muguet, M. Palmyre

    1995-03-01

    With the help of a new scheme to correct for the basis set superposition error (BSSE), we find that an eclipsed nonlinear geometry becomes energetically favored over the eclipsed linear hydrogen-bonded geometry. From a normal mode analysis of the potential energy surface (PES) in the vicinity of the nonlinear geometry, we suggest that several dynamical interchange pathways must be taken into account. The minimal molecular symmetry group to be considered should be the double group of G36, but still larger multiple groups may be required. An interpretation of experimental vibration-rotation-tunneling (VRT) data in terms of the G144 group, which implies monomer inversions, may not be the only alternative. It appears that group theoretical considerations alone are insufficient for understanding the complex VRT dynamics of the ammonia dimer.

  16. Improved hybrid algorithm with Gaussian basis sets and plane waves: First-principles calculations of ethylene adsorption on β-SiC(001)-(3×2)

    NASA Astrophysics Data System (ADS)

    Wieferink, Jürgen; Krüger, Peter; Pollmann, Johannes

    2006-11-01

    We present an algorithm for DFT calculations employing Gaussian basis sets for the wave function and a Fourier basis for the potential representation. In particular, a numerically very efficient calculation of the local potential matrix elements and the charge density is described. Special emphasis is placed on the consequences of periodicity and explicit k -vector dependence. The algorithm is tested by comparison with more straightforward ones for the case of adsorption of ethylene on the silicon-rich SiC(001)-(3×2) surface clearly revealing its substantial advantages. A complete self-consistency cycle is speeded up by roughly one order of magnitude since the calculation of matrix elements and of the charge density are accelerated by factors of 10 and 80, respectively, as compared to their straightforward calculation. Our results for C2H4:SiC(001)-(3×2) show that ethylene molecules preferentially adsorb in on-top positions above Si dimers on the substrate surface saturating both dimer dangling bonds per unit cell. In addition, a twist of the molecules around a surface-perpendicular axis is slightly favored energetically similar to the case of a complete monolayer of ethylene adsorbed on the Si(001)-(2×1) surface.

  17. Directional flow induced by synchronized longitudinal and zeta-potential controlling AC-electrical fields.

    PubMed

    van der Wouden, E J; Hermes, D C; Gardeniers, J G E; van den Berg, A

    2006-10-01

    Electroosmotic flow (EOF) in a microchannel can be controlled by electronic control of the surface charge using an electrode embedded in the wall of the channel. By setting a voltage to the electrode, the zeta-potential at the wall can be changed locally. Thus, the electrode acts as a "gate" for liquid flow, in analogy with a gate in a field-effect transistor. In this paper we will show three aspects of a Field Effect Flow Control (FEFC) structure. We demonstrate the induction of directional flow by the synchronized switching of the gate potential with the channel axial potential. The advantage of this procedure is that potential gas formation by electrolysis at the electrodes that provide the axial electric field is suppressed at sufficiently large switching frequencies, while the direction and magnitude of the EOF can be maintained. Furthermore we will give an analysis of the time constants involved in the charging of the insulator, and thus the switching of the zeta potential, in order to predict the maximum operating frequency. For this purpose an equivalent electrical circuit is presented and analyzed. It is shown that in order to accurately describe the charging dynamics and pH dependency the traditionally used three capacitor model should be expanded with an element describing the buffer capacitance of the silica wall surface.

  18. Binding of phosphoinositide-specific phospholipase C-zeta (PLC-zeta) to phospholipid membranes: potential role of an unstructured cluster of basic residues.

    PubMed

    Nomikos, Michail; Mulgrew-Nesbitt, Anna; Pallavi, Payal; Mihalyne, Gyongyi; Zaitseva, Irina; Swann, Karl; Lai, F Anthony; Murray, Diana; McLaughlin, Stuart

    2007-06-01

    Phospholipase C-zeta (PLC-zeta) is a sperm-specific enzyme that initiates the Ca2+ oscillations in mammalian eggs that activate embryo development. It shares considerable sequence homology with PLC-delta1, but lacks the PH domain that anchors PLC-delta1 to phosphatidylinositol 4,5-bisphosphate, PIP2. Thus it is unclear how PLC-zeta interacts with membranes. The linker region between the X and Y catalytic domains of PLC-zeta, however, contains a cluster of basic residues not present in PLC-delta1. Application of electrostatic theory to a homology model of PLC-zeta suggests this basic cluster could interact with acidic lipids. We measured the binding of catalytically competent mouse PLC-zeta to phospholipid vesicles: for 2:1 phosphatidylcholine/phosphatidylserine (PC/PS) vesicles, the molar partition coefficient, K, is too weak to be of physiological significance. Incorporating 1% PIP2 into the 2:1 PC/PS vesicles increases K about 10-fold, to 5x10(3) M-1, a biologically relevant value. Expressed fragments corresponding to the PLC-zeta X-Y linker region also bind with higher affinity to polyvalent than monovalent phosphoinositides on nitrocellulose filters. A peptide corresponding to the basic cluster (charge=+7) within the linker region, PLC-zeta-(374-385), binds to PC/PS vesicles with higher affinity than PLC-zeta, but its binding is less sensitive to incorporating PIP2. The acidic residues flanking this basic cluster in PLC-zeta may account for both these phenomena. FRET experiments suggest the basic cluster could not only anchor the protein to the membrane, but also enhance the local concentration of PIP2 adjacent to the catalytic domain.

  19. The spectral energy distribution of Zeta Puppis and HD 50896

    NASA Technical Reports Server (NTRS)

    Holm, A. V.; Cassinelli, J. P.

    1977-01-01

    The ultraviolet spectral energy distribution of the O5f star Zeta Pup and the WN5 star HD 50896 are derived from OAO-2 observations with the calibration of Bless, Code, and Fairchild (1976). An estimate of the interstellar reddening (0.12 magnitude) of the Wolf-Rayet star is determined from the size of the characteristic interstellar extinction bump at 4.6 inverse microns. After correction for extinction, both stars show a flat energy distribution in the ultraviolet. The distribution of HD 50896 from 1100 A to 2 microns is in good agreement with results of extended model atmospheres, but some uncertainty remains because of the interstellar-extinction correction. The absolute energy distribution of Zeta Pup is fitted by a 42,000-K plane-parallel model if the model's flux is adjusted for the effects of electron scattering in the stellar wind and for UV line blanketing that was determined empirically from high-resolution Copernicus satellite observations. To achieve this fit, it is necessary to push both the spectroscopically determined temperature and the ultraviolet calibration to the limits of their probable errors.

  20. Interlaboratory comparison for the measurement of particle size and zeta potential of silica nanoparticles in an aqueous suspension

    NASA Astrophysics Data System (ADS)

    Lamberty, Andrée; Franks, Katrin; Braun, Adelina; Kestens, Vikram; Roebben, Gert; Linsinger, Thomas P. J.

    2011-12-01

    The Institute for Reference Materials and Measurements has organised an interlaboratory comparison (ILC) to allow the participating laboratories to demonstrate their proficiency in particle size and zeta potential measurements on monomodal aqueous suspensions of silica nanoparticles in the 10-100 nm size range. The main goal of this ILC was to identify competent collaborators for the production of certified nanoparticle reference materials. 38 laboratories from four different continents participated in the ILC with different methods for particle sizing and determination of zeta potential. Most of the laboratories submitted particle size results obtained with centrifugal liquid sedimentation (CLS), dynamic light scattering (DLS) or electron microscopy (EM), or zeta potential values obtained via electrophoretic light scattering (ELS). The results of the laboratories were evaluated using method-specific z scores, calculated on the basis of consensus values from the ILC. For CLS (13 results) and EM (13 results), all reported values were within the ±2 | z| interval. For DLS, 25 of the 27 results reported were within the ±2 | z| interval, the two other results were within the ±3 | z| interval. The standard deviations of the corresponding laboratory mean values varied between 3.7 and 6.5%, which demonstrates satisfactory interlaboratory comparability of CLS, DLS and EM particle size values. From the received test reports, a large discrepancy was observed in terms of the laboratory's quality assurance systems, which are equally important for the selection of collaborators in reference material certification projects. Only a minority of the participating laboratories is aware of all the items that are mandatory in test reports compliant to ISO/IEC 17025 (ISO General requirements for the competence of testing and calibration laboratories. International Organisation for Standardization, Geneva, 2005b). The absence of measurement uncertainty values in the reports, for

  1. Radio and submillimetre observations of wind structure in zeta Puppis

    NASA Astrophysics Data System (ADS)

    Blomme, R.; van de Steene, G. C.; Prinja, R. K.; Runacres, M. C.; Clark, J. S.

    2003-09-01

    We present radio and submillimetre observations of the O4I(n)f star zeta Pup, and discuss structure in the outer region of its wind ( ~ 10-100 R_*). The properties of bremsstrahlung, the dominant emission process at these wavelengths, make it sensitive to structure and allow us to study how the amount of structure changes in the wind by comparing the fluxes at different wavelengths. Possible forms of structure at these distances include Corotating Interaction Regions (CIRs), stochastic clumping, a disk or a polar enhancement. As the CIRs are azimuthally asymmetric, they should result in variability at submillimetre or radio wavelengths. To look for this variability, we acquired 3.6 and 6 cm observations with the Australia Telescope Compact Array (ATCA), covering about two rotational periods of the star. We supplemented these with archive observations from the NRAO Very Large Array (VLA), which cover a much longer time scale. We did not find variability at more than the +/-20% level. The long integration time does allow an accurate determination of the fluxes at 3.6 and 6 cm. Converting these fluxes into a mass loss rate, we find dot {M} = 3.5 x 10-6 Msun/yr. This value confirms the significant discrepancy with the mass loss rate derived from the Hα profile, making zeta Pup an exception to the usually good agreement between the Hα and radio mass loss rates. To study the run of structure as a function of distance, we supplemented the ATCA data by observing zeta Pup at 850 mu m with the James Clerk Maxwell Telescope (JCMT) and at 20 cm with the VLA. A smooth wind model shows that the millimetre fluxes are too high compared to the radio fluxes. While recombination of helium in the outer wind cannot be discounted as an explanation, the wealth of evidence for structure strongly suggests this as the explanation for the discrepancy. Model calculations show that the structure needs to be present in the inner ~ 70 R_* of the wind, but that it decays significantly, or maybe

  2. Secondary electroosmotic flow in microchannels with nonuniform and asymmetric Zeta potential

    NASA Astrophysics Data System (ADS)

    Zhang, Jinbai; He, Guowei; Liu, Feng

    2004-11-01

    Microfluidics has a broad range of applications in biotechnology, such as sample injection, drug delivering, solution mixing, and separations. All of these techniques require handling fluids in the low Reynolds number (Re) regime. Electroosmotic flow (EOF) or electroosmocitcs is the bulk movement of liquid relative to a stationary surface due to an externally applied electronic field. It is an alternative to pressure-driven flows with convenient implementation The driving force for EOF is dependent on the zeta potential. Previous reseraches focus on the nonuniform Zeta potential. In the present work, we consider nonuniform and asymmetric Zeta potential. The effects of asymmetric Zeta potential on the EOF are investigated analytically and simulated numerically. It is demonstrated that the nonuniform and asymmetric Zeta potential can generate more flow patterns for microfluidic control compared to symmetric Zeta potential.

  3. Estimation of the zeta potential and the dielectric constant using velocity measurements in the electroosmotic flows.

    PubMed

    Park, H M; Hong, S M

    2006-12-15

    In this paper we develop a method for the determination of the zeta potential zeta and the dielectric constant epsilon by exploiting velocity measurements of the electroosmotic flow in microchannels. The inverse problem is solved through the minimization of a performance function utilizing the conjugate gradient method. The present method is found to estimate zeta and epsilon with reasonable accuracy even with noisy velocity measurements.

  4. Moments of zeta functions associated to hyperelliptic curves over finite fields

    PubMed Central

    Rubinstein, Michael O.; Wu, Kaiyu

    2015-01-01

    Let q be an odd prime power, and denote the set of square-free monic polynomials D(x)∈Fq[x] of degree d. Katz and Sarnak showed that the moments, over , of the zeta functions associated to the curves y2=D(x), evaluated at the central point, tend, as , to the moments of characteristic polynomials, evaluated at the central point, of matrices in USp(2⌊(d−1)/2⌋). Using techniques that were originally developed for studying moments of L-functions over number fields, Andrade and Keating conjectured an asymptotic formula for the moments for q fixed and . We provide theoretical and numerical evidence in favour of their conjecture. In some cases, we are able to work out exact formulae for the moments and use these to precisely determine the size of the remainder term in the predicted moments. PMID:25802418

  5. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

    NASA Astrophysics Data System (ADS)

    Goldfeld, Dahlia A.; Bochevarov, Arteum D.; Friesner, Richard A.

    2008-12-01

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G∗, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

  6. Estimation of zeta potential of electroosmotic flow in a microchannel using a reduced-order model.

    PubMed

    Park, H M; Hong, S M; Lee, J S

    2007-10-01

    A reduced-order model is derived for electroosmotic flow in a microchannel of nonuniform cross section using the Karhunen-Loève Galerkin (KLG) procedure. The resulting reduced-order model is shown to predict electroosmotic flows accurately with minimal consumption of computer time for a wide range of zeta potential zeta and dielectric constant epsilon. Using the reduced-order model, a practical method is devised to estimate zeta from the velocity measurements of the electroosmotic flow in the microchannel. The proposed method is found to estimate zeta with reasonable accuracy even with noisy velocity measurements.

  7. Roothaan’s approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior

    SciTech Connect

    Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M.

    2015-07-21

    In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energiesmore » always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.« less

  8. Roothaan's approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior.

    PubMed

    Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M; Vargas, Rubicelia; Garza, Jorge

    2015-07-21

    In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.

  9. Methodological basis for the optimization of a marine sea-urchin embryo test (SET) for the ecological assessment of coastal water quality.

    PubMed

    Saco-Alvarez, Liliana; Durán, Iria; Ignacio Lorenzo, J; Beiras, Ricardo

    2010-05-01

    The sea-urchin embryo test (SET) has been frequently used as a rapid, sensitive, and cost-effective biological tool for marine monitoring worldwide, but the selection of a sensitive, objective, and automatically readable endpoint, a stricter quality control to guarantee optimum handling and biological material, and the identification of confounding factors that interfere with the response have hampered its widespread routine use. Size increase in a minimum of n=30 individuals per replicate, either normal larvae or earlier developmental stages, was preferred to observer-dependent, discontinuous responses as test endpoint. Control size increase after 48 h incubation at 20 degrees C must meet an acceptability criterion of 218 microm. In order to avoid false positives minimums of 32 per thousand salinity, 7 pH and 2mg/L oxygen, and a maximum of 40 microg/L NH(3) (NOEC) are required in the incubation media. For in situ testing size increase rates must be corrected on a degree-day basis using 12 degrees C as the developmental threshold. Copyright 2010 Elsevier Inc. All rights reserved.

  10. Evaluation of the Volatility Basis-Set Approach for Modeling Primary and Secondary Organic Aerosol in the Mexico City Metropolitan Area

    NASA Astrophysics Data System (ADS)

    Tsimpidi, A. P.; Karydis, V. A.; Pandis, S. N.; Zavala, M.; Lei, W.; Molina, L. T.

    2007-12-01

    Anthropogenic air pollution is an increasingly serious problem for public health, agriculture, and global climate. Organic material (OM) contributes ~ 20-50% to the total fine aerosol mass at continental mid-latitudes. Although OM accounts for a large fraction of PM2.5 concentration worldwide, the contributions of primary and secondary organic aerosol have been difficult to quantify. In this study, new primary and secondary organic aerosol modules were added to PMCAMx, a three dimensional chemical transport model (Gaydos et al., 2007), for use with the SAPRC99 chemistry mechanism (Carter, 2000; ENVIRON, 2006) based on recent smog chamber studies (Robinson et al., 2007). The new modeling framework is based on the volatility basis-set approach (Lane et al., 2007): both primary and secondary organic components are assumed to be semivolatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. The emission inventory, which uses as starting point the MCMA 2004 official inventory (CAM, 2006), is modified and the primary organic aerosol (POA) emissions are distributed by volatility based on dilution experiments (Robinson et al., 2007). Sensitivity tests where POA is considered as nonvolatile and POA and SOA as chemically reactive are also described. In all cases PMCAMx is applied in the Mexico City Metropolitan Area during March 2006. The modeling domain covers a 180x180x6 km region in the MCMA with 3x3 km grid resolution. The model predictions are compared with Aerodyne's Aerosol Mass Spectrometry (AMS) observations from the MILAGRO Campaign. References Robinson, A. L.; Donahue, N. M.; Shrivastava, M. K.; Weitkamp, E. A.; Sage, A. M.; Grieshop, A. P.; Lane, T. E.; Pandis, S. N.; Pierce, J. R., 2007. Rethinking organic aerosols: semivolatile emissions and photochemical aging. Science 315, 1259-1262. Gaydos, T. M.; Pinder, R. W.; Koo, B.; Fahey, K. M.; Pandis, S. N., 2007. Development and application of a three- dimensional aerosol

  11. A basis set for exploration of sensitivity to prescribed ocean conditions for estimating human contributions to extreme weather in CAM5.1-1degree

    SciTech Connect

    Stone, Dáithí A.; Risser, Mark D.; Angélil, Oliver M.

    This paper presents two contributions for research into better understanding the role of anthropogenic warming in extreme weather. The first contribution is the generation of a large number of multi-decadal simulations using a medium-resolution atmospheric climate model, CAM5.1-1degree, under two scenarios of historical climate following the protocols of the C20C+ Detection and Attribution project: the one we have experienced (All-Hist), and one that might have been experienced in the absence of human interference with the climate system (Nat-Hist). These simulations are also specifically designed for understanding extreme weather and atmospheric variability in the context of anthropogenic climate change.The second contributionmore » takes advantage of the duration and size of these simulations in order to identify features of variability in the prescribed ocean conditions that may strongly influence calculated estimates of the role of anthropogenic emissions on extreme weather frequency (event attribution). There is a large amount of uncertainty in how much anthropogenic emissions should warm regional ocean surface temperatures, yet contributions to the C20C+ Detection and Attribution project and similar efforts so far use only one or a limited number of possible estimates of the ocean warming attributable to anthropogenic emissions when generating their Nat-Hist simulations. Thus, the importance of the uncertainty in regional attributable warming estimates to the results of event attribution studies is poorly understood. The identification of features of the anomalous ocean state that seem to strongly influence event attribution estimates should therefore be able to serve as a basis set for effective sampling of other plausible attributable warming patterns. The identification performed in this paper examines monthly temperature and precipitation output from the CAM5.1-1degree simulations averaged over 237 land regions, and compares interannual anomalous

  12. Antiferromagnetic vs. non-magnetic ε phase of solid oxygen. Periodic density functional theory studies using a localized atomic basis set and the role of exact exchange.

    PubMed

    Ramírez-Solís, A; Zicovich-Wilson, C M; Hernández-Lamoneda, R; Ochoa-Calle, A J

    2017-01-25

    The question of the non-magnetic (NM) vs. antiferromagnetic (AF) nature of the ε phase of solid oxygen is a matter of great interest and continuing debate. In particular, it has been proposed that the ε phase is actually composed of two phases, a low-pressure AF ε 1 phase and a higher pressure NM ε 0 phase [Crespo et al., Proc. Natl. Acad. Sci. U. S. A., 2014, 111, 10427]. We address this problem through periodic spin-restricted and spin-polarized Kohn-Sham density functional theory calculations at pressures from 10 to 50 GPa using calibrated GGA and hybrid exchange-correlation functionals with Gaussian atomic basis sets. The two possible configurations for the antiferromagnetic (AF1 and AF2) coupling of the 0 ≤ S ≤ 1 O 2 molecules in the (O 2 ) 4 unit cell were studied. Full enthalpy-driven geometry optimizations of the (O 2 ) 4 unit cells were done to study the pressure evolution of the enthalpy difference between the non-magnetic and both antiferromagnetic structures. We also address the evolution of structural parameters and the spin-per-molecule vs. pressure. We find that the spin-less solution becomes more stable than both AF structures above 50 GPa and, crucially, the spin-less solution yields lattice parameters in much better agreement with experimental data at all pressures than the AF structures. The optimized AF2 broken-symmetry structures lead to large errors of the a and b lattice parameters when compared with experiments. The results for the NM model are in much better agreement with the experimental data than those found for both AF models and are consistent with a completely non-magnetic (O 2 ) 4 unit cell for the low-pressure regime of the ε phase.

  13. A Combined Kinetic and Volatility Basis Set Approach to Model Secondary Organic Aerosol from Toluene and Diesel Exhaust/Meat Cooking Mixtures

    NASA Astrophysics Data System (ADS)

    Parikh, H. M.; Carlton, A. G.; Zhang, H.; Kamens, R.; Vizuete, W.

    2011-12-01

    Secondary organic aerosol (SOA) is simulated for 6 outdoor smog chamber experiments using a SOA model based on a kinetic chemical mechanism in conjunction with a volatility basis set (VBS) approach. The experiments include toluene, a non-SOA-forming hydrocarbon mixture, diesel exhaust or meat cooking emissions and NOx, and are performed under varying conditions of relative humidity. SOA formation from toluene is modeled using a condensed kinetic aromatic mechanism that includes partitioning of lumped semi-volatile products in particle organic-phase and incorporates particle aqueous-phase chemistry to describe uptake of glyoxal and methylglyoxal. Modeling using the kinetic mechanism alone, along with primary organic aerosol (POA) from diesel exhaust (DE) /meat cooking (MC) fails to simulate the rapid SOA formation at the beginning hours of the experiments. Inclusion of a VBS approach with the kinetic mechanism to characterize the emissions and chemistry of complex mixture of intermediate volatility organic compounds (IVOCs) from DE/MC, substantially improves SOA predictions when compared with observed data. The VBS model includes photochemical aging of IVOCs and evaporation of POA after dilution. The relative contribution of SOA mass from DE/MC is as high as 95% in the morning, but substantially decreases after mid-afternoon. For high humidity experiments, aqueous-phase SOA fraction dominates the total SOA mass at the end of the day (approximately 50%). In summary, the combined kinetic and VBS approach provides a new and improved framework to semi-explicitly model SOA from VOC precursors in conjunction with a VBS approach that can be used on complex emission mixtures comprised with hundreds of individual chemical species.

  14. A basis set for exploration of sensitivity to prescribed ocean conditions for estimating human contributions to extreme weather in CAM5.1-1degree

    DOE PAGES

    Stone, Dáithí A.; Risser, Mark D.; Angélil, Oliver M.; ...

    2018-03-01

    This paper presents two contributions for research into better understanding the role of anthropogenic warming in extreme weather. The first contribution is the generation of a large number of multi-decadal simulations using a medium-resolution atmospheric climate model, CAM5.1-1degree, under two scenarios of historical climate following the protocols of the C20C+ Detection and Attribution project: the one we have experienced (All-Hist), and one that might have been experienced in the absence of human interference with the climate system (Nat-Hist). These simulations are also specifically designed for understanding extreme weather and atmospheric variability in the context of anthropogenic climate change.The second contributionmore » takes advantage of the duration and size of these simulations in order to identify features of variability in the prescribed ocean conditions that may strongly influence calculated estimates of the role of anthropogenic emissions on extreme weather frequency (event attribution). There is a large amount of uncertainty in how much anthropogenic emissions should warm regional ocean surface temperatures, yet contributions to the C20C+ Detection and Attribution project and similar efforts so far use only one or a limited number of possible estimates of the ocean warming attributable to anthropogenic emissions when generating their Nat-Hist simulations. Thus, the importance of the uncertainty in regional attributable warming estimates to the results of event attribution studies is poorly understood. The identification of features of the anomalous ocean state that seem to strongly influence event attribution estimates should therefore be able to serve as a basis set for effective sampling of other plausible attributable warming patterns. The identification performed in this paper examines monthly temperature and precipitation output from the CAM5.1-1degree simulations averaged over 237 land regions, and compares interannual anomalous

  15. A systematic study of basis set, electron correlation, and geometry effects on the electric multipole moments, polarizability, and hyperpolarizability of HCl

    NASA Astrophysics Data System (ADS)

    Maroulis, George

    1998-04-01

    The electric multipole moments, dipole and quadrupole polarizability and hyperpolarizability of hydrogen chloride have been determined from an extensive and systematic study based on finite-field fourth-order many-body perturbation theory and coupled-cluster calculations. Our best values for the dipole, quadrupole, octopole and hexadecapole moment at the experimental internuclear separation of Re=2.408645a0 are μ=0.4238ea0, Θ=2.67ea02, Ω=3.94ea03, and Φ=13.37ea04, respectively. For the mean and the anisotropy of the dipole polarizability ααβ we recommend ᾱ=17.41±0.02 and Δα=1.60±0.03e2a02Eh-1. For the mean value of the first dipole hyperpolarizability βαβγ we advance β¯=-6.8±0.3e3a03Eh-2. Extensive calculations with a [8s6p6d3f/5s4p2d1f] basis set at the CCSD(T) level of theory yield the R-dependence of the Cartesian components and the mean of the second dipole hyperpolarizability γαβγδ(R)/e4a04Eh-3 around Re as γzzzz(R)=1907+1326(R-Re)+570(R-Re)2+10(R-Re)3-40(R-Re)4, γxxxx(R)=3900+747(R-Re)-65(R-Re)2-38(R-Re)3-7(R-Re)4, γxxzz(R)=962+222(R-Re)+88(R-Re)2+49(R-Re)3+5(R-Re)4, γ¯(R)=3230+841(R-Re)+151(R-Re)2+21(R-Re)3-9(R-Re)4, with z as the molecular axis. The present investigation suggests an estimate of (26.7±0.3)×102e4a04Eh-3 for the Hartree-Fock limit of the mean value γ¯ at Re. CCSD(T) calculations with basis sets of [8s6p6d3f/5s4p2d1f] and [9s7p5d4f/6s5p4d1f] size and MP4 calculations with the even larger [15s12p7d3f/12s7p2d1f] give (7.0±0.3)×102e4a04Eh-3 for the electron correlation effects for this property, thus leading to a recommended value of γ¯=(33.7±0.6)×102e4a04Eh-3. For the quadrupole polarizability Cαβ,γδ/e2a04Eh-1 at Re our best values are Czz,zz=41.68, Cxz,xz=26.11, and Cxx,xx=35.38, calculated with the [9s7p5d4f/6s5p4d1f] basis set at the CCSD(T) level of theory. The following CCSD(T) values were obtained with [8s6p6d3f/5s4p2d1f] at Re: dipole-quadrupole polarizability Aα,βγ/e2a03Eh-1, Az,zz=14.0, and

  16. Zeta potential of microfluidic substrates: 1. Theory, experimental techniques, and effects on separations.

    PubMed

    Kirby, Brian J; Hasselbrink, Ernest F

    2004-01-01

    This paper summarizes theory, experimental techniques, and the reported data pertaining to the zeta potential of silica and silicon with attention to use as microfluidic substrate materials, particularly for microchip chemical separations. Dependence on cation concentration, buffer and cation type, pH, cation valency, and temperature are discussed. The Debye-Hückel limit, which is often correctly treated as a good approximation for describing the ion concentration in the double layer, can lead to serious errors if it is extended to predict the dependence of zeta potential on the counterion concentration. For indifferent univalent electrolytes (e.g., sodium and potassium), two simple scalings for the dependence of zeta potential on counterion concentration can be derived in high- and low-zeta limits of the nonlinear Poisson-Boltzman equation solution in the double layer. It is shown that for most situations relevant to microchip separations, the high-zeta limit is most applicable, leading to the conclusion that the zeta potential on silica substrates is approximately proportional to the logarithm of the molar counterion concentration. The zeta vs. pH dependence measurements from several experiments are compared by normalizing the zeta based on concentration.

  17. Retention of membrane charge attributes by cryopreserved-thawed sperm and zeta selection.

    PubMed

    Kam, Tricia L; Jacobson, John D; Patton, William C; Corselli, Johannah U; Chan, Philip J

    2007-09-01

    Mature sperm can be selected based on their negative zeta electrokinetic potential. The zeta selection of cryopreserved sperm is unknown. The objective was to study the effect of zeta processing on the morphology and kinematic parameters of cryopreserved-thawed sperm. Colloid-washed sperm (N = 9 cases) were cryopreserved for 24 h, thawed and diluted in serum-free medium in positive-charged tubes. After centrifugation, the tubes were decanted, serum-supplemented medium was added and the resuspended sperm were analyzed. Untreated sperm and fresh sperm served as the controls. There were improvements in strict normal morphology in fresh (11.8 +/- 0.3 versus control 8.8 +/- 0.3 %, mean +/- SEM) and thawed (8.7 +/- 0.2 versus control 5.4 +/- 0.2%) sperm after zeta processing. Percent sperm necrosis was reduced after zeta processing (66.0 +/- 0.6 versus unprocessed 74.6 +/- 0.3%). Progression decreased by 50% but not total motility after zeta processing of thawed sperm. The results suggested that the cryopreservation process did not impact the sperm membrane net zeta potential and higher percentages of sperm with normal strict morphology, acrosome integrity and reduced necrosis were recovered. The zeta method was simple and improved the selection of quality sperm after cryopreservation but more studies would be needed before routine clinical application.

  18. Oscillatory electroosmotic flow in a parallel-plate microchannel under asymmetric zeta potentials

    NASA Astrophysics Data System (ADS)

    Peralta, M.; Arcos, J.; Méndez, F.; Bautista, O.

    2017-06-01

    In this work, we conduct a theoretical analysis of the start-up of an oscillatory electroosmotic flow (EOF) in a parallel-plate microchannel under asymmetric zeta potentials. It is found that the transient evolution of the flow field is controlled by the parameters {R}ω , {R}\\zeta , and \\bar{κ }, which represent the dimensionless frequency, the ratio of the zeta potentials of the microchannel walls, and the electrokinetic parameter, which is defined as the ratio of the microchannel height to the Debye length. The analysis is performed for both low and high zeta potentials; in the former case, an analytical solution is derived, whereas in the latter, a numerical solution is obtained. These solutions provide the fundamental characteristics of the oscillatory EOFs for which, with suitable adjustment of the zeta potential and the dimensionless frequency, the velocity profiles of the fluid flow exhibit symmetric or asymmetric shapes.

  19. IUE observations of the atmospheric eclipsing binary system Zeta Aurigae

    NASA Technical Reports Server (NTRS)

    Champman, R. D.

    1980-01-01

    IUE observations of the eclipsing binary system Zeta Aurigae made prior to and during the eclipse of the relatively small B8 V star by the cool supergiant star (spectral type K2 II) are reported. Spectral lines produced by the absorption of B star radiation in the atmosphere of the K star during eclipse can be used as a probe of the extended K star atmosphere, due to the negligible cool star continuum in the 1200-3200 A region. Spectra taken prior to eclipse are found to be similar to those of the single B8 V star 64 Ori, with the exception of very strong multi-component absorption lines of Si II, Si IV, C IV and the Mg resonance doublet with strong P Cygni profiles, indicating a double shell. Absorption lines including those corresponding to Al II, Al III, Cr II, Mn II, Fe II, Ni II and Ca II are observed to increase in strength and number as the eclipse progresses, with high-ionization-potential lines formed far from the K star, possibly in a shock wave, and low-ionization potential lines, formed in cool plasma, probably a cool wind, nearer to the K star. Finally, an emission-line spectra with lines corresponding to those previously observed in absorption is noted at the time the B-star continuum had disappeared.

  20. Zeta potentials in the flotation of oxide and silicate minerals.

    PubMed

    Fuerstenau, D W; Pradip

    2005-06-30

    Adsorption of collectors and modifying reagents in the flotation of oxide and silicate minerals is controlled by the electrical double layer at the mineral-water interface. In systems where the collector is physically adsorbed, flotation with anionic or cationic collectors depends on the mineral surface being charged oppositely. Adjusting the pH of the system can enhance or prevent the flotation of a mineral. Thus, the point of zero charge (PZC) of the mineral is the most important property of a mineral in such systems. The length of the hydrocarbon chain of the collector is important because of chain-chain association enhances the adsorption once the surfactant ions aggregate to form hemimicelles at the surface. Strongly chemisorbing collectors are able to induce flotation even when collector and the mineral surface are charged similarly, but raising the pH sufficiently above the PZC can repel chemisorbing collectors from the mineral surface. Zeta potentials can be used to delineate interfacial phenomena in these various systems.

  1. Comparison of one-particle basis set extrapolation to explicitly correlated methods for the calculation of accurate quartic force fields, vibrational frequencies, and spectroscopic constants: Application to H2O, N2H+, NO2+, and C2H2

    NASA Astrophysics Data System (ADS)

    Huang, Xinchuan; Valeev, Edward F.; Lee, Timothy J.

    2010-12-01

    One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H2O, N2H+, NO2+, and C2H2 molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N2H+ where it is concluded that basis set extrapolation is still preferred. The differences for H2O and NO2+ are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C2H2, however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)R12, incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N2H+ and NO2+ were computed, including basis set extrapolation, core-correlation, scalar relativity, and higher

  2. Influence of surface conductivity on the apparent zeta potential of calcite.

    PubMed

    Li, Shuai; Leroy, Philippe; Heberling, Frank; Devau, Nicolas; Jougnot, Damien; Chiaberge, Christophe

    2016-04-15

    Zeta potential is a physicochemical parameter of particular importance in describing the surface electrical properties of charged porous media. However, the zeta potential of calcite is still poorly known because of the difficulty to interpret streaming potential experiments. The Helmholtz-Smoluchowski (HS) equation is widely used to estimate the apparent zeta potential from these experiments. However, this equation neglects the influence of surface conductivity on streaming potential. We present streaming potential and electrical conductivity measurements on a calcite powder in contact with an aqueous NaCl electrolyte. Our streaming potential model corrects the apparent zeta potential of calcite by accounting for the influence of surface conductivity and flow regime. We show that the HS equation seriously underestimates the zeta potential of calcite, particularly when the electrolyte is diluted (ionic strength ⩽ 0.01 M) because of calcite surface conductivity. The basic Stern model successfully predicted the corrected zeta potential by assuming that the zeta potential is located at the outer Helmholtz plane, i.e. without considering a stagnant diffuse layer at the calcite-water interface. The surface conductivity of calcite crystals was inferred from electrical conductivity measurements and computed using our basic Stern model. Surface conductivity was also successfully predicted by our surface complexation model. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Observations of H II regions around Zeta OPH and other O-B stars

    NASA Astrophysics Data System (ADS)

    Shestakova, L. I.; Kutirev, A. S.; Ataev, A. Sh.

    1988-01-01

    A Fabry-Perot spectrometer was used to measure the emission intensities in H-beta near Zeta Oph, Alpha Vir, Alpha Cam, and HD 188209. The spectrometer sensitivity is 0.2 rayleighs, the intensity measurement accuracy is 20 percent. Ionization zone boundaries are determined for Zeta Oph and Alpha Vir; the angular diameters of both regions are about 15 deg. The contour of the H II region near Zeta Oph on the level of the double background in the southwest does not close; instead, it expands again and incorporates the region associated with the B-association II Sco.

  4. Tunnel determinants from spectral zeta functions. Instanton effects in quantum mechanics

    SciTech Connect

    Izquierdo, A. Alonso; Guilarte, J. Mateos

    2014-07-23

    In this paper we develop an spectral zeta function regularization procedure on the determinants of instanton fluctuation operators that describe the semi-classical order of tunnel effects between degenerate vacua.

  5. Surface Complexation Modeling of Calcite Zeta Potential Measurement in Mixed Brines for Carbonate Wettability Characterization

    NASA Astrophysics Data System (ADS)

    Song, J.; Zeng, Y.; Biswal, S. L.; Hirasaki, G. J.

    2017-12-01

    We presents zeta potential measurements and surface complexation modeling (SCM) of synthetic calcite in various conditions. The systematic zeta potential measurement and the proposed SCM provide insight into the role of four potential determining cations (Mg2+, SO42- , Ca2+ and CO32-) and CO2 partial pressure in calcite surface charge formation and facilitate the revealing of calcite wettability alteration induced by brines with designed ionic composition ("smart water"). Brines with varying potential determining ions (PDI) concentration in two different CO2 partial pressure (PCO2) are investigated in experiments. Then, a double layer SCM is developed to model the zeta potential measurements. Moreover, we propose a definition for contribution of charged surface species and quantitatively analyze the variation of charged species contribution when changing brine composition. After showing our model can accurately predict calcite zeta potential in brines containing mixed PDIs, we apply it to predict zeta potential in ultra-low and pressurized CO2 environments for potential applications in carbonate enhanced oil recovery including miscible CO2 flooding and CO2 sequestration in carbonate reservoirs. Model prediction reveals that pure calcite surface will be positively charged in all investigated brines in pressurized CO2 environment (>1atm). Moreover, the sensitivity of calcite zeta potential to CO2 partial pressure in the various brine is found to be in the sequence of Na2CO3 > Na2SO4 > NaCl > MgCl2 > CaCl2 (Ionic strength=0.1M).

  6. Mapping Protein-Protein Interactions of the Resistance-Related Bacterial Zeta Toxin-Epsilon Antitoxin Complex (ε₂ζ₂) with High Affinity Peptide Ligands Using Fluorescence Polarization.

    PubMed

    Fernández-Bachiller, María Isabel; Brzozowska, Iwona; Odolczyk, Norbert; Zielenkiewicz, Urszula; Zielenkiewicz, Piotr; Rademann, Jörg

    2016-07-16

    Toxin-antitoxin systems constitute a native survival strategy of pathogenic bacteria and thus are potential targets of antibiotic drugs. Here, we target the Zeta-Epsilon toxin-antitoxin system, which is responsible for the stable maintenance of certain multiresistance plasmids in Gram-positive bacteria. Peptide ligands were designed on the basis of the ε₂ζ₂ complex. Three α helices of Zeta forming the protein-protein interaction (PPI) site were selected and peptides were designed conserving the residues interacting with Epsilon antitoxin while substituting residues binding intramolecularly to other parts of Zeta. Designed peptides were synthesized with an N-terminal fluoresceinyl-carboxy-residue for binding assays and provided active ligands, which were used to define the hot spots of the ε₂ζ₂ complex. Further shortening and modification of the binding peptides provided ligands with affinities <100 nM, allowing us to determine the most relevant PPIs and implement a robust competition binding assay.

  7. Antiholomorphic perturbations of Weierstrass Zeta functions and Green’s function on tori

    NASA Astrophysics Data System (ADS)

    Bogdanov, Konstantin; Mamayusupov, Khudoyor; Mukherjee, Sabyasachi; Schleicher, Dierk

    2017-08-01

    In Bergweiler and Eremenko (2016 Proc. Am. Math. Soc. 144 2911-22), Bergweiler and Eremenko computed the number of critical points of the Green’s function on a torus by investigating the dynamics of a certain family of antiholomorphic meromorphic functions on tori. They also observed that hyperbolic maps are dense in this family of meromorphic functions in a rather trivial way. In this paper, we study the parameter space of this family of meromorphic functions, which can be written as antiholomorphic perturbations of Weierstrass Zeta functions. On the one hand, we give a complete topological description of the hyperbolic components and their boundaries, and on the other hand, we show that these sets admit natural parametrizations by associated dynamical invariants. This settles a conjecture, made in Lin and Wang (2010 Ann. Math. 172 911-54), on the topology of the regions in the upper half plane {H} where the number of critical points of the Green’s function remains constant.

  8. Electronic Structure and Bonding in Transition Metal Inorganic and Organometallic Complexes: New Basis Sets, Linear Semibridging Carbonyls and Thiocarbonyls, and Oxidative Addition of Molecular Hydrogen to Square - Iridium Complexes.

    NASA Astrophysics Data System (ADS)

    Sargent, Andrew Landman

    Approximate molecular orbital and ab initio quantum chemical techniques are used to investigate the electronic structure, bonding and reactivity of several transition metal inorganic and organometallic complexes. Modest-sized basis sets are developed for the second-row transition metal atoms and are designed for use in geometry optimizations of inorganic and organometallic complexes incorporating these atoms. The basis sets produce optimized equilibrium geometries which are slightly better than those produced with standard 3-21G basis sets, and which are significantly better than those produced with effective core potential basis sets. Linear semibridging carbonyl ligands in heterobimetallic complexes which contain a coordinatively unsaturated late transition metal center are found to accept electron density from, rather than donate electron density to, these centers. Only when the secondary metal center is a coordinatively unsaturated early transition metal center does the semibridging ligand donate electron density to this center. Large holes in the d shell around the metal center are more prominent and prevalent in early than in late transition metal centers, and the importance of filling in these holes outweighs the importance of mitigating the charge imbalance due to the dative metal-metal interaction. Semibridging thiocarbonyl ligands are more effective donors of electron density than the carbonyl ligands since the occupied donor orbitals of pi symmetry are higher in energy. The stereoselectivity of H_2 addition to d^8 square-planar transition metal complexes is controlled by the interactions between the ligands in the plane of addition and the concentrations of electronic charge around the metal center as the complex evolves from a four-coordinate to a six-coordinate species. Electron -withdrawing ligands help stabilize the five-coordinate species while strong electron donor ligands contribute only to the destabilizing repulsive interactions. The relative

  9. An Approach To Using All Location Tagged Numerical Data Sets As Continuous Fields With User-Assigned Continuity As A Basis For User-Driven Data Assimilation

    NASA Astrophysics Data System (ADS)

    Vernon, F.; Arrott, M.; Orcutt, J. A.; Mueller, C.; Case, J.; De Wardener, G.; Kerfoot, J.; Schofield, O.

    2013-12-01

    Any approach sophisticated enough to handle a variety of data sources and scale, yet easy enough to promote wide use and mainstream adoption is required to address the following mappings: - From the authored domain of observation to the requested domain of interest; - From the authored spatiotemporal resolution to the requested resolution; and - From the representation of data placed on wide variety of discrete mesh types to the use of that data as a continuos field with a selectable continuity. The Open Geospatial Consortium's (OGC) Reference Model[1] with its direct association with the ISO 19000 series standards provides a comprehensive foundation to represent all data on any type of mesh structure, aka "Discrete Coverages". The Reference Model also provides the specification for the core operations required to utilize any Discrete Coverage. The FEniCS Project[2] provides a comprehensive model for how to represent the Basis Functions on mesh structures as "Degrees of Freedom" to present discrete data as continuous fields with variable continuity. In this talk, we will present the research and development the OOI Cyberinfrastructure Project is pursuing to integrate these approaches into a comprehensive Application Programming Interface (API) to author, acquire and operate on the broad range of data formulation from time series, trajectories and tables through to time variant finite difference grids and finite element meshes.

  10. Measurement of Zeta-Potential at Microchannel Wall by a Nanoscale Laser Induced Fluorescence Imaging

    NASA Astrophysics Data System (ADS)

    Kazoe, Yutaka; Sato, Yohei

    A nanoscale laser induced fluorescence imaging was proposed by using fluorescent dye and the evanescent wave with total internal reflection of a laser beam. The present study focused on the two-dimensional measurement of zeta-potential at the microchannel wall, which is an electrostatic potential at the wall surface and a dominant parameter of electroosmotic flow. The evanescent wave, which decays exponentially from the wall, was used as an excitation light of the fluorescent dye. The fluorescent intensity detected by a CCD camera is closely related to the zeta-potential. Two kinds of fluorescent dye solution at different ionic concentrations were injected into a T-shaped microchannel, and formed a mixing flow field in the junction area. The two-dimensional distribution of zeta-potential at the microchannel wall in the pressure-driven flow field was measured. The obtained zeta-potential distribution has a transverse gradient toward the mixing flow field and was changed by the difference in the averaged velocity of pressure-driven flow. To understand the ion motion in the mixing flow field, the three-dimensional flow structure was analyzed by the velocity measurement using micron-resolution particle image velocimetry and the numerical simulation. It is concluded that the two-dimensional distribution of zeta-potential at the microchannel wall was dependent on the ion motion in the flow field, which was governed by the convection and molecular diffusion.

  11. An induced current method for measuring zeta potential of electrolyte solution-air interface.

    PubMed

    Song, Yongxin; Zhao, Kai; Wang, Junsheng; Wu, Xudong; Pan, Xinxiang; Sun, Yeqing; Li, Dongqing

    2014-02-15

    This paper reports a novel and very simple method for measuring the zeta potential of electrolyte solution-air interface. When a measuring electrode contacts the electrolyte solution-air interface, an electrical current will be generated due to the potential difference between the electrode-air surface and the electrolyte solution-air interface. The amplitude of the measured electric signal is linearly proportional to this potential difference; and depends only on the zeta potential at the electrolyte solution-air interface, regardless of the types and concentrations of the electrolyte. A correlation between the zeta potential and the measured voltage signal is obtained based on the experimental data. Using this equation, the zeta potential of any electrolyte solution-air interface can be evaluated quickly and easily by inserting an electrode through the electrolyte solution-air interface and measuring the electrical signal amplitude. This method was verified by comparing the obtained results of NaCl, MgCl2 and CaCl2 solutions of different pH values and concentrations with the zeta potential data reported in the published journal papers. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. A gene variation of 14-3-3 zeta isoform in rat hippocampus.

    PubMed

    Murakami, K; Situ, S Y; Eshete, F

    1996-11-14

    A variant form of 14-3-3 zeta was isolated from the rat hippocampal cDNA library. The cloned cDNA is 1687 bp in length and it contains an entire ORF (nt = 63-797) with 245 amino acids that is characteristic to 14-3-3 zeta subtype. By comparing with reported sequences of 14-3-3 zeta, we found three nucleotide substitutions within the coding sequence in our clone; C<-->T transition at nt = 325 and G<-->C transversions at nt = 387 and 388. Both are missense mutations, leading ACG (Thr) to ATG (Met) and CGT (Arg) to GCT (Ala) conversions at residue 88 and 109, respectively. Our results show that at least three different genetic variants of 14-3-3 zeta are present in rat species which results in protein variations. Such mutation in the amino acid sequence is an important indication of the diverse functions of this protein and may also contribute to the recent contradictory observations regarding the role of the 14-3-3 zeta subtype.

  13. LETTER TO THE EDITOR: Fractal diffusion coefficient from dynamical zeta functions

    NASA Astrophysics Data System (ADS)

    Cristadoro, Giampaolo

    2006-03-01

    Dynamical zeta functions provide a powerful method to analyse low-dimensional dynamical systems when the underlying symbolic dynamics is under control. On the other hand, even simple one-dimensional maps can show an intricate structure of the grammar rules that may lead to a non-smooth dependence of global observables on parameters changes. A paradigmatic example is the fractal diffusion coefficient arising in a simple piecewise linear one-dimensional map of the real line. Using the Baladi-Ruelle generalization of the Milnor-Thurnston kneading determinant, we provide the exact dynamical zeta function for such a map and compute the diffusion coefficient from its smallest zero.

  14. Zeta Function Regularization in Casimir Effect Calculations and J. S. DOWKER's Contribution

    NASA Astrophysics Data System (ADS)

    Elizalde, Emilio

    2012-06-01

    A summary of relevant contributions, ordered in time, to the subject of operator zeta functions and their application to physical issues is provided. The description ends with the seminal contributions of Stephen Hawking and Stuart Dowker and collaborators, considered by many authors as the actual starting point of the introduction of zeta function regularization methods in theoretical physics, in particular, for quantum vacuum fluctuation and Casimir effect calculations. After recalling a number of the strengths of this powerful and elegant method, some of its limitations are discussed. Finally, recent results of the so-called operator regularization procedure are presented.

  15. Zeta Function Regularization in Casimir Effect Calculations and J. S. Dowker's Contribution

    NASA Astrophysics Data System (ADS)

    Elizalde, Emilio

    2012-07-01

    A summary of relevant contributions, ordered in time, to the subject of operator zeta functions and their application to physical issues is provided. The description ends with the seminal contributions of Stephen Hawking and Stuart Dowker and collaborators, considered by many authors as the actual starting point of the introduction of zeta function regularization methods in theoretical physics, in particular, for quantum vacuum fluctuation and Casimir effect calculations. After recalling a number of the strengths of this powerful and elegant method, some of its limitations are discussed. Finally, recent results of the so called operator regularization procedure are presented.

  16. Dynamic interaction between 14-3-3zeta and bax during TNF-α-induced apoptosis in living cells

    NASA Astrophysics Data System (ADS)

    Gao, Xuejuan; Xing, Da; Chen, Tongsheng

    2006-09-01

    Bax, a proapoptotic member of the Bcl-2 family, localizes largely in the cytoplasm but redistributes to mitochondria and undergoes oligomerization to induce the release of apoptogenic factors such as cytochrome c in response to apoptotic stimuli. Cytoplasmic protein 14-3-3zeta binds to Bax and, upon apoptotic stimulation, releases Bax by a caspase-independent mechanism. However, the direct interaction of the cytoplasmic 14-3-3zeta and Bax in living cells has not been observed. In present study, to monitor the dynamic interaction between 14-3-3zeta and Bax in living cells in real time during apoptosis induced by tumor necrosis factor (TNF-α), DsRed-14-3-3zeta plasmid is constructed. By cotransfecting DsRed- 14-3-3zeta and GFP-Bax plasmids into human lung adenocarcinoma cells (ASTC-a-1), we observe the dynamic interaction between Bax and 14-3-3zeta using fluorescence resonance energy transfer (FRET) technique on laser scanning confocal microscope. The results show that 14-3-3zeta remains in the cytoplasm but GFP-Bax translocates to mitochondria completely after TNF-α stimulation. These results reveal that 14-3-3zeta binds directly to Bax in healthy cells, and that 14-3-3zeta negatively regulates Bax translocation to mitochondria during TNF-α-induced apoptosis.

  17. Asymptotic analysis on a pseudo-Hermitian Riemann-zeta Hamiltonian

    NASA Astrophysics Data System (ADS)

    Bender, Carl M.; Brody, Dorje C.

    2018-04-01

    The differential-equation eigenvalue problem associated with a recently-introduced Hamiltonian, whose eigenvalues correspond to the zeros of the Riemann zeta function, is analyzed using Fourier and WKB analysis. The Fourier analysis leads to a challenging open problem concerning the formulation of the eigenvalue problem in the momentum space. The WKB analysis gives the exact asymptotic behavior of the eigenfunction.

  18. Preliminary X-ray crystallographic analysis of glutathione transferase zeta 1 (GSTZ1a-1a)

    SciTech Connect

    Boone, Christopher D.; Zhong, Guo; Smeltz, Marci

    2014-01-21

    Crystals of glutathione transferase zeta 1 were grown and shown to diffract X-rays to 3.1 Å resolution. They belonged to space group P1, with unit-cell parameters a = 42.0, b = 49.6, c = 54.6 Å, α = 82.9, β = 69.9, γ = 73.4°.

  19. Boundary Conditions for the Maintenance of Memory by PKM[zeta] in Neocortex

    ERIC Educational Resources Information Center

    Shema, Reul; Hazvi, Shoshi; Sacktor, Todd C.; Dudai, Yadin

    2009-01-01

    We report here that ZIP, a selective inhibitor of the atypical protein kinase C isoform PKM[zeta], abolishes very long-term conditioned taste aversion (CTA) associations in the insular cortex of the behaving rat, at least 3 mo after encoding. The effect of ZIP is not replicated by a general serine/threonine protein kinase inhibitor that is…

  20. High-concentration zeta potential measurements using light-scattering techniques

    PubMed Central

    Kaszuba, Michael; Corbett, Jason; Watson, Fraser Mcneil; Jones, Andrew

    2010-01-01

    Zeta potential is the key parameter that controls electrostatic interactions in particle dispersions. Laser Doppler electrophoresis is an accepted method for the measurement of particle electrophoretic mobility and hence zeta potential of dispersions of colloidal size materials. Traditionally, samples measured by this technique have to be optically transparent. Therefore, depending upon the size and optical properties of the particles, many samples will be too concentrated and will require dilution. The ability to measure samples at or close to their neat concentration would be desirable as it would minimize any changes in the zeta potential of the sample owing to dilution. However, the ability to measure turbid samples using light-scattering techniques presents a number of challenges. This paper discusses electrophoretic mobility measurements made on turbid samples at high concentration using a novel cell with reduced path length. Results are presented on two different sample types, titanium dioxide and a polyurethane dispersion, as a function of sample concentration. For both of the sample types studied, the electrophoretic mobility results show a gradual decrease as the sample concentration increases and the possible reasons for these observations are discussed. Further, a comparison of the data against theoretical models is presented and discussed. Conclusions and recommendations are made from the zeta potential values obtained at high concentrations. PMID:20732896

  1. Synthesis, bioactivity and zeta potential investigations of chlorine and fluorine substituted hydroxyapatite.

    PubMed

    Fahami, Abbas; Beall, Gary W; Betancourt, Tania

    2016-02-01

    Chlorine and fluorine substituted hydroxyapatites (HA-Cl-F) with different degrees of ion replacement were successfully prepared by the one step mechanochemical activation method. X-ray diffraction (XRD) and FT-IR spectra indicated that substitution of these anions in milled powders resulted in the formation of pure hydroxyapatite phase except for the small observed change in the lattice parameters and unit cell volumes of the resultant hydroxyapatite. Microscopic observations showed that the milled product had a cluster-like structure made up of polygonal and spherical particles with an average particle size of approximately ranged from 20±5 to 70±5nm. The zeta potential of milled samples was performed at three different pH (5, 7.4, and 9). The obtained zeta potential values were negative for all three pH values. Negative zeta potential was described to favor osseointegration, apatite nucleation, and bone regeneration. The bioactivity of samples was investigated on sintered pellets soaked in simulated body fluid (SBF) solution and apatite crystals formed on the surface of the pellets after being incubated for 14days. Zeta potential analysis and bioactivity experiment suggested that HA-Cl-F will lead to the formation of new apatite particles and therefore be a potential implant material. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Zeta-potential Analyses using Micro Electrical Field Flow Fractionation with Fluorescent Nanoparticles

    PubMed Central

    Chang, Moon-Hwan; Dosev, Dosi; Kennedy, Ian M.

    2007-01-01

    Increasingly growing application of nanoparticles in biotechnology requires fast and accessible tools for their manipulation and for characterization of their colloidal properties. In this work we determine the zeta-potentials for polystyrene nanoparticles using micro electrical field flow fractionation (μ–EFFF) which is an efficient method for sorting of particles by size. The data obtained by μ–EFFF were compared to zeta potentials determined by standard capillary electrophoresis. For proof of concept, we used polystyrene nanoparticles of two different sizes, impregnated with two different fluorescent dyes. Fluorescent emission spectra were used to evaluate the particle separation in both systems. Using the theory of electrophoresis, we estimated the zeta-potentials as a function of size, dielectric permittivity, viscosity and electrophoretic mobility. The results obtained by the μ–EFFF technique were confirmed by the conventional capillary electrophoresis measurements. These results demonstrate the applicability of the μ–EFFF method not only for particle size separation but also as a simple and inexpensive tool for measurements of nanoparticles zeta potentials. PMID:18542710

  3. The white dwarf companion of the B a 2 star zeta Cap

    NASA Technical Reports Server (NTRS)

    Boehm-Vitense, E.

    1981-01-01

    The Ba II star zeta Cap has a white dwarf companion. Its T (sub eff) is determined to be 22000 K, its mass is approximately one solar mass. The importance of this finding for the explanation of abundance peculiarities is discussed.

  4. Chitosan-magnesium aluminum silicate composite dispersions: characterization of rheology, flocculate size and zeta potential.

    PubMed

    Khunawattanakul, Wanwisa; Puttipipatkhachorn, Satit; Rades, Thomas; Pongjanyakul, Thaned

    2008-03-03

    Composite dispersions of chitosan (CS), a positively charged polymer, and magnesium aluminum silicate (MAS), a negatively charged clay, were prepared and rheology, flocculate size and zeta potential of the CS-MAS dispersions were investigated. High and low molecular weights of CS (HCS and LCS, respectively) were used in this study. Moreover, the effects of heat treatment at 60 degrees C on the characteristics of the CS-MAS dispersions and the zeta potential of MAS upon addition of CS at different pHs were examined. Incorporation of MAS into CS dispersions caused an increase in viscosity and a shift of CS flow type from Newtonian to pseudoplastic flow with thixotropic properties. Heat treatment brought about a significant decrease in viscosity and hysteresis area of the composite dispersions. Microscopic studies showed that flocculation of MAS occurred after mixing with CS. The size and polydispersity index of the HCS-MAS flocculate were greater than those of the LCS-MAS flocculate. However, a narrower size distribution and the smaller size of the HCS-MAS flocculate were found after heating at 60 degrees C. Zeta potentials of the CS-MAS flocculates were positive and slightly increased with increasing MAS content. In the zeta potential studies, the negative charge of the MAS could be neutralized by the addition of CS. Increasing the pH and molecular weight of CS resulted in higher CS concentrations required to neutralize the charge of MAS. These findings suggest that the electrostatic interaction between CS and MAS caused a change in flow behavior and flocculation of the composite dispersions, depending on the molecular weight of CS. Heat treatment affected the rheological properties and the flocculate size of the composite dispersions. Moreover, pH of medium and molecular weight of CS influence the zeta potential of MAS.

  5. Line identifications in the ultraviolet spectra of Tau Herculis, B5 IV, and Zeta Draconis, B6 III

    NASA Technical Reports Server (NTRS)

    Underhill, A. B.; Adelman, S. J.

    1976-01-01

    Tables of the lines found on two tracings each of the ultraviolet spectrum of Tau Her, B5 IV, and Zeta Dra, B6 III, made by the Copernicus satellite and possible identifications are given. The ranges 1025-1451A for Tau Her and 1035 to 1425A for Zeta Dra are covered by the U2 spectrometer at a resolution of 0.2A; the ranges 2028 to 2959A for Tau Her and 2000 to 3000A for Zeta Dra are covered by the V2 spectrometer at a resolution of 0.4A. The observed density of lines in the U2 region is 1.1 lines/A for Tau Her and 1.7 lines/A for Zeta Dra. In the V2 region it is 0.8 lines/A for Tau Her and 0.9 lines/A for Zeta Dra.

  6. Stimulation and inhibition of enzymatic hydrolysis by organosolv lignins as determined by zeta potential and hydrophobicity.

    PubMed

    Huang, Yang; Sun, Shaolong; Huang, Chen; Yong, Qiang; Elder, Thomas; Tu, Maobing

    2017-01-01

    Lignin typically inhibits enzymatic hydrolysis of cellulosic biomass, but certain organosolv lignins or lignosulfonates enhance enzymatic hydrolysis. The hydrophobic and electrostatic interactions between lignin and cellulases play critical roles in the enzymatic hydrolysis process. However, how to incorporate these two interactions into the consideration of lignin effects has not been investigated. We examined the physicochemical properties and the structures of ethanol organosolv lignins (EOL) from hardwood and softwood and ascertained the association between lignin properties and their inhibitory and stimulatory effects on enzymatic hydrolysis. The zeta potential and hydrophobicity of EOL lignin samples, isolated from organosolv pretreatment of cottonwood (CW), black willow (BW), aspen (AS), eucalyptus (EH), and loblolly pine (LP), were determined and correlated with their effects on enzymatic hydrolysis of Avicel. EOLs from CW, BW, and AS improved the 72 h hydrolysis yield by 8-12%, while EOLs from EH and LP decreased the 72 h hydrolysis yield by 6 and 16%, respectively. The results showed a strong correlation between the 72 h hydrolysis yield with hydrophobicity and zeta potential. The correlation indicated that the hydrophobicity of EOL had a negative effect and the negative zeta potential of EOL had a positive effect. HSQC NMR spectra showed that β- O -4 linkages in lignin react with ethanol to form an α -ethoxylated β- O -4' substructure (A') during organosolv pretreatment. Considerable amounts of C 2,6 -H 2,6 correlation in p -hydroxybenzoate (PB) units were observed for EOL-CW, EOL-BW, and EOL-AS, but not for EOL-EH and EOL-LP. This study revealed that the effect of lignin on enzymatic hydrolysis is a function of both hydrophobic interactions and electrostatic repulsions. The lignin inhibition is controlled by lignin hydrophobicity and the lignin stimulation is governed by the negative zeta potential. The net effect of lignin depends on the combined

  7. Carbon and nitrogen abundances in the supergiants HD 93840 and zeta Per

    NASA Technical Reports Server (NTRS)

    Massa, Derck; Altner, Bruce; Wynne, David; Lamers, H. J. G. L. M.

    1990-01-01

    The BN supergiant HD 93840 is shown to have the same temperature and surface gravity as the normal Bi Ib zeta Per. Differential abundance analysis of their C 4 and N 5 wind line profiles are found. The results are independent of the usual model atmosphere analyses and, therefore, a valuable check on them. Ratios for the C and N surface abundances in HD 93840 compared to Per of 1:10 and 4.6:1 are found respectively. By introducing a simple model for the compositions of both atmospheres the fraction of material in each atmosphere which has undergone CNO processing, more than 90 percent for HD 93840 and less than about 15 percent for zeta Per, is derived.

  8. Averages of ratios of the Riemann zeta-function and correlations of divisor sums

    NASA Astrophysics Data System (ADS)

    Conrey, Brian; Keating, Jonathan P.

    2017-10-01

    Nonlinearity has published articles containing a significant number-theoretic component since the journal was first established. We examine one thread, concerning the statistics of the zeros of the Riemann zeta function. We extend this by establishing a connection between the ratios conjecture for the Riemann zeta-function and a conjecture concerning correlations of convolutions of Möbius and divisor functions. Specifically, we prove that the ratios conjecture and an arithmetic correlations conjecture imply the same result. This provides new support for the ratios conjecture, which previously had been motivated by analogy with formulae in random matrix theory and by a heuristic recipe. Our main theorem generalises a recent calculation pertaining to the special case of two-over-two ratios.

  9. Effect of additive on Zeta potential and particle size of nickel nanoparticles

    NASA Astrophysics Data System (ADS)

    Sharma, Vikash; Tarachand, Chotia, Chandrabhan; Okram, G. S.

    2017-05-01

    Nickel nanoparticles (NPs) were prepared by thermal decomposition method using Oleylamine (OLY) as a solvent and Trioctylphosphine (TOP) as a surfactant. We have investigated the effect of pH and addition of Ethylenediamine tetraacetic acid (EDTA) on the stability and particle size of Ni NPs using zeta potential and particle size analyser. Coating of the surfactants on the surface of Ni NPs was confirmed by Fourier transform infrared (FTIR) spectroscopy. Autotitration study of zeta potential of these NPs in ethanol by dynamic light scattering (DLS) at different pH values confirmed an isoelectric point (IEP) at pH = 3.64 in ethanol and pH = 3.04 after addition of EDTA in ethanol. It was observed that addition of EDTA in nanosuspension enhances stability of Ni-NPs significantly.

  10. Cursory examination of the zeta potential behaviors of two optical materials

    SciTech Connect

    Tesar, A.; Oja, T.

    1992-01-02

    When an oxide surface is placed in water, a difference in potential across the interface occurs due to dipole orientation. Hydroxyl groups or bound oxygen atoms on the oxide surface will orient adjacent water molecules which balance the dipole charge. This occurs over some small distance called the electrical double layer. Trace amounts of high field strength ions present in the vicinity of the double layer can have significant effects on the double layer. When there is movement of the oxide surface with respect to the water, a shearing of the double layer occurs. The electrical potential at this surfacemore » of shear is termed the zeta potential. The impetus for this study was to document the zeta potential behavior in water of two optical materials. (1) a multicomponent phosphate glass; and (2) Zerodur, a silicate glass-ceramic.« less

  11. Electrokinetically driven active micro-mixers utilizing zeta potential variation induced by field effect

    NASA Astrophysics Data System (ADS)

    Lee, Chia-Yen; Lee, Gwo-Bin; Fu, Lung-Ming; Lee, Kuo-Hoong; Yang, Ruey-Jen

    2004-10-01

    This paper presents a new electrokinetically driven active micro-mixer which uses localized capacitance effects to induce zeta potential variations along the surface of silica-based microchannels. The mixer is fabricated by etching bulk flow and shielding electrode channels into glass substrates and then depositing Au/Cr thin films within the latter to form capacitor electrodes, which establish localized zeta potential variations near the electrical double layer (EDL) region of the electroosmotic flow (EOF) within the microchannels. The potential variations induce flow velocity changes within a homogeneous fluid and a rapid mixing effect if an alternating electric field is provided. The current experimental data confirm that the fluid velocity can be actively controlled by using the capacitance effect of the buried shielding electrodes to vary the zeta potential along the channel walls. While compared with commonly used planar electrodes across the microchannels, the buried shielding electrodes prevent current leakage caused by bad bonding and allow direct optical observation during operation. It also shows that the buried shielding electrodes can significantly induce the field effect, resulting in higher variations of zeta potential. Computational fluid dynamic simulations are also used to study the fluid characteristics of the developed active mixers. The numerical and experimental results demonstrate that the developed microfluidic device permits a high degree of control over the fluid flow and an efficient mixing effect. Moreover, the developed device could be used as a pumping device as well. The development of the active electrokinetically driven micro-mixer could be crucial for micro-total-analysis-systems.

  12. Electroosmotic flow of Phan-Thien-Tanner fluids at high zeta potentials: An exact analytical solution

    NASA Astrophysics Data System (ADS)

    Sarma, Rajkumar; Deka, Nabajit; Sarma, Kuldeep; Mondal, Pranab Kumar

    2018-06-01

    We present a mathematical model to study the electroosmotic flow of a viscoelastic fluid in a parallel plate microchannel with a high zeta potential, taking hydrodynamic slippage at the walls into account in the underlying analysis. We use the simplified Phan-Thien-Tanner (s-PTT) constitutive relationships to describe the rheological behavior of the viscoelastic fluid, while Navier's slip law is employed to model the interfacial hydrodynamic slip. Here, we derive analytical solutions for the potential distribution, flow velocity, and volumetric flow rate based on the complete Poisson-Boltzmann equation (without considering the frequently used Debye-Hückel linear approximation). For the underlying electrokinetic transport, this investigation primarily reveals the influence of fluid rheology, wall zeta potential as modulated by the interfacial electrochemistry and interfacial slip on the velocity distribution, volumetric flow rate, and fluid stress, as well as the apparent viscosity. We show that combined with the viscoelasticity of the fluid, a higher wall zeta potential and slip coefficient lead to a phenomenal enhancement in the volumetric flow rate. We believe that this analysis, besides providing a deep theoretical insight to interpret the transport process, will also serve as a fundamental design tool for microfluidic devices/systems under electrokinetic influence.

  13. Three proposed B-associations in the vicinity of zeta puppis

    NASA Technical Reports Server (NTRS)

    Upton, E. K. L.

    1971-01-01

    There appear to be three loose B associations in the general vicinity of zeta Puppis, all at distances of approximately 300 to 400 parsecs from the sun. Their diameters, perpendicular to the line of sight, are 20 to 50 parsecs, and their separations are of similar size. All three are situated in bright areas of the Gum nebula. The proposed associations A and C lie in the two brightest parts of the nebula. The three associations are not all of the same age. Association C is about 50 million years old, whereas A and B are decidedly younger. The ages of A and B cannot be determined from the present data, as their color-magnitude diagrams show no clear turnoff from the main sequence. Association A may be young enough to qualify as the birthplace of zeta Puppis. There is no other identifiable association in which zeta Puppis can have originated, unless its age is substantially greater than the 3 million years assumed.

  14. Electrokinetic mixing at high zeta potentials: ionic size effects on cross stream diffusion.

    PubMed

    Ahmadian Yazdi, Alireza; Sadeghi, Arman; Saidi, Mohammad Hassan

    2015-03-15

    The electrokinetic phenomena at high zeta potentials may show several unique features which are not normally observed. One of these features is the ionic size (steric) effect associated with the solutions of high ionic concentration. In the present work, attention is given to the influences of finite ionic size on the cross stream diffusion process in an electrokinetically actuated Y-shaped micromixer. The method consists of a finite difference based numerical approach for non-uniform grid which is applied to the dimensionless form of the governing equations, including the modified Poisson-Boltzmann equation. The results reveal that, neglecting the ionic size at high zeta potentials gives rise to the overestimation of the mixing length, because the steric effects retard liquid flow, thereby enhancing the mixing efficiency. The importance of steric effects is found to be more intense for channels of smaller width to height ratio. It is also observed that, in sharp contrast to the conditions that the ions are treated as point charges, increasing the zeta potential improves the cross stream diffusion when incorporating the ionic size. Moreover, increasing the EDL thickness decreases the mixing length, whereas the opposite is true for the channel aspect ratio. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Coagulation-flocculation mechanisms in wastewater treatment plants through zeta potential measurements.

    PubMed

    López-Maldonado, E A; Oropeza-Guzman, M T; Jurado-Baizaval, J L; Ochoa-Terán, A

    2014-08-30

    Based on the polyelectrolyte-contaminant physical and chemical interactions at the molecular level, this article analyzed and discussed the coagulation-flocculation and chemical precipitation processes in order to improve their efficiency. Bench experiments indicate that water pH, polyelectrolyte (PE) dosing strategy and cationic polyelectrolyte addition are key parameters for the stability of metal-PE complexes. The coagulation-flocculation mechanism is proposed based on zeta potential (ζ) measurement as the criteria to define the electrostatic interaction between pollutants and coagulant-flocculant agents. Polyelectrolyte and wastewater dispersions are exposed to an electrophoretic effect to determine ζ. Finally, zeta potential values are compared at pH 9, suggesting the optimum coagulant dose at 162mg/L polydadmac and 67mg/L of flocculant, since a complete removal of TSS and turbidity is achieved. Based on the concentration of heavy metals (0.931mg/L Sn, 0.7mg/L Fe and 0.63mg/L Pb), treated water met the Mexican maximum permissible limits. In addition, the treated water has 45mg O2/L chemical oxygen demand (COD) and 45mg C/L total organic carbon (TOC). The coagulation-flocculation mechanism is proposed taking into account both: zeta potential (ζ)-pH measurement and chemical affinity, as the criteria to define the electrostatic and chemical interaction between pollutants and polyelectrolytes. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Entrapment of ovalbumin into liposomes--factors affecting entrapment efficiency, liposome size, and zeta potential.

    PubMed

    Brgles, Marija; Jurasin, Darija; Sikirić, Maja Dutour; Frkanec, Ruza; Tomasić, Jelka

    2008-01-01

    Various amounts of Ovalbumin (OVA) were encapsulated into positively and negatively charged multilamellar liposomes, with the aim to investigate the entrapment efficiency in different buffers and to study their effects on the liposome size and zeta potential. Results showed that the entrapment efficiency of OVA in anionic liposomes was the same in 10 mM Phosphate Buffer (PB) as in Phosphate-Buffered Saline (PBS; PB + 0.15 M NaCl). Also, liposome size was approximately 1200 nm for all anionic liposomes incorporating OVA. The entrapment efficiency of OVA in cationic liposomes was highly dependent on ionic strength. The size of cationic liposomes was approximately 1200 nm in PBS, regardless of protein content, but increased with the amount of the incorporated protein in PB. Aggregation of cationic liposomes in PB was observed when the mass of the protein was 2.5 mg or greater. The zeta potential of anionic liposomes was negative and of cationic liposomes positive in the whole range of protein mass tested. These results show how different compositions of lipid and aqueous phases can be used to vary the entrapment efficiency, liposome size, and zeta potential--the factors that are of great importance for the use of liposomes as drug carriers.

  17. Complete sequence of Enterococcus faecium pVEF3 and the detection of an omega-epsilon-zeta toxin-antitoxin module and an ABC transporter.

    PubMed

    Sletvold, H; Johnsen, P J; Hamre, I; Simonsen, G S; Sundsfjord, A; Nielsen, K M

    2008-07-01

    Glycopeptide resistant Enterococcus faecium (GREF) persists on Norwegian poultry farms despite the ban on the growth promoter avoparcin. The biological basis for long-term persistence of avoparcin resistance is not fully understood. This study presents the complete DNA sequence of the E. faecium R-plasmid pVEF3 and functional studies of some plasmid-encoded traits (a toxin-antitoxin (TA) system and an ABC transporter) that may be of importance for plasmid persistence. The pVEF3 (63.1 kbp), isolated from an E. faecium strain of poultry origin sampled in Norway in 1999, has 71 coding sequences including the vanA avoparcin/vancomycin resistance encoding gene cluster. pVEF3 encodes the TA system omega-epsilon-zeta, and plasmid stability tests and transcription analysis show that omega-epsilon-zeta is functional in Enterococcus faecalis OGIX, although with decreasing effect over time. The predicted ABC transporter was not found to confer reduced susceptibility to any of the 28 substances tested. The TA system identified in the pVEF-type plasmids may contribute to vanA plasmid persistence on Norwegian poultry farms. However, size and compositional heterogeneity among E. faecium vanA plasmids suggest that additional plasmid maintenance systems in combination with host specific factors and frequent horizontal gene transfer and rearrangement causes the observed plasmid composition and distribution patterns.

  18. A Comparison of Streaming and Microelectrophoresis Methods for Obtaining the zeta Potential of Granular Porous Media Surfaces.

    PubMed

    Johnson

    1999-01-01

    The electrokinetic behavior of granular quartz sand in aqueous solution is investigated by both microelectrophoresis and streaming potential methods. zeta potentials of surfaces composed of granular quartz obtained via streaming potential methods are compared to electrophoretic mobility zeta potential values of colloid-sized quartz fragments. The zeta values generated by these alternate methods are in close agreement over a wide pH range and electrolyte concentrations spanning several orders of magnitude. Streaming measurements performed on chemically heterogeneous mixtures of physically homogeneous sand are shown to obey a simple mixing model based on the surface area-weighted average of the streaming potentials associated with the individual end members. These experimental results support the applicability of the streaming potential method as a means of determining the zeta potential of granular porous media surfaces. Copyright 1999 Academic Press.

  19. Relations between elliptic multiple zeta values and a special derivation algebra

    NASA Astrophysics Data System (ADS)

    Broedel, Johannes; Matthes, Nils; Schlotterer, Oliver

    2016-04-01

    We investigate relations between elliptic multiple zeta values (eMZVs) and describe a method to derive the number of indecomposable elements of given weight and length. Our method is based on representing eMZVs as iterated integrals over Eisenstein series and exploiting the connection with a special derivation algebra. Its commutator relations give rise to constraints on the iterated integrals over Eisenstein series relevant for eMZVs and thereby allow to count the indecomposable representatives. Conversely, the above connection suggests apparently new relations in the derivation algebra. Under https://tools.aei.mpg.de/emzv we provide relations for eMZVs over a wide range of weights and lengths.

  20. Effective charges and zeta potentials of oil in water microemulsions in the presence of Hofmeister salts

    NASA Astrophysics Data System (ADS)

    dos Santos, Alexandre P.; Levin, Yan

    2018-06-01

    We present a theory which allows us to calculate the effective charge and zeta potential of oil droplets in microemulsions containing Hofmeister salts. A modified Poisson-Boltzmann equation is used to account for the surface and ion polarizations and hydrophobic and dispersion interactions. The ions are classified as kosmotropes and chaotropes according to their Jones-Dole viscosity B coefficient. Kosmotropes stay hydrated and do not enter into the oil phase, while chaotropes can adsorb to the oil-water interface. The effective interaction potentials between ions and oil-water interface are parametrized so as to accurately account for the excess interfacial tension.

  1. Effective charges and zeta potentials of oil in water microemulsions in the presence of Hofmeister salts.

    PubMed

    Dos Santos, Alexandre P; Levin, Yan

    2018-06-14

    We present a theory which allows us to calculate the effective charge and zeta potential of oil droplets in microemulsions containing Hofmeister salts. A modified Poisson-Boltzmann equation is used to account for the surface and ion polarizations and hydrophobic and dispersion interactions. The ions are classified as kosmotropes and chaotropes according to their Jones-Dole viscosity B coefficient. Kosmotropes stay hydrated and do not enter into the oil phase, while chaotropes can adsorb to the oil-water interface. The effective interaction potentials between ions and oil-water interface are parametrized so as to accurately account for the excess interfacial tension.

  2. The 1979-1980 eclipse of Zeta Aurigae. I - The circumstellar envelope

    NASA Technical Reports Server (NTRS)

    Chapman, R. D.

    1981-01-01

    A model of the K-star wind far from the K star, and its interaction with the B star, has been derived from a study of Mg(+) and C(+++) resonance lines in the spectrum of Zeta Aurigae during 1979 and 1980. A mass loss rate from the K star of 2 x 10 to the -8th solar masses/year is suggested by the data; the rate of accretion of the K supergiant's material by the B star then being such that the matter accreted over a period of ten years is of the order of the total mass of the photosphere of the B star.

  3. Thickness determination of biological samples with a zeta-calibrated scanning tunneling microscope.

    PubMed Central

    Wang, Z H; Hartmann, T; Baumeister, W; Guckenberger, R

    1990-01-01

    A single-tube scanning tunneling microscope has been zeta-calibrated by using atomic steps of crystalline gold and was used for measuring the thickness of two biological samples, metal-coated as well as uncoated. The hexagonal surface layer of the bacterium Deinococcus radiodurans with an open network-type structure shows thickness values that are strongly influenced by the substrate and the preparation method. In contrast, the thickness of the purple membrane of Halobacterium halobium with its densely packed less-corrugated structure exhibits very little variation in thickness in coated preparations and the values obtained are in good agreement with x-ray data. Images PMID:2251276

  4. The effect of basis set and exchange-correlation functional on time-dependent density functional theory calculations within the Tamm-Dancoff approximation of the x-ray emission spectroscopy of transition metal complexes.

    PubMed

    Roper, Ian P E; Besley, Nicholas A

    2016-03-21

    The simulation of X-ray emission spectra of transition metal complexes with time-dependent density functional theory (TDDFT) is investigated. X-ray emission spectra can be computed within TDDFT in conjunction with the Tamm-Dancoff approximation by using a reference determinant with a vacancy in the relevant core orbital, and these calculations can be performed using the frozen orbital approximation or with the relaxation of the orbitals of the intermediate core-ionised state included. Both standard exchange-correlation functionals and functionals specifically designed for X-ray emission spectroscopy are studied, and it is shown that the computed spectral band profiles are sensitive to the exchange-correlation functional used. The computed intensities of the spectral bands can be rationalised by considering the metal p orbital character of the valence molecular orbitals. To compute X-ray emission spectra with the correct energy scale allowing a direct comparison with experiment requires the relaxation of the core-ionised state to be included and the use of specifically designed functionals with increased amounts of Hartree-Fock exchange in conjunction with high quality basis sets. A range-corrected functional with increased Hartree-Fock exchange in the short range provides transition energies close to experiment and spectral band profiles that have a similar accuracy to those from standard functionals.

  5. The receptor protein tyrosine phosphatase (RPTP){beta}/{zeta} is expressed in different subtypes of human breast cancer

    SciTech Connect

    Perez-Pinera, Pablo; Garcia-Suarez, Olivia; Instituto Universitario de Oncologia del Principado de Asturias, Oviedo

    2007-10-12

    Increasing evidence suggests mutations in human breast cancer cells that induce inappropriate expression of the 18-kDa cytokine pleiotrophin (PTN, Ptn) initiate progression of breast cancers to a more malignant phenotype. Pleiotrophin signals through inactivating its receptor, the receptor protein tyrosine phosphatase (RPTP){beta}/{zeta}, leading to increased tyrosine phosphorylation of different substrate proteins of RPTP{beta}/{zeta}, including {beta}-catenin, {beta}-adducin, Fyn, GIT1/Cat-1, and P190RhoGAP. PTN signaling thus has wide impact on different important cellular systems. Recently, PTN was found to activate anaplastic lymphoma kinase (ALK) through the PTN/RPTP{beta}/{zeta} signaling pathway; this discovery potentially is very important, since constitutive ALK activity of nucleophosmin (NPM)-ALK fusionmore » protein is causative of anaplastic large cell lymphomas, and, activated ALK is found in other malignant cancers. Recently ALK was identified in each of 63 human breast cancers from 22 subjects. We now demonstrate that RPTP{beta}/{zeta} is expressed in each of these same 63 human breast cancers that previously were found to express ALK and in 10 additional samples of human breast cancer. RPTP{beta}/{zeta} furthermore was localized not only in its normal association with the cell membrane but also scattered in cytoplasm and in nuclei in different breast cancer cells and, in the case of infiltrating ductal carcinomas, the distribution of RPTP{beta}/{zeta} changes as the breast cancer become more malignant. The data suggest that the PTN/RPTP{beta}/{zeta} signaling pathway may be constitutively activated and potentially function to constitutively activate ALK in human breast cancer.« less

  6. Zeta potential in oil-brine-sandstone system and its role in oil recovery during controlled salinity waterflooding

    NASA Astrophysics Data System (ADS)

    Li, S.; Jackson, M.

    2017-12-01

    Wettability alteration is widely recognised as a primary role in improved oil recovery (IOR) during controlled salinity waterflooding (CSW) by modifying brine composition. The change of wettability of core sample depends on adsorption of polar oil compounds into the mineral surface which influences its surface charge density and zeta potential. It has been proved that zeta potentials can be useful to quantify the wettability and incremental oil recovery in natural carbonates. However, the study of zeta potential in oil-brine-sandstone system has not investigated yet. In this experimental study, the zeta potential is used to examine the controlled salinity effects on IOR in nature sandstone (Doddington) aged with two types of crude oils (Oil T and Oil D) over 4 weeks at 80 °C. Results show that the zeta potential measured in the Oil T-brine-sandstone system following primary waterflooding decreases compared to that in fully water saturation, which is consistent with the negative oil found in carbonates study, and IOR response during secondary waterflooding using diluted seawater was observed. In the case of negative oil, the injected low salinity brine induces a more repulsive electrostatic force between the mineral-brine interface and oil-brine interface, which results in an increase disjoining pressure and alters the rock surface to be more water-wet. For Oil D with a positive oil-brine interface, the zeta potential becomes more positive compared to that under single phase condition. The conventional waterflooding fails to observe the IOR in Oil D-brine-sandstone system due to a less repulsive electrostatic force built up between the two interfaces. After switching the injection brine from low salinity brine to formation brine, the IOR was observed. Measured zeta potentials shed some light on the mechanism of wettability alteration in the oil-brine-sandstone system and oil recovery during CSW.

  7. Differential interaction and aggregation of 3-repeat and 4-repeat tau isoforms with 14-3-3{zeta} protein

    SciTech Connect

    Sadik, Golam; Tanaka, Toshihisa, E-mail: tanaka@psy.med.osaka-u.ac.jp; Kato, Kiyoko

    2009-05-22

    Tau isoforms, 3-repeat (3R) and 4-repeat tau (4R), are differentially involved in neuronal development and in several tauopathies. 14-3-3 protein binds to tau and 14-3-3/tau association has been found both in the development and in tauopathies. To understand the role of 14-3-3 in the differential regulation of tau isoforms, we have performed studies on the interaction and aggregation of 3R-tau and 4R-tau, either phosphorylated or unphosphorylated, with 14-3-3{zeta}. We show by surface plasmon resonance studies that the interaction between unphosphorylated 3R-tau and 14-3-3{zeta} is {approx}3-folds higher than that between unphosphorylated 4R-tau and 14-3-3{zeta}. Phosphorylation of tau by protein kinase Amore » (PKA) increases the affinity of both 3R- and 4R-tau for 14-3-3{zeta} to a similar level. An in vitro aggregation assay employing both transmission electron microscopy and fluorescence spectroscopy revealed the aggregation of unphosphorylated 4R-tau to be significantly higher than that of unphosphorylated 3R-tau following the induction of 14-3-3{zeta}. The filaments formed from 3R- and 4R-tau were almost similar in morphology. In contrast, the aggregation of both 3R- and 4R-tau was reduced to a similar low level after phosphorylation with PKA. Taken together, these results suggest that 14-3-3{zeta} exhibits a similar role for tau isoforms after PKA-phosphorylation, but a differential role for unphosphorylated tau. The significant aggregation of 4R-tau by 14-3-3{zeta} suggests that 14-3-3 may act as an inducer in the generation of 4R-tau-predominant neurofibrillary tangles in tauopathies.« less

  8. The Structural Evolution of Milky-Way-Like Star-Forming Galaxies zeta is approximately 1.3

    NASA Technical Reports Server (NTRS)

    Patel, Shannon G.; Fumagalli, Mattia; Franx, Marun; VanDokkum, Pieter G.; VanDerWel, Arjen; Leja, Joel; Labbe, Ivo; Brammr, Gabriel; Whitaker, Katherine E.; Skelton, Rosalind E.; hide

    2013-01-01

    We follow the structural evolution of star-forming galaxies (SFGs) like the Milky Way by selecting progenitors to zeta is approx. 1.3 based on the stellar mass growth inferred from the evolution of the star-forming sequence. We select our sample from the 3D-HT survey, which utilizes spectroscopy from the HST-WFC3 G141 near-IR grism and enables precise redshift measurements for our sample of SFGs. Structural properties are obtained from Sersic profile fits to CANDELS WFC3 imaging. The progenitors of zeta = 0 SFGs with stellar mass M = 10(exp 10.5) solar mass are typically half as massive at zeta is approx. 1. This late-time stellar mass grow is consistent with recent studies that employ abundance matching techniques. The descendant SFGs at zeta is approx. 0 have grown in half-light radius by a factor of approx. 1.4 zeta is approx. 1. The half-light radius grows with stellar mass as r(sub e) alpha stellar mass(exp 0.29). While most of the stellar mass is clearly assembling at large radii, the mass surface density profiles reveal ongoing mass growth also in the central regions where bulges and pseudobulges are common features in present day late-type galaxies. Some portion of this growth in the central regions is due to star formation as recent observations of H(a) maps for SFGs at zeta approx. are found to be extended but centrally peaked. Connecting our lookback study with galactic archeology, we find the stellar mass surface density at R - 8 kkpc to have increased by a factor of approx. 2 since zeta is approx. 1, in good agreement with measurements derived for the solar neighborhood of the Milky Way.

  9. Organization of the human [zeta]-crystallin/quinone reductase gene (CRYZ)

    SciTech Connect

    Gonzalez, P.; Rao, P.V.; Zigler, J.S. Jr.

    1994-05-15

    [zeta]-Crystallin is a protein highly expressed in the lens of guinea pigs and camels, where it comprises about 10% of the total soluble protein. It has recently been characterized as a novel quinone oxidoreductase present in a variety of mammalian tissues. The authors report here the isolation and characterization of the human [zeta]-crystallin gene (CRYZ) and its processed pseudogene. The functional gene is composed of nine exons and spans about 20 kb. The 5[prime]-flanking region of the gene is rich in G and C (58%) and lacks TATA and CAAT boxes. Previous analysis of the guinea pig gene revealed themore » presence of two different promoters, one responsible for the high lens-specific expression and the other for expression at the enzymatic level in numerous tissues. Comparative analysis with the guinea pig gene shows that a region of [approximately]2.5 kb that includes the promoter responsible for the high expression in the lens in guinea pig is not present in the human gene. 34 refs., 6 figs., 1 tab.« less

  10. Casimir force in brane worlds: Coinciding results from Green's and zeta function approaches

    SciTech Connect

    Linares, Roman; Morales-Tecotl, Hugo A.; Pedraza, Omar

    2010-06-15

    Casimir force encodes the structure of the field modes as vacuum fluctuations and so it is sensitive to the extra dimensions of brane worlds. Now, in flat spacetimes of arbitrary dimension the two standard approaches to the Casimir force, Green's function, and zeta function yield the same result, but for brane world models this was only assumed. In this work we show that both approaches yield the same Casimir force in the case of universal extra dimensions and Randall-Sundrum scenarios with one and two branes added by p compact dimensions. Essentially, the details of the mode eigenfunctions that enter themore » Casimir force in the Green's function approach get removed due to their orthogonality relations with a measure involving the right hypervolume of the plates, and this leaves just the contribution coming from the zeta function approach. The present analysis corrects previous results showing a difference between the two approaches for the single brane Randall-Sundrum; this was due to an erroneous hypervolume of the plates introduced by the authors when using the Green's function. For all the models we discuss here, the resulting Casimir force can be neatly expressed in terms of two four-dimensional Casimir force contributions: one for the massless mode and the other for a tower of massive modes associated with the extra dimensions.« less

  11. Nanoparticle Tracking Analysis for Determination of Hydrodynamic Diameter, Concentration, and Zeta-Potential of Polyplex Nanoparticles.

    PubMed

    Wilson, David R; Green, Jordan J

    2017-01-01

    Nanoparticle tracking analysis (NTA) is a recently developed nanoparticle characterization technique that offers certain advantages over dynamic light scattering for characterizing polyplex nanoparticles in particular. Dynamic light scattering results in intensity-weighted average measurements of nanoparticle characteristics. In contrast, NTA directly tracks individual particles, enabling concentration measurements as well as the direct determination of number-weighted particle size and zeta-potential. A direct number-weighted assessment of nanoparticle characteristics is particularly useful for polydisperse samples of particles, including many varieties of gene delivery particles that can be prone to aggregation. Here, we describe the synthesis of poly(beta-amino ester)/deoxyribonucleic acid (PBAE/DNA) polyplex nanoparticles and their characterization using NTA to determine hydrodynamic diameter, zeta-potential, and concentration. Additionally, we detail methods of labeling nucleic acids with fluorophores to assess only those polyplex nanoparticles containing plasmids via NTA. Polymeric gene delivery of exogenous plasmid DNA has great potential for treating a wide variety of diseases by inducing cells to express a gene of interest.

  12. Effective flocculation of Chlorella vulgaris using chitosan with zeta potential measurement

    NASA Astrophysics Data System (ADS)

    Low, Y. J.; Lau, S. W.

    2017-06-01

    Microalgae are considered as one promising source of third-generation biofuels due to their fast growth rates, potentially higher yield rates and wide ranges of growth conditions. However, the extremely low biomass concentration in microalgae cultures presents a great challenge to the harvesting of microalgae because a large volume of water needs to be removed to obtain dry microalgal cells for the subsequent oil extraction process. In this study, the fresh water microalgae Chlorella vulgaris (C. vulgaris) was effectively harvested using both low molecular weight (MW) and high MW chitosan flocculants. The flocculation efficiency was evaluated by physical appearance, supernatant absorbance, zeta potential and solids content after centrifugal dewatering. High flocculation efficiency of 98.0-99.0% was achieved at the optimal dosage of 30-40 mg/g with formation of large microalgae flocs. This study suggests that the polymer bridging mechanism was governing the flocculation behaviour of C. vulgaris using high MW chitosan. Besides, charge patch neutralisation mechanism prevailed at low MW chitosan where lower dosage was sufficient to reach near-zero zeta potential compared with the high MW chitosan. The amount of chitosan polymer present in the culture may also affect the mechanism of flocculation.

  13. An interstellar cloud density from Copernicus observations of CO in the spectrum of Zeta Ophiuchi

    NASA Technical Reports Server (NTRS)

    Smith, A. M.; Stecher, T. P.; Krishna Swamy, K. S.

    1978-01-01

    Interstellar CO absorption bands in Copernicus spectra of Zeta Oph have been studied. Absorption profiles, computed under the assumption that excitation is due to collisions with H2 molecules and interaction with the 3-K background radiation field, were fitted to the reduced data of nine bands. When a gas kinetic temperature of 56 K is assumed, the best-fit condition implies a hydrogen-nucleus density of 120 per cu cm, a CO column density of 1.2 by 10 to the 15th power per sq cm, and a radial-velocity dispersion of 0.9 km/s. The relevance of these results to existing ideas concerning the Zeta Oph interstellar clouds is discussed. It is suggested that the strongest interstellar component is not circumstellar in origin but is instead part of a supernova remnant. Simple calculations are made to establish the plausibility of the supernova-remnant identification. This suggestion is also supported by Heiles's (1976) 21-cm pictures.

  14. Optimal aluminum/zirconium: Protein interactions for predicting antiperspirant efficacy using zeta potential measurements.

    PubMed

    Yuan, Shaotang; Vaughn, John; Pappas, Iraklis; Fitzgerald, Michael; Masters, James G; Pan, Long

    2015-01-01

    The interactions between commercial antiperspirant (AP) salts [aluminum chlorohydrate (ACH), activated ACH, aluminum sesquichlorohydrate (ASCH), zirconium aluminum glycine (ZAG), activated ZAG), pure aluminum polyoxocations (Al13-mer, Al30-mer), and the zirconium(IV)-glycine complex Zr6 (O)4 (OH)4 (H2O)8 (Gly)8]12+(-) (CP-2 or ZG) with Bovine serum albumin (BSA) were studied using zeta potential and turbidity measurements. The maximal turbidity, which revealed the optimal interactions between protein and metal salts, for all protein-metal salt samples was observed at the isoelectric point (IEP), where the zeta potential of the solution was zero. Efficacy of AP salts was determined via three parameters: the amount of salt required to flocculate BSA to reach IEP, the turbidity of solution at the IEP, and the pH range over which the turbidity of the solution remains sufficiently high. By comparing active salt performance from this work to traditional prescreening methods, this methodology was able to provide a consistent efficacy assessment for metal actives in APs or in water treatment.

  15. Stability of fenbendazole suspensions for veterinary use. Correlation between zeta potential and sedimentation.

    PubMed

    Arias, José L; López-Viota, Margarita; Clares, Beatriz; Ruiz, Ma Adolfina

    2008-08-07

    In this paper we have carried out a detailed investigation of the stability and redispersibility characteristics of fenbendazole aqueous suspensions, through a thermodynamic and electrokinetic characterization, considering the effect of both pH and ionic strength. The hydrophobic character of the drug, and the surface charge and electrical double-layer thickness play an essential role in the stability of the system, hence the need for a full characterization of fenbendazole. It was found that the drug suspensions displays "delayed" or "hindered" sedimentation, determined by their hydrophobic character and their low zeta potential (indicating a small electrokinetic charge on the particles). The electrostatic repulsion between the particles is responsible for the low sedimentation volume and poor redispersibility of the drug. However, only low concentrations of AlCl(3) induced a significant effect on both the zeta potential and stability of the drug, leading to a "free-layered" sedimentation and a very easy redispersion which could be of great interest in the design of an oral pharmaceutical dosage form for veterinary.

  16. p62 modulates Akt activity via association with PKC{zeta} in neuronal survival and differentiation

    SciTech Connect

    Joung, Insil; Kim, Hak Jae; Kwon, Yunhee Kim

    2005-08-26

    p62 is a ubiquitously expressed phosphoprotein that interacts with a number of signaling molecules and a major component of neurofibrillary tangles in the brain of Alzheimer's disease patients. It has been implicated in important cellular functions such as cell proliferation and anti-apoptotic pathways. In this study, we have addressed the potential role of p62 during neuronal differentiation and survival using HiB5, a rat neuronal progenitor cell. We generated a recombinant adenovirus encoding T7-epitope tagged p62 to reliably transfer p62 cDNA into the neuronal cells. The results show that an overexpression of p62 led not only to neuronal differentiation, but alsomore » to decreased cell death induced by serum withdrawal in HiB5 cells. In this process p62-dependent Akt phosphorylation occurred via the release of Akt from PKC{zeta} by association of p62 and PKC{zeta}, which is known as a negative regulator of Akt activation. These findings indicate that p62 facilitates cell survival through novel signaling cascades that result in Akt activation. Furthermore, we found that p62 expression was induced during neuronal differentiation. Taken together, the data suggest p62 is a regulator of neuronal cell survival and differentiation.« less

  17. Implementation of the Baldwin-Barth turbulence model into the ZETA code and its diagnosis. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Low, Scott L.

    1993-01-01

    The Baldwin-Barth turbulence model was implemented into Zeta, a time-accurate, zonal, integro-differential code for incompressible laminar and turbulent flows. The implementation procedure is patterned after the model subroutine in ARC2D. The results of ZETA with the Baldwin-Barth turbulence model were compared with experimental data, with ZETA using Baldwin-Lomax model, and with ARC2D using the Baldwin-Barth model. The Baldwin-Barth model subroutine was tested by inputting an ARC2D velocity solution of an NACA-0012 airfoil at R(sub e) = 3.9 x 10(exp 6) and alpha = 5 deg. The resultant turbulent viscosity and Reynolds stresses compared favorably with the original data. For the same grid having grid points inside the laminar sublayer, which is necessary due to the one-equation nature of the model, ZETA however predicts early separation. It was found that the current ZETA has problem with such a fine grid. Further work is in progress to solve this problem.

  18. Interstellar detection of the intersystem line Si II lambda 2335 toward zeta Ophiuchi

    NASA Technical Reports Server (NTRS)

    Cardelli, Jason A.; Sofia, Ulysses J.; Savage, Blair D.; Keenan, Francis P.; Dufton, Philip L.

    1994-01-01

    We report on the detection of the weak intersystem transistion of Si II lambda 2335 A in the sight line toward zeta Oph using the Ech-B mode (3.5 km/s resolution) of the Goddard High Resolution Spectrograph. The high-quality spectrum is characterized by an empirically measured signal-to-noise of 450, in excellent agreement with that expected from photon-statistics. The measured equivalent width of the Si II line is W(sub lambda) = 0.48 +/- 0.12 mA. Using the new experimental f-value of Calamai, Smith, and Bergeson, we find a Si II column density of 2.34 (+/- 0.58) x 10(exp 15) atoms/sq cm and (Si/H)(sub zeta Oph) = 1.78 (+/- 0.44) x 10(exp -6) for the principal absorbing component(s) at v(sub sun) approx. = -15 km/s. Analysis of the Si II lambda 1808 absorption over the same velocity range using the new experimental f-value of Bergeson & Lawler yields a column density (corrected for saturation) that is consistent within the weak line errors and confirms the relative accuracies of these new f-values. Furthermore, these results indicate that accurate abundances can now be derived for Si II, particularly from the weak Si II lambda 2335 A since it is free of saturation effects. For the zeta Oph v(sub sun) approx. = -15 km/s component(s), we find that greater than 95% of the available cosmic abundance (i.e. the 1989 meteoritic abundances of Anders & Grevesse) of Mg, Fe, and Si is 'missing' from the gas phase and is presumably locked up in the dust. These elements are present in the dust grains in ratios of Fe/Si approximately equals 0.9 and Mg/Si approximately equals 1.1, consistent with the ratio of their cosmic abundances. These ratios are in sharp contrast to more diffuse clouds like those seen toward the high-latitude halo star HD 93521 where in the dust Fe/Si approximately equals 1.8 and Mg/Si approximately equals 2.1.

  19. Catalytic properties of an expressed and purified higher plant type zeta-carotene desaturase from Capsicum annuum.

    PubMed

    Breitenbach, J; Kuntz, M; Takaichi, S; Sandmann, G

    1999-10-01

    The zeta-carotene desaturase from Capsicum annuum (EC 1.14.99.-) was expressed in Escherichia coli, purified and characterized biochemically. The enzyme acts as a monomer with lipophilic quinones as cofactors. Km values for the substrate zeta-carotene or the intermediate neurosporene in the two-step desaturation reaction are almost identical. Product analysis showed that different lycopene isomers are formed, including substantial amounts of the all-trans form, together with 7,7',9,9'-tetracis prolycopene via the corresponding neurosporene isomers. The application of different geometric isomers as substrates revealed that the zeta-carotene desaturase has no preference for certain isomers and that the nature of the isomers formed during catalysis depends strictly on the isomeric composition of the substrate.

  20. High mobility group box-1 is phosphorylated by protein kinase C zeta and secreted in colon cancer cells

    SciTech Connect

    Lee, Hanna; Park, Minhee; Shin, Nara

    2012-07-27

    Highlights: Black-Right-Pointing-Pointer Specific enzyme for HMGB1 phosphorylation and its secretion is proposed. Black-Right-Pointing-Pointer Inhibition of PKC-{zeta} leads to significant reduction of the secreted HMGB1. Black-Right-Pointing-Pointer Phosphorylation of specific site of HMGB1 redirects its secretion in cancer cells. Black-Right-Pointing-Pointer Activation of PKC-{zeta} in cancers explains the enhanced HMGB1 secretion. -- Abstract: High mobility group box-1 (HMGB1), a nuclear protein, is overexpressed and secreted in cancer cells. Phosphorylation on two different nuclear localization signal regions are known to be important for the nuclear-to-cytoplasmic transport and secretion of HMGB1. However, little is known about the biochemical mechanism of HMGB1 modifications and its subsequentmore » secretion from cancer cells. To identify the specific enzyme and important sites for HMGB1 phosphorylation, we screened the protein kinase C (PKC) family in a colon cancer cell line (HCT116) for HMGB1 binding by pull-down experiments using a 3XFLAG-HMGB1 construct. Strong interactions between atypical PKCs (PKC-{zeta}, {lambda}, and {iota}) and cytoplasmic HMGB1 were observed in HCT116 cells. We further identified the most critical PKC isotype that regulates HMGB1 secretion is PKC-{zeta} by using PKC inhibitors and siRNA experiments. The serine residues at S39, S53 and S181 of HMGB1 were related to enhancing HMGB1 secretion. We also demonstrated overexpression and activation of PKC-{zeta} in colon cancer tissues. Our findings suggest that PKC-{zeta} is involved in the phosphorylation of HMGB1, and the phosphorylation of specific serine residues in the nuclear localization signal regions is related to enhanced HMGB1 secretion in colon cancer cells.« less

  1. The Italian cross-sectional survey of the management of bone metastasis: ZeTa study

    PubMed Central

    Santini, Daniele; Bertoldo, Francesco; Dell'Aquila, Emanuela; Cecchini, Isabella; Fregosi, Stefania; Bortolussi, Paolo

    2012-01-01

    Background Several studies have emphasized the importance of the maintenance of bone health in a comprehensive cancer care. However, no survey about approach to bone metastasis care is currently available. The ZeTa study provides a picture of the Italian oncologists' therapeutics habits in this area, in a real clinical-practice scenario. Design This study was based on online questionnaire-based interviews to Italian oncologists that included 145 questions. The aim was to collect information on the treatment of bone metastasis, the current use of bisphosphonates, the awareness of guidelines and the concerns about ONJ, the use of vitamin D supplementation. Results 445 oncologists were contacted, 283 agreed to participate. The results show that the current management of bone metastasis is still sub-optimal, as the recommendations from current clinical guidelines are not completely followed by all specialists. Conclusions This survey highlights the urgent need to improve management of bone metastasis in cancer patients. PMID:26909253

  2. Zeta-potential and particle size studies of silver sulphide nanoparticles

    SciTech Connect

    Sharma, Vikash, E-mail: vikash@csr.res.in; Tarachand,; Ganesan, V.

    Silver sulfide (Ag{sub 2}S) nanoparticles (NPs) were prepared successfully for the first time using diethylene glycol (DEG) as a surfactant. X-ray diffraction (XRD) data revealed single phase nature of the compound and energy-dispersive X-ray (EDX) confirmed its nominal composition. Their sizes were 43 nm from XRD, 50 nm from atomic force microscopy (AFM) and 19 nm & 213 nm from dynamic light scattering (DLS); their differences have been discussed. Autotitration study of zeta potential of these NPs in deionized water by DLS at different pH values confirmed an isoelectric point at pH = 5.14 and their very unstable nature in deionized water.

  3. Interstellar gas phase abundance of carbon, oxygen, nitrogen, copper, gallium, germanium, and krypton toward Zeta Ophiuchi

    NASA Technical Reports Server (NTRS)

    Cardelli, Jason A.; Savage, Blair D.; Ebbets, Dennis C.

    1991-01-01

    An analysis of weak (less than 10 mA) UV interstellar absorption line data obtained for the line of sight to the O9.5 IV star Zeta Oph is presented. Measurements of weak semiforbidden lines of N I, O I, Cu II, and a new UV detection of Na I are reported along with a small upper limit for C II. Interstellar detections of Ga II, Ge II, and Kr I are also presented. Ga, Ge, and Kr represent the heaviest elements detected in the ISM. A comparison of the derived column densities to cosmic abundances shows Ga to be depleted by about -1.2 dex while Ge is overabundant by +0.2 dex. Assuming Kr to be undepleted, a logarithmic cosmic abundance of Kr/H = 2.95 is obtained on the scale where H = 12.00.

  4. Cellular internalization of polycation-coated microparticles and its dependence on their zeta potential

    NASA Astrophysics Data System (ADS)

    Kato, Noritaka; Kondo, Ryosuke

    2018-03-01

    By applying microparticles to HeLa cells, the number of particles adhered on the cell and that of the ones internalized in the cells were evaluated. Three-dimensional tomographic images of the cells with the particles were obtained by multiphoton excitation laser scanning microscopy, and the adhered and internalized particles were counted separately. When the surface charge of the particles was reversed from negative to positive by coating the particles with polycations, both numbers significantly increased owing to the electrostatic attraction between the cells and the polycation-coated particles. Four different positively charged particles were prepared using four different polycations, and the numbers of adhered and internalized particles were compared. Our results suggest that these numbers depended on the zeta potential rather than the molecular structure of the polycation.

  5. A new biphasic osteoinductive calcium composite material with a negative Zeta potential for bone augmentation

    PubMed Central

    Smeets, Ralf; Kolk, Andreas; Gerressen, Marcus; Driemel, Oliver; Maciejewski, Oliver; Hermanns-Sachweh, Benita; Riediger, Dieter; Stein, Jamal M

    2009-01-01

    The aim of the present study was to analyze the osteogenic potential of a biphasic calcium composite material (BCC) with a negative surface charge for maxillary sinus floor augmentation. In a 61 year old patient, the BCC material was used in a bilateral sinus floor augmentation procedure. Six months postoperative, a bone sample was taken from the augmented regions before two titanium implants were inserted at each side. We analyzed bone neoformation by histology, bone density by computed tomography, and measured the activity of voltage-activated calcium currents of osteoblasts and surface charge effects. Control orthopantomograms were carried out five months after implant insertion. The BCC was biocompatible and replaced by new mineralized bone after being resorbed completely. The material demonstrated a negative surface charge (negative Zeta potential) which was found to be favorable for bone regeneration and osseointegration of dental implants. PMID:19523239

  6. Surfactants, not size or zeta-potential influence blood-brain barrier passage of polymeric nanoparticles.

    PubMed

    Voigt, Nadine; Henrich-Noack, Petra; Kockentiedt, Sarah; Hintz, Werner; Tomas, Jürgen; Sabel, Bernhard A

    2014-05-01

    Nanoparticles (NP) can deliver drugs across the blood-brain barrier (BBB), but little is known which of the factors surfactant, size and zeta-potential are essential for allowing BBB passage. To this end we designed purpose-built fluorescent polybutylcyanoacrylate (PBCA) NP and imaged the NP's passage over the blood-retina barrier - which is a model of the BBB - in live animals. Rats received intravenous injections of fluorescent PBCA-NP fabricated by mini-emulsion polymerisation to obtain various NP's compositions that varied in surfactants (non-ionic, anionic, cationic), size (67-464nm) and zeta-potential. Real-time imaging of retinal blood vessels and retinal tissue was carried out with in vivo confocal neuroimaging (ICON) before, during and after NP's injection. Successful BBB passage with subsequent cellular labelling was achieved if NP were fabricated with non-ionic surfactants or cationic stabilizers but not when anionic compounds were added. NP's size and charge had no influence on BBB passage and cell labelling. This transport was not caused by an unspecific opening of the BBB because control experiments with injections of unlabelled NP and fluorescent dye (to test a "door-opener" effect) did not lead to parenchymal labelling. Thus, neither NP's size nor chemo-electric charge, but particle surface is the key factor determining BBB passage. This result has important implications for NP engineering in medicine: depending on the surfactant, NP can serve one of two opposite functions: while non-ionic tensides enhance brain up-take, addition of anionic tensides prevents it. NP can now be designed to specifically enhance drug delivery to the brain or, alternatively, to prevent brain penetration so to reduce unwanted psychoactive effects of drugs or prevent environmental nanoparticles from entering tissue of the central nervous system. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Investigation of the influence of the zeta-potential on the filtration rate in the presence of collectors

    NASA Technical Reports Server (NTRS)

    Provirnina, E. V.; Barbin, M. B.

    1984-01-01

    The value of the zeta-potential does not have an explicit effect, which is expressed by a simple math correlation, on filtration rate when a solution of the tested collector is filtered through a cake prepared under standard conditions from the examined particulate material. The zeta-potential measurements and filtration tests were carried out on silica and galena with solutions contg. a cationic container ANP and Et xanthane, resp. at PH = 6.5, varying concentration of the agent (0-2500 g/ton), and under a vacuum of 100 to 600 mm Hg.

  8. Multiwavelength Characterization of an ACT-Selected, Lensed Dusty Star-Forming Galaxy at zeta 2.64

    NASA Technical Reports Server (NTRS)

    Roberts-Borsani, G. W.; Jimenez-Donaire, M. J.; Dapra, M.; Alatalo, K.; Aretxaga, I.; Alvarez-Marquez, J.; Baker, A. J.; Fujimoto, S.; Gallardo, P. A.; Gralla, M.; hide

    2017-01-01

    We present C I(21) and multi-transition C-12 O observations of a dusty star-forming galaxy, ACT J2029+0120,which we spectroscopically confirm to lie at zeta = 2.64. We detect CO(3-2), CO(5-4), CO(7-6), CO(8-7), and C I(2-1) at high significance, tentatively detect HCO+(4-3), and place strong upper limits on the integrated strength of dense gas tracers (HCN(4-3) and CS(7-6)). Multi-transition CO observations and dense gas tracers can provide valuable constraints on the molecular gas content and excitation conditions in high-redshift galaxies. We therefore use this unique data set to construct a CO spectral line energy distribution (SLED) of the source, which is most consistent with that of a ULIRG Seyfert or QSO host object in the taxonomy of the Herschel Comprehensive ULIRG Emission Survey. We employ RADEX models to fit the peak of the CO SLED, inferring a temperature of T approximately 117 K and n(sub H2) approximately 10(exp5) cm(exp -3), most consistent with a ULIRGQSO object and the presence of high-density tracers. We also find that the velocity width of the C I line is potentially larger than seen in all CO transitions forth is object, and that the L'(sub Ci(2-1))/L'(sub CO(3-2))ratio is also larger than seen in other lensed and unlensed submillimeter galaxies and QSO hosts; if confirmed, this anomaly could be an effect of differential lensing of a shocked molecular outflow.

  9. Constraining a hybrid volatility basis-set model for aging of wood-burning emissions using smog chamber experiments: a box-model study based on the VBS scheme of the CAMx model (v5.40)

    NASA Astrophysics Data System (ADS)

    Ciarelli, Giancarlo; El Haddad, Imad; Bruns, Emily; Aksoyoglu, Sebnem; Möhler, Ottmar; Baltensperger, Urs; Prévôt, André S. H.

    2017-06-01

    In this study, novel wood combustion aging experiments performed at different temperatures (263 and 288 K) in a ˜ 7 m3 smog chamber were modelled using a hybrid volatility basis set (VBS) box model, representing the emission partitioning and their oxidation against OH. We combine aerosol-chemistry box-model simulations with unprecedented measurements of non-traditional volatile organic compounds (NTVOCs) from a high-resolution proton transfer reaction mass spectrometer (PTR-MS) and with organic aerosol measurements from an aerosol mass spectrometer (AMS). Due to this, we are able to observationally constrain the amounts of different NTVOC aerosol precursors (in the model) relative to low volatility and semi-volatile primary organic material (OMsv), which is partitioned based on current published volatility distribution data. By comparing the NTVOC / OMsv ratios at different temperatures, we determine the enthalpies of vaporization of primary biomass-burning organic aerosols. Further, the developed model allows for evaluating the evolution of oxidation products of the semi-volatile and volatile precursors with aging. More than 30 000 box-model simulations were performed to retrieve the combination of parameters that best fit the observed organic aerosol mass and O : C ratios. The parameters investigated include the NTVOC reaction rates and yields as well as enthalpies of vaporization and the O : C of secondary organic aerosol surrogates. Our results suggest an average ratio of NTVOCs to the sum of non-volatile and semi-volatile organic compounds of ˜ 4.75. The mass yields of these compounds determined for a wide range of atmospherically relevant temperatures and organic aerosol (OA) concentrations were predicted to vary between 8 and 30 % after 5 h of continuous aging. Based on the reaction scheme used, reaction rates of the NTVOC mixture range from 3.0 × 10-11 to 4. 0 × 10-11 cm3 molec-1 s-1. The average enthalpy of vaporization of secondary organic aerosol

  10. Study of a binary interpenetrated polymeric complex by correlation of rheological parameters with zeta potential and conductivity.

    PubMed

    Nita, Loredana Elena; Chiriac, Aurica P; Neamtu, Iordana; Bercea, Maria

    2010-03-01

    The interpenetrated macromolecular chains complexation between poly(aspartic acid) and poly(vinyl alcohol) in aqueous solution it was investigated. The interpolymer complexation process was evaluated through dynamic rheology. The aspects concerning the stability of the tested homopolymers and the prepared interpolymeric complex there were achieved from the evaluation of the aqueous solutions'zeta potential and also by determining the pH influence upon the zeta potential and the conductivity. The data obtained through the rheological dynamic measurements were correlated with the composition of the polymeric mixture, the dependence of zeta potential and conductivity. The study reveals the conditions for the formation of interpenetrated polymeric complex as being a ratio of 70wt.% PAS to 30wt.% PVA at 22 degrees C and 50/50 PAS/PVA ratio at 37 degrees C temperature. From the pH influence upon the zeta potential values it was evidenced the PAS aqueous solution does not reach the isoelectric point. At the same time, PVA solution and the complex PAS/PVA reaches the isoelectric point at strongly acid pH. The better stability of PAS, PVA and their mixture in solution is recorded in the alkaline domain (7.5or=12). The conductivity increases with the rising of the PAS content, pH and temperature. Other characteristics of the prepared interpenetrated polymeric structure, as for example thermal stability, there are also presented.

  11. The adsorption of cationic and amphoteric copolymers on glass surfaces: zeta potential measurements, adsorption isotherm determination, and FT Raman characterization.

    PubMed

    Tartakovsky, Alla; Drutis, Dane M; Carnali, Joseph O

    2003-07-15

    The adsorption of cationic and amphoteric copolymers onto controlled pore glass (CPG) powders has been studied by measurement of the powder particle zeta (zeta) potential, by determination of the adsorption isotherm, and by FT Raman measurements of the polymer-coated powder. The cationic polymers consisted chiefly of homopolymers of dimethyldiallylammonium chloride (DMDAAC) or copolymers of DMDAAC and acrylamide. The amphoteric polymers studied included copolymers of DMDAAC and acrylic acid. The comonomer ratio was varied to explore the dependence of cationic charge density on the extent and effect of adsorption. Both types of polymers adsorb onto the anionic glass surface via an ion-exchange mechanism. Consequently, a correspondingly higher mass of a low-charge-density copolymer adsorbs than of a cationic homopolymer. The presence of the anionic portion in the amphoteric polymers does not significantly alter this picture. The zeta potential, however, reflects the overall nature of the polymer. Cationic polymers effectively neutralize the glass surface, while amphoteric polymers leave the zeta potential net negative. Adsorption isotherms, determined via the depletion technique using colloidal titration, were used to "calibrate" a FT Raman method. The latter was used to determined the amount of adsorbed polymer under solution conditions in which colloidal titration could not be performed.

  12. Development of a novel in silico model of zeta potential for metal oxide nanoparticles: a nano-QSPR approach

    NASA Astrophysics Data System (ADS)

    Wyrzykowska, Ewelina; Mikolajczyk, Alicja; Sikorska, Celina; Puzyn, Tomasz

    2016-11-01

    Once released into the aquatic environment, nanoparticles (NPs) are expected to interact (e.g. dissolve, agglomerate/aggregate, settle), with important consequences for NP fate and toxicity. A clear understanding of how internal and environmental factors influence the NP toxicity and fate in the environment is still in its infancy. In this study, a quantitative structure-property relationship (QSPR) approach was employed to systematically explore factors that affect surface charge (zeta potential) under environmentally realistic conditions. The nano-QSPR model developed with multiple linear regression (MLR) was characterized by high robustness ({{{Q}}{{2}}}{{CV}}=0.90) and external predictivity ({{{Q}}{{2}}}{{EXT}}=0.93). The results clearly showed that zeta potential values varied markedly as functions of the ionic radius of the metal atom in the metal oxides, confirming that agglomeration and the extent of release of free MexOy largely depend on their intrinsic properties. A developed nano-QSPR model was successfully applied to predict zeta potential in an ionized solution of NPs for which experimentally determined values of response have been unavailable. Hence, the application of our model is possible when the values of zeta potential in the ionized solution for metal oxide nanoparticles are undetermined, without the necessity of performing more time consuming and expensive experiments. We believe that our studies will be helpful in predicting the conditions under which MexOy is likely to become problematic for the environment and human health.

  13. Hydrodynamic dispersion in a combined magnetohydrodynamic- electroosmotic-driven flow through a microchannel with slowly varying wall zeta potentials

    NASA Astrophysics Data System (ADS)

    Vargas, C.; Arcos, J.; Bautista, O.; Méndez, F.

    2017-09-01

    The effective dispersion coefficient of a neutral solute in the combined electroosmotic (EO) and magnetohydrodynamic (MHD)-driven flow of a Newtonian fluid through a parallel flat plate microchannel is studied. The walls of the microchannel are assumed to have modulated and low zeta potentials that vary slowly in the axial direction in a sinusoidal manner. The flow field required to obtain the dispersion coefficient is solved using the lubrication approximation theory. The solution of the electrical potential is based on the Debye-Hückel approximation for a symmetric (Z :Z ) electrolyte solution. The EO and MHD effects, together with the variations in the zeta potentials of the walls, are observed to notably modify the axial distribution of the effective dispersion coefficient. The problem is formulated for two cases of the zeta potential function. Note that the dispersion coefficient primarily depends on the Hartmann number, on the ratio of the half height of the microchannel to the Debye length, and on the assumed variation in the zeta potentials of the walls.

  14. EFFECT OF AQUEOUS PHASE PROPERTIES ON CLAY PARTICLE ZETA POTENTIAL AND ELECTRO-OSMOTIC PERMEABILITY: IMPLICATIONS FOR ELECTRO-KINETIC SOIL REMEDIATION PROCESSES

    EPA Science Inventory

    The influence of aqueous phase properties (pH, ionic strength and divalent metal ion concentration) on clay particle zeta potential and packed-bed electro-osmotic permeability was quantified. Although pH strongly altered the zeta potential of a Georgia kaolinite, it did not signi...

  15. Interrelationship between the zeta potential and viscoelastic properties in coacervates complexes.

    PubMed

    Espinosa-Andrews, Hugo; Enríquez-Ramírez, Karina Esmeralda; García-Márquez, Eristeo; Ramírez-Santiago, Cesar; Lobato-Calleros, Consuelo; Vernon-Carter, Jaime

    2013-06-05

    The formation of the complex coacervate (CC) phases between gum Arabic (GA) and low molecular weight chitosan (Ch) and the interrelationship between the zeta-potential and viscoelastic properties of the coacervate phase were investigated. The maximum charge difference of biopolymers stock dispersion was displayed in a range of pH between 4.0 and 5.5. Titration experiment between the oppositely charged biopolymers showed that the isoelectric point was found at a biopolymers mass ratio (R[GA:Ch]) of R[5.5:1]. Turbidity, size and ζ-potential of the soluble complexes (SC) showed an interrelation with the complex coacervate yield (CCY). Higher CCY values (82.2-88.1%) were obtained in the range from R[3:1] to R[5.5:1]. Change the R[GA:Ch] in dispersion, make possible to produce CC's phases exhibiting cationic (R[1:1] and R[3:1]), neutral (R[5.5:1]) or anionic (R[9:1] and R[7:1]) charged. All CC's exhibited liquid-viscoelastic behavior at lower frequencies and a crossover between G″ and G' at higher frequencies. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Hippocampal Infusion of Zeta Inhibitory Peptide Impairs Recent, but Not Remote, Recognition Memory in Rats

    PubMed Central

    Hales, Jena B.; Ocampo, Amber C.; Broadbent, Nicola J.; Clark, Robert E.

    2015-01-01

    Spatial memory in rodents can be erased following the infusion of zeta inhibitory peptide (ZIP) into the dorsal hippocampus via indwelling guide cannulas. It is believed that ZIP impairs spatial memory by reversing established late-phase long-term potentiation (LTP). However, it is unclear whether other forms of hippocampus-dependent memory, such as recognition memory, are also supported by hippocampal LTP. In the current study, we tested recognition memory in rats following hippocampal ZIP infusion. In order to combat the limited targeting of infusions via cannula, we implemented a stereotaxic approach for infusing ZIP throughout the dorsal, intermediate, and ventral hippocampus. Rats infused with ZIP 3–7 days after training on the novel object recognition task exhibited impaired object recognition memory compared to control rats (those infused with aCSF). In contrast, rats infused with ZIP 1 month after training performed similar to control rats. The ability to form new memories after ZIP infusions remained intact. We suggest that enhanced recognition memory for recent events is supported by hippocampal LTP, which can be reversed by hippocampal ZIP infusion. PMID:26380123

  17. Effect of zeta potential on the performance of a ring-type electroosmotic mixer.

    PubMed

    Kim, T A; Koo, K H; Kim, Y J

    2009-12-01

    In order to achieve faster mixing, a new type of electrokinetic mixer with a T-type channel is introduced. The proposed mixer takes two fluids from different inlets and combines them into a single channel. The fluids then enter a mixing chamber with different inner and outer radii. Four microelectrodes are positioned on the outer wall of the mixing chamber. The electric potentials on the four microelectrodes are sinusoidal with respect to time and have various maximum voltages, zeta potentials and frequency values. The working fluid is water and each inlet has a different initial concentration values. The incompressible Navier-Stokes equation is solved in the channel, with a slip boundary condition on the inner and outer walls of the mixing chamber. The convection-diffusion equation is used to describe the concentration of the dissolved substances in the fluid. The pressure, concentration and flow fields in the channel are calculated and the results are graphically depicted for various flow and electric conditions.

  18. Tc Trends and Terrestrial Planet Formation: The Case of Zeta Reticuli

    NASA Astrophysics Data System (ADS)

    Adibekyan, Vardan; Delgado-Mena, Elisa; Figueira, Pedro; Sousa, Sergio; Santos, Nuno; Faria, Joao; González Hernández, Jonay; Israelian, Garik; Harutyunyan, Gohar; Suárez-Andrés, Lucia; Hakobyan, Artur

    2016-11-01

    During the last decade astronomers have been trying to search for chemical signatures of terrestrial planet formation in the atmospheres of the hosting stars. Several studies suggested that the chemical abundance trend with the condensation temperature, Tc, is a signature of rocky planet formation. In particular, it was suggested that the Sun shows 'peculiar' chemical abundances due to the presence of the terrestrial planets in our solar-system. However, the rocky material accretion or the trap of rocky materials in terrestrial planets is not the only explanation for the chemical 'peculiarity' of the Sun, or other Sun-like stars with planets. In this talk I madea very brief review of this topic, and presented our last results for the particular case of Zeta Reticuli binary system: A very interesting and well-known system (known in science fiction and ufology as the world of Grey Aliens, or Reticulans) where one of the components hosts an exo-Kuiper belt, and the other component is a 'single', 'lonely' star.

  19. A study of EUV emission from the O4f star Zeta Puppis

    NASA Technical Reports Server (NTRS)

    Waldron, Wayne L.; Vallerga, John

    1995-01-01

    Our 20 ks observation did not allow us to carry out our primary objective, i.e., to test the limitations of deeply embedded EUV and X-ray sources. However, it did provide a very useful constraint in our analysis of a newly acquired high S/N ROSAT PSPC X-ray spectrum of Zeta Pup. In addition, modifications to our stellar wind opacity code have been preformed to investigate the sensitivity of the EUV opacity energy range to different photospheric model flux inputs and different wind structures. These analyses provided the justification for a 140 ks follow up EUVE Cycle III observation of this star. We have recently been informed that our requested observation has been accepted as a Type 1 target for Cycle III. The remainder of this report focuses on the following: (1) a brief background on the status of X-ray emission from OB stars; (2) a discussion on the importance of EUV observations; (3) a discussion of our scientific objectives; and (4) a summary of our technical approach for our Cycle III observation (including the predicted EUV counts for various lines.)

  20. A Search for EUV Emission from the O4f Star Zeta Puppis

    NASA Technical Reports Server (NTRS)

    Waldron, Wayne L.; Vallerga, John

    1996-01-01

    We obtained a 140 ks EUVE observation of the O4f star, zeta Puppis. Because of its low ISM column density and highly ionized stellar wind, a unique EUV window is accessible for viewing between 128 to 140 A, suggesting that this star may he the only O star observable with the EUVE. Although no SW spectrometer wavelength bin had a signal to noise greater than 3, a bin at 136 A had a signal to noise of 2.4. This bin is where models predict the brightest line due to OV emission should occur. We present several EUV line emission models. These models were constrained by fitting the ROSAT PSPC X-ray data and our EUVE data. If the OV emission is real, the best fits to the data suggest that there are discrepancies in our current understanding of EUV/X-ray production mechanisms. In particular, the emission measure of the EUV source is found to be much greater than the total wind emission measure, suggesting that the EUV shock must produce a very large density enhancement. In addition, the location of the EUV and X-ray shocks are found to be separated by approx. 0.3 stellar radii, but the EUV emission region is found to be approx. 400 times larger than the X-ray emission region. We also discuss the implications of a null detection and present relevant upper limits.

  1. The use of zeta potential as a tool to study phase transitions in binary phosphatidylcholines mixtures.

    PubMed

    Sierra, M B; Pedroni, V I; Buffo, F E; Disalvo, E A; Morini, M A

    2016-06-01

    Temperature dependence of the zeta potential (ZP) is proposed as a tool to analyze the thermotropic behavior of unilamellar liposomes prepared from binary mixtures of phosphatidylcholines in the absence or presence of ions in aqueous suspensions. Since the lipid phase transition influences the surface potential of the liposome reflecting a sharp change in the ZP during the transition, it is proposed as a screening method for transition temperatures in complex systems, given its high sensitivity and small amount of sample required, that is, 70% less than that required in the use of conventional calorimeters. The sensitivity is also reflected in the pre-transition detection in the presence of ions. Plots of phase boundaries for these mixed-lipid vesicles were constructed by plotting the delimiting temperatures of both main phase transition and pre-transition vs. the lipid composition of the vesicle. Differential scanning calorimetry (DSC) studies, although subject to uncertainties in interpretation due to broad bands in lipid mixtures, allowed the validation of the temperature dependence of the ZP method for determining the phase transition and pre-transition temperatures. The system chosen was dipalmitoylphosphatidylcholine/dimyristoyl phosphatidylcholine (DMPC/DPPC), the most common combination in biological membranes. This work may be considered as a starting point for further research into more complex lipid mixtures with functional biological importance. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Pleiotrophin and its receptor protein tyrosine phosphatase beta/zeta as regulators of angiogenesis and cancer.

    PubMed

    Papadimitriou, Evangelia; Pantazaka, Evangelia; Castana, Penelope; Tsalios, Thomas; Polyzos, Alexandros; Beis, Dimitris

    2016-12-01

    Pleiotrophin (PTN) is a secreted heparin-binding growth factor that through its receptor protein tyrosine phosphatase beta/zeta (RPTPβ/ζ) has a significant regulatory effect on angiogenesis and cancer. PTN and RPTPβ/ζ are over-expressed in several types of human cancers and regulate important cancer cell functions in vitro and cancer growth in vivo. This review begins with a brief introduction of PTN and the regulation of its expression. PTN receptors are described with special emphasis on RPTPβ/ζ, which also interacts with and/or affects the function of other important targets for cancer therapy, such as vascular endothelial growth factor A, α ν β 3 and cell surface nucleolin. PTN biological activities related to angiogenesis and cancer are extensively discussed. Finally, up to date approaches of targeting PTN or RPTPβ/ζ for cancer treatment are presented. Insights into the regulatory role of PTN/RPTPβ/ζ on angiogenesis will be extremely beneficial for future development of alternative anti-angiogenic approaches in cancer therapy. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics Simulations.

    PubMed

    Ge, Zhenpeng; Wang, Yi

    2017-04-20

    Molecular dynamics simulations of nanoparticles (NPs) are increasingly used to study their interactions with various biological macromolecules. Such simulations generally require detailed knowledge of the surface composition of the NP under investigation. Even for some well-characterized nanoparticles, however, this knowledge is not always available. An example is nanodiamond, a nanoscale diamond particle with surface dominated by oxygen-containing functional groups. In this work, we explore using the harmonic restraint method developed by Venable et al., to estimate the surface charge density (σ) of nanodiamonds. Based on the Gouy-Chapman theory, we convert the experimentally determined zeta potential of a nanodiamond to an effective charge density (σ eff ), and then use the latter to estimate σ via molecular dynamics simulations. Through scanning a series of nanodiamond models, we show that the above method provides a straightforward protocol to determine the surface charge density of relatively large (> ∼100 nm) NPs. Overall, our results suggest that despite certain limitation, the above protocol can be readily employed to guide the model construction for MD simulations, which is particularly useful when only limited experimental information on the NP surface composition is available to a modeler.

  4. Optimal MEMS device for mobility and zeta potential measurements using DC electrophoresis.

    PubMed

    Karam, Pascal R; Dukhin, Andrei; Pennathur, Sumita

    2017-05-01

    We have developed a novel microchannel geometry that allows us to perform simple DC electrophoresis to measure the electrophoretic mobility and zeta potential of analytes and particles. In standard capillary geometries, mobility measurements using DC fields are difficult to perform. Specifically, measurements in open capillaries require knowledge of the hard to measure and often dynamic wall surface potential. Although measurements in closed capillaries eliminate this requirement, the measurements must be performed at infinitesimally small regions of zero flow where the pressure driven-flow completely cancels the electroosmotic flow (Komagata Planes). Furthermore, applied DC fields lead to electrode polarization, further questioning the reliability and accuracy of the measurement. In contrast, our geometry expands and moves the Komagata planes to where velocity gradients are at a minimum, and thus knowledge of the precise location of a Komagata plane is not necessary. Additionally, our microfluidic device prevents electrode polarization because of fluid recirculation around the electrodes. We fabricated our device using standard MEMS fabrication techniques and performed electrophoretic mobility measurements on 500 nm fluorescently tagged polystyrene particles at various buffer concentrations. Results are comparable to two different commercial dynamic light scattering based particle sizing instruments. We conclude with guidelines to further develop this robust electrophoretic tool that allows for facile and efficient particle characterization. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Can Eccentric Debris Disks Be Long-lived? A First Numerical Investigation and Application to Zeta(exp 2) Reticuli

    NASA Technical Reports Server (NTRS)

    Faramaz, V.; Beust, H.; Thebault, P.; Augereau, J.-C.; Bonsor, A.; delBurgo, C.; Ertel, S.; Marshall, J. P.; Milli, J.; Montesinos, B.; hide

    2014-01-01

    Context. Imaging of debris disks has found evidence for both eccentric and offset disks. One hypothesis is that they provide evidence for massive perturbers, for example, planets or binary companions, which sculpt the observed structures. One such disk was recently observed in the far-IR by the Herschel Space Observatory around Zeta2 Reticuli. In contrast with previously reported systems, the disk is significantly eccentric, and the system is several Gyr old. Aims. We aim to investigate the long-term evolution of eccentric structures in debris disks caused by a perturber on an eccentric orbit around the star. We hypothesise that the observed eccentric disk around Zeta2 Reticuli might be evidence of such a scenario. If so, we are able to constrain the mass and orbit of a potential perturber, either a giant planet or a binary companion. Methods. Analytical techniques were used to predict the effects of a perturber on a debris disk. Numerical N-body simulations were used to verify these results and further investigate the observable structures that may be produced by eccentric perturbers. The long-term evolution of the disk geometry was examined, with particular application to the Zeta2 Reticuli system. In addition, synthetic images of the disk were produced for direct comparison with Herschel observations. Results. We show that an eccentric companion can produce both the observed offsets and eccentric disks. These effects are not immediate, and we characterise the timescale required for the disk to develop to an eccentric state (and any spirals to vanish). For Zeta2 Reticuli, we derive limits on the mass and orbit of the companion required to produce the observations. Synthetic images show that the pattern observed around Zeta2 Reticuli can be produced by an eccentric disk seen close to edge-on, and allow us to bring additional constraints on the disk parameters of our model (disk flux and extent). Conclusions. We conclude that eccentric planets or stellar companions

  6. Zeta potentials of the rare earth element fluorcarbonate minerals focusing on bastnäsite and parisite.

    PubMed

    Owens, C L; Nash, G R; Hadler, K; Fitzpatrick, R S; Anderson, C G; Wall, F

    2018-06-01

    Rare earth elements (REE) are critical to a wide range of technologies ranging from mobile phones to wind turbines. Processing and extraction of REE minerals from ore bodies is, however, both challenging and relatively poorly understood, as the majority of deposits contain only limited enrichment of REEs. An improved understanding of the surface properties of the minerals is important in informing and optimising their processing, in particular for separation by froth flotation. The measurement of zeta potential can be used to extract information regarding the electrical double layer, and hence surface properties of these minerals. There are over 34 REE fluorcarbonate minerals currently identified, however bastnäsite, synchysite and parisite are of most economic importance. Bastnäsite-(Ce), the most common REE fluorcarbonate, supplies over 50% of the world's REE. Previous studies of bastnäsite have showed a wide range of surface behaviour, with the iso-electric point (IEP), being measured between pH values of 4.6 and 9.3. In contrast, no values of IEP have been reported for parisite or synchysite. In this work, we review previous studies of the zeta potentials of bastnäsite to investigate the effects of different methodologies and sample preparation. In addition, measurements of zeta potentials of parisite under water, collector and supernatant conditions were conducted, the first to be reported. These results showed an iso-electric point for parisite of 5.6 under water, with a shift to a more negative zeta potential with both collector (hydroxamic and fatty acids) and supernatant conditions. The IEP with collectors and supernatant was <3.5. As zeta potential measurements in the presence of reagents and supernatants are the most rigorous way of determining the efficiency of a flotation reagent, the agreement between parisite zeta potentials obtained here and previous work on bastnäsite suggests that parisite may be processed using similar reagent schemes to

  7. Flotation of algae for water reuse and biomass production: role of zeta potential and surfactant to separate algal particles.

    PubMed

    Kwak, Dong-Heui; Kim, Mi-Sug

    2015-01-01

    The effect of chemical coagulation and biological auto-flocculation relative to zeta potential was examined to compare flotation and sedimentation separation processes for algae harvesting. Experiments revealed that microalgae separation is related to auto-flocculation of Anabaena spp. and requires chemical coagulation for the whole period of microalgae cultivation. In addition, microalgae separation characteristics which are associated with surfactants demonstrated optimal microalgae cultivation time and separation efficiency of dissolved CO2 flotation (DCF) as an alternative to dissolved air flotation (DAF). Microalgae were significantly separated in response to anionic surfactant rather than cationic surfactant as a function of bubble size and zeta potential. DAF and DCF both showed slightly efficient flotation; however, application of anionic surfactant was required when using DCF.

  8. Influence of temperature, anions and size distribution on the zeta potential of DMPC, DPPC and DMPE lipid vesicles.

    PubMed

    Morini, M A; Sierra, M B; Pedroni, V I; Alarcon, L M; Appignanesi, G A; Disalvo, E A

    2015-07-01

    The purpose of the work is to compare the influence of the multilamellarity, phase state, lipid head groups and ionic media on the origin of the surface potential of lipid membranes. With this aim, we present a new analysis of the zeta potential of multilamellar and unilamellar vesicles composed by phosphatidylcholines (PC) and phosphatidylethanolamines (PE) dispersed in water and ionic solutions of polarizable anions, at temperatures below and above the phase transition. In general, the adsorption of anions seems to explain the origin of the zeta potential in vesicles only above the transition temperature (Tc). In this case, the sign of the surface potential is ascribed to a partial orientation of head group moiety toward the aqueous phase. This is noticeable in PC head groups but not in PEs, due to the strong lateral interaction between PO and NH group in PE. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Reduced Zeta potential through use of cationic adhesion promoter for improved resist process performance and minimizing material consumption

    NASA Astrophysics Data System (ADS)

    Hodgson, Lorna; Thompson, Andrew

    2012-03-01

    This paper presents the results of a non-HMDS (non-silane) adhesion promoter that was used to reduce the zeta potential for very thin (proprietary) polymer on silicon. By reducing the zeta potential, as measured by the minimum sample required to fully coat a wafer, the amount of polymer required to coat silicon substrates was significantly reduced in the manufacture of X-ray windows used for high transmission of low-energy X-rays. Moreover, this approach used aqueous based adhesion promoter described as a cationic surface active agent that has been shown to improve adhesion of photoresists (positive, negative, epoxy [SU8], e-beam and dry film). As well as reducing the amount of polymer required to coat substrates, this aqueous adhesion promoter is nonhazardous, and contains non-volatile solvents.

  10. Rheological behavior, zeta potential, and accelerated stability tests of Buriti oil (Mauritia flexuosa) emulsions containing lyotropic liquid crystals.

    PubMed

    Zanatta, Cinthia Fernanda; de Faria Sato, Anne Miwa Callejón; de Camargo, Flavio Bueno; Campos, Patrícia Maria Berardo Gonçalves Maia; Rocha-Filho, Pedro Alves

    2010-01-01

    It is well known that the Amazon region presents a huge biodiversity; therefore, countless natural resources are being employed in the production of phytocosmetics and phytomedicines. The purpose of this work was to obtain emulsions produced with Buriti oil and non-ionic surfactants. Two surfactant systems were employed (Steareth-2 associated to Ceteareth-5 and to Ceteareth-20) to produce the emulsions using phase diagram method. Emulsions were obtained by echo-planar imaging method at 75°C. Rheological behavior and zeta potential were evaluated, and accelerated stability tests were performed. All emulsions analyzed presented pseudoplastic behavior. Zeta potential values were obtained between -14.2 and -53.3 mV. The formulations did not show changes in either physical stability, pH, or rheological behavior after accelerated stability tests. Significant differences were observed only after temperature cycling test. Based on these results, the emulsions obtained could be considered as promising delivery systems.

  11. Relationship between phospholipase C-zeta, semen parameters, and chromatin status.

    PubMed

    Tavalaee, Marziyeh; Kiani-Esfahani, Abbas; Nasr-Esfahani, Mohammad H

    2017-08-01

    The need for additional tests to complement basic sperm analysis in clinics is well appreciated. In this regard, a number of tests such as sperm DNA integrity test as a tool in diagnosis and treatment of infertility are suggested. But recent studies have focused on main sperm factors involved in oocyte activation such as phospholipase C-zeta (PLCζ) that initiate intracellular Ca 2+ signaling and embryogenesis. Therefore, this study aimed to investigate the relationship between PLCζ, basic semen parameters, sperm DNA fragmentation (SDF), and protamine deficiency in men with normal (n=32) and abnormal (n=23) semen parameters. Unlike SDF and protamine deficiency, as negative factors related to fertility, the mean value of PLCζ as positive factor related to infertility was significantly lower in men with abnormal semen parameters compared to men with normal semen parameters. Significant correlations were also observed between sperm concentration, motility, and abnormal morphology with the percentage of PLCζ positive spermatozoa. In addition, logistic regression analysis revealed that sperm morphology is more predictive than sperm motility and concentration for PLCζ presence. In addition, a statistically significant negative relationship was observed between the percentage of PLCζ positive spermatozoa and SDF. These findings suggested during ICSI, selection of sperm based on morphology has a profound effect on its ability to induce oocyte activation based on the likelihood of PLCζ expression. Therefore, assessment of PLCζ as an index for fertilization potential of a semen sample in men with severe teratozoospermia may define individuals who are candidates for artificial oocyte activation (AOA) and may avoid failed fertilization post ICSI.

  12. Zeta Potential Measurements on Three Clays from Turkey and Effects of Clays on Coal Flotation

    PubMed

    Hussain; Dem&idot;rc&idot;; özbayoğlu

    1996-12-25

    There is a growing trend of characterizing coal and coal wastes in order to study the effect of clays present in them during coal washing. Coarse wastes from the Zonguldak Coal Washery, Turkey, were characterized and found to contain kaolinite, illite, and chlorite. These three clays, obtained in almost pure form from various locations in Turkey, have been subjected to X-ray diffraction (XRD) analysis to assess their purity and zeta potential measurements in order to evaluate their properties in terms of their surface charge and point of zero charge (pzc) values. It was found from XRD data that these clays were almost pure and their electrokinetic potential should therefore be representative of their colloidal behavior. All three clay minerals were negatively charged over the range from pH 2.5 to 11. Chlorite and illite have pzc at pH 3 and pH 2.5, respectively, whereas kaolinite has no pzc. The effect of these clays in Zonguldak coal, wastes, and black waters on coal flotation was studied by floating artificial mixtures of Zonguldak clean coal (4.5% ash) and individual clay. The flotation tests on coal/individual clay revealed that each clay influences coal flotation differently according to its type and amount. Illite had the worst effect on coal floated, followed by chlorite and kaolinite. The loss of yield in coal was found to be 18% for kaolinite, 20% for chlorite, and 28% for illite, indicating the worst effect of illite and least for kaolinite during coal flotation.

  13. The zeta potential of extended dielectrics and conductors in terms of streaming potential and streaming current measurements.

    PubMed

    Gallardo-Moreno, Amparo M; Vadillo-Rodríguez, Virginia; Perera-Núñez, Julia; Bruque, José M; González-Martín, M Luisa

    2012-07-21

    The electrical characterization of surfaces in terms of the zeta potential (ζ), i.e., the electric potential contributing to the interaction potential energy, is of major importance in a wide variety of industrial, environmental and biomedical applications in which the integration of any material with the surrounding media is initially mediated by the physico-chemical properties of its outer surface layer. Among the different existing electrokinetic techniques for obtaining ζ, streaming potential (V(str)) and streaming current (I(str)) are important when dealing with flat-extended samples. Mostly dielectric materials have been subjected to this type of analysis and only a few papers can be found in the literature regarding the electrokinetic characterization of conducting materials. Nevertheless, a standardized procedure is typically followed to calculate ζ from the measured data and, importantly, it is shown in this paper that such a procedure leads to incorrect zeta potential values when conductors are investigated. In any case, assessment of a reliable numerical value of ζ requires careful consideration of the origin of the input data and the characteristics of the experimental setup. In particular, it is shown that the cell resistance (R) typically obtained through a.c. signals (R(a.c.)), and needed for the calculations of ζ, always underestimates the zeta potential values obtained from streaming potential measurements. The consideration of R(EK), derived from the V(str)/I(str) ratio, leads to reliable values of ζ when dielectrics are investigated. For metals, the contribution of conductivity of the sample to the cell resistance provokes an underestimation of R(EK), which leads to unrealistic values of ζ. For the electrical characterization of conducting samples I(str) measurements constitute a better choice. In general, the findings gathered in this manuscript establish a measurement protocol for obtaining reliable zeta potentials of dielectrics and

  14. 14-3-3 sigma and 14-3-3 zeta plays an opposite role in cell growth inhibition mediated by transforming growth factor-beta 1.

    PubMed

    Hong, Hye-Young; Jeon, Woo-Kwang; Bae, Eun-Jin; Kim, Shin-Tae; Lee, Ho-Jae; Kim, Seong-Jin; Kim, Byung-Chul

    2010-03-01

    The expression of 14-3-3 proteins is dysregulated in various types of cancer. This study was undertaken to investigate the effects of 14-3-3 zeta and 14-3-3 sigma on cell growth inhibition mediated by transforming growth factor-beta 1 (TGF-beta1). Mouse mammary epithelial cells (Eph4) that are transformed with oncogenic c-H-Ras (EpRas) and no longer sensitive to TGF-beta1-mediated growth inhibition displayed increased expression of 14-3-3 zeta and decreased expression of 14-3-3 sigma compared with parental Eph4 cells. Using small interfering RNA-mediated knockdown and overexpression of 14-3-3 sigma or 14-3-3 zeta, we showed that 14-3-3 sigma is required for TGF-beta1-mediated growth inhibition whereas 14-3-3 zeta negatively modulates this growth inhibitory response. Notably, overexpression of 14-3-3 zeta increased the level of Smad3 protein that is phosphorylated at linker regions and cannot mediate the TGF-beta1 growth inhibitory response. Consistent with this finding, mutation of the 14-3-3 zeta phosphorylation sites in Smad3 markedly reduced the 14-3-3 zeta-mediated inhibition of TGF-beta1-induced p15 promoter-reporter activity and cell cycle arrest, suggesting that these residues are critical targets of 14-3-3 zeta in the suppression of TGF-beta1-mediated growth. Taken together, our findings indicate that dysregulation of 14-3-3 sigma or 14-3-3 zeta contributes to TGF-beta1 resistance in cancer cells.

  15. Zeta potential study of Sb2S3 nanoparticles synthesized by a facile polyol method in various surfactants

    NASA Astrophysics Data System (ADS)

    Saxena, Monika; Okram, Gunadhor Singh

    2018-05-01

    In the present work, we report the successful synthesis of stibnite Sb2S3 nanoparticles (NPs) by a facile polyol method using various surfactant. The structural and optical properties were investigated by X-ray diffraction (XRD), Raman spectroscopy and Zeta potential. Rietveld refinement of XRD data confirms the single phase orthorhombic crystal structure of stibnite Sb2S3. Presence of six obvious Raman modes further confirmed their stoichiometric formation. Effect of different surfactants on the surface charge of Sb2S3 NPs was studied using Zeta potential measurement in deionized water at different pH values. They reveal that these NPs are more stable when it was synthesized in presence of EDTA than that of CTAB or without surfactant samples with high zeta potential. The isoelectronic point was found at pH = 6.4 for pure sample, 3.5 and 7.2 for CTAB and not found for EDTA Sb2S3 samples. This information can be useful for many industrial applications like pharmaceuticals, ceramics, waste water treatment and medicines.

  16. Zeta potential in oil-water-carbonate systems and its impact on oil recovery during controlled salinity water-flooding

    PubMed Central

    Jackson, Matthew D.; Al-Mahrouqi, Dawoud; Vinogradov, Jan

    2016-01-01

    Laboratory experiments and field trials have shown that oil recovery from carbonate reservoirs can be increased by modifying the brine composition injected during recovery in a process termed controlled salinity water-flooding (CSW). However, CSW remains poorly understood and there is no method to predict the optimum CSW composition. This work demonstrates for the first time that improved oil recovery (IOR) during CSW is strongly correlated to changes in zeta potential at both the mineral-water and oil-water interfaces. We report experiments in which IOR during CSW occurs only when the change in brine composition induces a repulsive electrostatic force between the oil-brine and mineral-brine interfaces. The polarity of the zeta potential at both interfaces must be determined when designing the optimum CSW composition. A new experimental method is presented that allows this. Results also show for the first time that the zeta potential at the oil-water interface may be positive at conditions relevant to carbonate reservoirs. A key challenge for any model of CSW is to explain why IOR is not always observed. Here we suggest that failures using the conventional (dilution) approach to CSW may have been caused by a positively charged oil-water interface that had not been identified. PMID:27876833

  17. High-resolution ultraviolet observations of interstellar lines toward Zeta Persei observed with the balloon-borne ultraviolet stellar spectrometer

    SciTech Connect

    Snow, T.P.; Lamers, H.J.G.L.M.; Joseph, C.L.

    1987-10-01

    The balloon-borne ultraviolet stellar spectrometer payload has been used to obtain high-resolution data on interstellar absorption lines toward Zeta Per. The only lines clearly present in the 2150-2450 region were several Fe II features, which show double structure. The two velocity components were sufficiently well separated that it was possible to construct separate curves of growth to derive the Fe II column densities for the individual components. These column densities and the component velocity separation were then used to compute a realistic two-component curve of growth for the line of sight to Zeta Per, which was then used to reanalyzemore » existing ultraviolet data from Copernicus. The results were generally similar to an earlier two-component analysis of the Copernicus data, with the important exception that the silicon depletion increased from near zero to about 1 dex. This makes the Zeta Per depletion pattern quite similar to those derived for other reddened lines of sight, supporting the viewpoint that the general diffuse interstellar medium has a nearly constant pattern of depletions. 31 references.« less

  18. Mapping Protein–Protein Interactions of the Resistance-Related Bacterial Zeta Toxin–Epsilon Antitoxin Complex (ε2ζ2) with High Affinity Peptide Ligands Using Fluorescence Polarization

    PubMed Central

    Fernández-Bachiller, María Isabel; Brzozowska, Iwona; Odolczyk, Norbert; Zielenkiewicz, Urszula; Zielenkiewicz, Piotr; Rademann, Jörg

    2016-01-01

    Toxin–antitoxin systems constitute a native survival strategy of pathogenic bacteria and thus are potential targets of antibiotic drugs. Here, we target the Zeta–Epsilon toxin–antitoxin system, which is responsible for the stable maintenance of certain multiresistance plasmids in Gram-positive bacteria. Peptide ligands were designed on the basis of the ε2ζ2 complex. Three α helices of Zeta forming the protein–protein interaction (PPI) site were selected and peptides were designed conserving the residues interacting with Epsilon antitoxin while substituting residues binding intramolecularly to other parts of Zeta. Designed peptides were synthesized with an N-terminal fluoresceinyl-carboxy-residue for binding assays and provided active ligands, which were used to define the hot spots of the ε2ζ2 complex. Further shortening and modification of the binding peptides provided ligands with affinities <100 nM, allowing us to determine the most relevant PPIs and implement a robust competition binding assay. PMID:27438853

  19. 14-3-3 zeta is a molecular target in guggulsterone induced apoptosis in head and neck cancer cells.

    PubMed

    Macha, Muzafar A; Matta, Ajay; Chauhan, Ss; Siu, Kw Michael; Ralhan, Ranju

    2010-11-30

    The five-year survival rates for head and neck squamous cell carcinoma (HNSCC) patients are less than 50%, and the prognosis has not improved, despite advancements in standard multi-modality therapies. Hence major emphasis is being laid on identification of novel molecular targets and development of multi-targeted therapies. 14-3-3 zeta, a multifunctional phospho-serine/phospho-threonine binding protein, is emerging as an effector of pro-survival signaling by binding to several proteins involved in apoptosis (Bad, FKHRL1 and ASK1) and may serve as an appropriate target for head and neck cancer therapy. Herein, we determined effect of guggulsterone (GS), a farnesoid X receptor antagonist, on 14-3-3 zeta associated molecular pathways for abrogation of apoptosis in head and neck cancer cells. Head and neck cancer cells were treated with guggulsterone (GS). Effect of GS-treatment was evaluated using cell viability (MTT) assay and apoptosis was verified by annexin V, DNA fragmentation and M30 CytoDeath antibody assay. Mechanism of GS-induced apoptosis was determined by western blotting and co-IP assays using specific antibodies. Using in vitro models of head and neck cancer, we showed 14-3-3 zeta as a key player regulating apoptosis in GS treated SCC4 cells. Treatment with GS releases BAD from the inhibitory action of 14-3-3 zeta in proliferating HNSCC cells by activating protein phosphatase 2A (PP2A). These events initiate the intrinsic mitochondrial pathway of apoptosis, as revealed by increased levels of cytochrome c in cytoplasmic extracts of GS-treated SCC4 cells. In addition, GS treatment significantly reduced the expression of anti-apoptotic proteins, Bcl-2, xIAP, Mcl1, survivin, cyclin D1 and c-myc, thus committing cells to apoptosis. These events were followed by activation of caspase 9, caspase 8 and caspase 3 leading to cleavage of its downstream target, poly-ADP-ribose phosphate (PARP). GS targets 14-3-3 zeta associated cellular pathways for reducing

  20. Dynamic Light Scattering and Zeta Potential of Colloidal Mixtures of Amelogenin and Hydroxyapatite in Calcium and Phosphate Rich Ionic Milieus

    PubMed Central

    Uskoković, Vuk; Odsinada, Roselyn; Djordjevic, Sonia; Habelitz, Stefan

    2011-01-01

    The concept of zeta-potential has been used for more than a century as a basic parameter in controlling the stability of colloidal suspensions, irrespective of the nature of their particulate ingredients – organic or inorganic. There are prospects that self-assembly of peptide species and the protein-mineral interactions related to biomineralization may be controlled using this fundamental physicochemical parameter. In this study, we have analyzed the particle size and zeta-potential of the full-length recombinant human amelogenin (rH174), the main protein of the developing enamel matrix, in the presence of calcium and phosphate ions and hydroxyapatite (HAP) particles. As calcium and phosphate salts are introduced to rH174 sols in increments, zeta-potential of the rH174 nanospheres is more affected by negatively charged ions, suggesting their tendency to locate within the double charge layer. Phosphate ions have a more pronounced effect on both the zeta-potential and aggregation propensity of rH174 nanospheres compared to calcium ions. The isoelectric point of amelogenin was independent on the ionic strength of the solution and the concentration of calcium and/or phosphate ions. Whereas rH174 shows a higher affinity for phosphate than for calcium, HAP attracts both of these ions to the shear plane of the double layer. The parallel size and zeta-potential analysis of HAP and rH174 colloidal mixtures indicated that at pH 7.4, despite both HAP and rH174 particles being negatively charged, rH174 adsorbs well onto HAP particles. The process is slower at pH 7.4 than at pH 4.5 when the HAP surface is negatively charged and the rH174 nanosphere carries an overall positive charge. The results presented hereby demonstrate that electrostatic interactions can affect the kinetics of the adsorption of rH174 onto HAP. PMID:21146151

  1. Joint Task Force on Undergraduate Physics Programs (J-TUPP): What skills and knowledge are needed for a diverse set of careers and what's the basis for these recommendations?

    NASA Astrophysics Data System (ADS)

    Woolf, Lawrence

    2016-03-01

    A wide variety of reports have been issued recently concerning the skills, knowledge, and attitudes needed by employees to be successful. This talk will review findings from reports from the major science and engineering disciplines, from surveys of employers, and from interviews with recent undergraduate physics graduates. Also to be discussed is the correlation between these findings and the detailed J-TUPP recommendations for the skills and knowledge needed by the next generation of undergraduate physics degree holders to be prepared for a diverse set of careers.

  2. Clinical Trials Using Anti-CD19/CD28/CD3zeta CAR Gammaretroviral Vector-transduced Autologous T Lymphocytes KTE-C19

    Cancer.gov

    NCI supports clinical trials that test new and more effective ways to treat cancer. Find clinical trials studying anti-cd19/cd28/cd3zeta car gammaretroviral vector-transduced autologous t lymphocytes kte-c19.

  3. A Diverse Set of Single-domain Antibodies (VHHs) against the Anthrax Toxin Lethal and Edema Factors Provides a Basis for Construction of a Bispecific Agent That Protects against Anthrax Infection*

    PubMed Central

    Vrentas, Catherine E.; Moayeri, Mahtab; Keefer, Andrea B.; Greaney, Allison J.; Tremblay, Jacqueline; O'Mard, Danielle; Leppla, Stephen H.; Shoemaker, Charles B.

    2016-01-01

    Infection with Bacillus anthracis, the causative agent of anthrax, can lead to persistence of lethal secreted toxins in the bloodstream, even after antibiotic treatment. VHH single-domain antibodies have been demonstrated to neutralize diverse bacterial toxins both in vitro and in vivo, with protein properties such as small size and high stability that make them attractive therapeutic candidates. Recently, we reported on VHHs with in vivo activity against the protective antigen component of the anthrax toxins. Here, we characterized a new set of 15 VHHs against the anthrax toxins that act by binding to the edema factor (EF) and/or lethal factor (LF) components. Six of these VHHs are cross-reactive against both EF and LF and recognize the N-terminal domain (LFN, EFN) of their target(s) with subnanomolar affinity. The cross-reactive VHHs block binding of EF/LF to the protective antigen C-terminal binding interface, preventing toxin entry into the cell. Another VHH appears to recognize the LF C-terminal domain and exhibits a kinetic effect on substrate cleavage by LF. A subset of the VHHs neutralized against EF and/or LF in murine macrophage assays, and the neutralizing VHHs that were tested improved survival of mice in a spore model of anthrax infection. Finally, a bispecific VNA (VHH-based neutralizing agent) consisting of two linked toxin-neutralizing VHHs, JMN-D10 and JMO-G1, was fully protective against lethal anthrax spore infection in mice as a single dose. This set of VHHs should facilitate development of new therapeutic VNAs and/or diagnostic agents for anthrax. PMID:27539858

  4. A Diverse Set of Single-domain Antibodies (VHHs) against the Anthrax Toxin Lethal and Edema Factors Provides a Basis for Construction of a Bispecific Agent That Protects against Anthrax Infection.

    PubMed

    Vrentas, Catherine E; Moayeri, Mahtab; Keefer, Andrea B; Greaney, Allison J; Tremblay, Jacqueline; O'Mard, Danielle; Leppla, Stephen H; Shoemaker, Charles B

    2016-10-07

    Infection with Bacillus anthracis, the causative agent of anthrax, can lead to persistence of lethal secreted toxins in the bloodstream, even after antibiotic treatment. VHH single-domain antibodies have been demonstrated to neutralize diverse bacterial toxins both in vitro and in vivo, with protein properties such as small size and high stability that make them attractive therapeutic candidates. Recently, we reported on VHHs with in vivo activity against the protective antigen component of the anthrax toxins. Here, we characterized a new set of 15 VHHs against the anthrax toxins that act by binding to the edema factor (EF) and/or lethal factor (LF) components. Six of these VHHs are cross-reactive against both EF and LF and recognize the N-terminal domain (LF N , EF N ) of their target(s) with subnanomolar affinity. The cross-reactive VHHs block binding of EF/LF to the protective antigen C-terminal binding interface, preventing toxin entry into the cell. Another VHH appears to recognize the LF C-terminal domain and exhibits a kinetic effect on substrate cleavage by LF. A subset of the VHHs neutralized against EF and/or LF in murine macrophage assays, and the neutralizing VHHs that were tested improved survival of mice in a spore model of anthrax infection. Finally, a bispecific VNA (VHH-based neutralizing agent) consisting of two linked toxin-neutralizing VHHs, JMN-D10 and JMO-G1, was fully protective against lethal anthrax spore infection in mice as a single dose. This set of VHHs should facilitate development of new therapeutic VNAs and/or diagnostic agents for anthrax. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Effect of the adsorption of lithium and borate species on the zeta potential of particles of cobalt ferrite, nickel ferrite, and magnetite.

    PubMed

    Barale, M; Lefèvre, G; Carrette, F; Catalette, H; Fédoroff, M; Cote, G

    2008-12-01

    Zetametric measurements on suspensions of oxide particles (cobalt ferrite, nickel ferrite, and magnetite) representative of corrosion products from primary circuits of pressurized water reactors were performed at 25 and 70 degrees C in the presence of lithium and borate species. No effect of lithium ions was observed. Borate species cause a decrease of the isoelectric point (IEP), attributed to the sorption of borate as a negative complex MOB(OH)3(-). A predictive model based on thermodynamic calculations (2-pK and diffuse layer models) of the surface acidity constants from the data of acid-base titrations combined with an empirical relationship between the surface potential Psi 0 and the zeta potential determined by zetametry was developed. A whole set of parameters valid at 25 degrees C, in a range of ionic strength between 10(-4) and 10(-2) molL(-1) and in a range of pH between 4 and 8, was determined for this model. Increase of temperature to 70 degrees C in the presence of borate results in a decrease of IEP for cobalt ferrite and an increase of the IEP for nickel ferrite.

  6. The Basis System

    SciTech Connect

    Dubois, P.F.

    1989-05-16

    This paper discusses the basis system. Basis is a program development system for scientific programs. It has been developed over the last five years at Lawrence Livermore National Laboratory (LLNL), where it is now used in about twenty major programming efforts. The Basis System includes two major components, a program development system and a run-time package. The run-time package provides the Basis Language interpreter, through which the user does input, output, plotting, and control of the program's subroutines and functions. Variables in the scientific packages are known to this interpreter, so that the user may arbitrarily print, plot, and calculatemore » with, any major program variables. Also provided are facilities for dynamic memory management, terminal logs, error recovery, text-file i/o, and the attachment of non-Basis-developed packages.« less

  7. Protein adsorption on dopamine-melanin films: role of electrostatic interactions inferred from zeta-potential measurements versus chemisorption.

    PubMed

    Bernsmann, Falk; Frisch, Benoît; Ringwald, Christian; Ball, Vincent

    2010-04-01

    We recently showed the possibility to build dopamine-melanin films of controlled thickness by successive immersions of a substrate in alkaline solutions of dopamine [F. Bernsmann, A. Ponche, C. Ringwald, J. Hemmerlé, J. Raya, B. Bechinger, J.-C. Voegel, P. Schaaf, V. Ball, J. Phys. Chem. C 113 (2009) 8234-8242]. In this work the structure and properties of such films are further explored. The zeta-potential of dopamine-melanin films is measured as a function of the total immersion time to build the film. It appears that the film bears a constant zeta-potential of (-39+/-3) mV after 12 immersion steps. These data are used to calculate the surface density of charged groups of the dopamine-melanin films at pH 8.5 that are mostly catechol or quinone imine chemical groups. Furthermore the zeta-potential is used to explain the adsorption of three model proteins (lysozyme, myoglobin, alpha-lactalbumin), which is monitored by quartz crystal microbalance. We come to the conclusion that protein adsorption on dopamine-melanin is not only determined by possible covalent binding between amino groups of the proteins and catechol groups of dopamine-melanin but that electrostatic interactions contribute to protein binding. Part of the adsorbed proteins can be desorbed by sodium dodecylsulfate solutions at the critical micellar concentration. The fraction of weakly bound proteins decreases with their isoelectric point. Additionally the number of available sites for covalent binding of amino groups on melanin grains is quantified. Copyright 2009 Elsevier Inc. All rights reserved.

  8. The role of zeta potential in the adhesion of E. coli to suspended intertidal sediments.

    PubMed

    Wyness, Adam J; Paterson, David M; Defew, Emma C; Stutter, Marc I; Avery, Lisa M

    2018-05-29

    The extent of pathogen transport to and within aquatic systems depends heavily on whether the bacterial cells are freely suspended or in association with suspended particles. The surface charge of both bacterial cells and suspended particles affects cell-particle adhesion and subsequent transport and exposure pathways through settling and resuspension cycles. This study investigated the adhesion of Faecal Indicator Organisms (FIOs) to natural suspended intertidal sediments over the salinity gradient encountered at the transition zone from freshwater to marine environments. Phenotypic characteristics of three E. coli strains, and the zeta potential (surface charge) of the E. coli strains and 3 physically different types of intertidal sediments was measured over a salinity gradient from 0 to 5 Practical Salinity Units (PSU). A batch adhesion microcosm experiment was constructed with each combination of E. coli strain, intertidal sediment and 0, 2, 3.5 and 5 PSU. The zeta potential profile of one E. coli strain had a low negative charge and did not change in response to an increase in salinity, and the remaining E. coli strains and the sediments exhibited a more negative charge that decreased with an increase in salinity. Strain type was the most important factor in explaining cell-particle adhesion, however adhesion was also dependant on sediment type and salinity (2, 3.5 PSU > 0, 5 PSU). Contrary to traditional colloidal (Derjaguin, Landau, Vervey, and Overbeek (DLVO)) theory, zeta potential of strain or sediment did not correlate with cell-particle adhesion. E. coli strain characteristics were the defining factor in cell-particle adhesion, implying that diverse strain-specific transport and exposure pathways may exist. Further research applying these findings on a catchment scale is necessary to elucidate these pathways in order to improve accuracy of FIO fate and transport models. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. In vitro phosphorylation of insulin receptor substrate 1 by protein kinase C-zeta: functional analysis and identification of novel phosphorylation sites.

    PubMed

    Sommerfeld, Mark R; Metzger, Sabine; Stosik, Magdalene; Tennagels, Norbert; Eckel, Jürgen

    2004-05-18

    Protein kinase C-zeta (PKC-zeta) participates both in downstream insulin signaling and in the negative feedback control of insulin action. Here we used an in vitro approach to identify PKC-zeta phosphorylation sites within insulin receptor substrate 1 (IRS-1) and to characterize the functional implications. A recombinant IRS-1 fragment (rIRS-1(449)(-)(664)) containing major tyrosine motifs for interaction with phosphatidylinositol (PI) 3-kinase strongly associated to the p85alpha subunit of PI 3-kinase after Tyr phosphorylation by the insulin receptor. Phosphorylation of rIRS-1(449)(-)(664) by PKC-zeta induced a prominent inhibition of this process with a mixture of classical PKC isoforms being less effective. Both PKC-zeta and the classical isoforms phosphorylated rIRS-1(449)(-)(664) on Ser(612). However, modification of this residue did not reduce the affinity of p85alpha binding to pTyr-containing peptides (amino acids 605-615 of rat IRS-1), as determined by surface plasmon resonance. rIRS-1(449)(-)(664) was then phosphorylated by PKC-zeta using [(32)P]ATP and subjected to tryptic phosphopeptide mapping based on two-dimensional HPLC coupled to mass spectrometry. Ser(498) and Ser(570) were identified as novel phosphoserine sites targeted by PKC-zeta. Both sites were additionally confirmed by phosphopeptide mapping of the corresponding Ser --> Ala mutants of rIRS-1(449)(-)(664). Ser(570) was specifically targeted by PKC-zeta, as shown by immunoblotting with a phosphospecific antiserum against Ser(570) of IRS-1. Binding of p85alpha to the S570A mutant was less susceptible to inhibition by PKC-zeta, when compared to the S612A mutant. In conclusion, our in vitro data demonstrate a strong inhibitory action of PKC-zeta at the level of IRS-1/PI 3-kinase interaction involving multiple serine phosphorylation sites. Whereas Ser(612) appears not to participate in the negative control of insulin signaling, Ser(570) may at least partly contribute to this process.

  10. Zeta Sperm Selection Improves Pregnancy Rate and Alters Sex Ratio in Male Factor Infertility Patients: A Double-Blind, Randomized Clinical Trial

    PubMed Central

    Nasr Esfahani, Mohammad Hossein; Deemeh, Mohammad Reza; Tavalaee, Marziyeh; Sekhavati, Mohammad Hadi; Gourabi, Hamid

    2016-01-01

    Background Selection of sperm for intra-cytoplasmic sperm injection (ICSI) is usually considered as the ultimate technique to alleviate male-factor infertility. In routine ICSI, selection is based on morphology and viability which does not necessarily preclude the chance injection of DNA-damaged or apoptotic sperm into the oocyte. Sperm with high negative surface electrical charge, named “Zeta potential”, are mature and more likely to have intact chromatin. In addition, X-bearing spermatozoa carry more negative charge. Therefore, we aimed to compare the clinical outcomes of Zeta procedure with routine sperm selection in infertile men candidate for ICSI. Materials and Methods From a total of 203 ICSI cycles studied, 101 cycles were allocated to density gradient centrifugation (DGC)/Zeta group and the remaining 102 were included in the DGC group in this prospective study. Clinical outcomes were com- pared between the two groups. The ratios of Xand Y bearing sperm were assessed by fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR) methods in 17 independent semen samples. Results In the present double-blind randomized clinical trial, a significant increase in top quality embryos and pregnancy rate were observed in DGC/Zeta group compared to DGC group. Moreover, sex ratio (XY/XX) at birth significantly was lower in the DGC/Zeta group compared to DGC group despite similar ratio of X/Y bearings sper- matozoa following Zeta selection. Conclusion Zeta method not only improves the percentage of top embryo quality and pregnancy outcome but also alters the sex ratio compared to the conventional DGC method, despite no significant change in the ratio of Xand Ybearing sperm population (Registration number: IRCT201108047223N1). PMID:27441060

  11. Authorization basis requirements comparison report

    SciTech Connect

    Brantley, W.M.

    The TWRS Authorization Basis (AB) consists of a set of documents identified by TWRS management with the concurrence of DOE-RL. Upon implementation of the TWRS Basis for Interim Operation (BIO) and Technical Safety Requirements (TSRs), the AB list will be revised to include the BIO and TSRs. Some documents that currently form part of the AB will be removed from the list. This SD identifies each - requirement from those documents, and recommends a disposition for each to ensure that necessary requirements are retained when the AB is revised to incorporate the BIO and TSRs. This SD also identifies documentsmore » that will remain part of the AB after the BIO and TSRs are implemented. This document does not change the AB, but provides guidance for the preparation of change documentation.« less

  12. Hydrogen bonding and interparticle forces in platelet alpha-Al2O3 dispersions: yield stress and zeta potential.

    PubMed

    Khoo, Kay-Sen; Teh, E-Jen; Leong, Yee-Kwong; Ong, Ban Choon

    2009-04-09

    Adsorbed phosphate on smooth platelet alpha-Al2O3 particles at saturation surface coverage gives rise to strong interparticle attractive forces in dispersion. The maximum yield stress at the point of zero charge was increased by 2-fold. This was attributed to a high density of intermolecular hydrogen bonding between the adsorbed phosphate layers of the interacting particles. Adsorbed citrate at saturation surface coverage, however, reduced the maximum yield stress by 50%. It adsorbed to form a very effective steric barrier as intramolecular hydrogen bonding between -OH and the free terminal carboxylic group prevented strong interactions with other adsorbed citrate molecules residing on the second interacting particle. This steric barrier kept the interacting platelet particles further apart, thereby weakening the van der Waals attraction. The platelet alpha-Al2O3 dispersions were flocculated at all pH level. These dispersions displayed a maximum yield stress at the point of zero zeta potential at the pH approximately 8.0. They also obeyed the yield stress-DLVO force model as characterized by a linear decrease in the yield stress with the square of the zeta potential.

  13. The Isolation of DNA by Polycharged Magnetic Particles: An Analysis of the Interaction by Zeta Potential and Particle Size

    PubMed Central

    Haddad, Yazan; Xhaxhiu, Kledi; Kopel, Pavel; Hynek, David; Zitka, Ondrej; Adam, Vojtech

    2016-01-01

    Magnetic isolation of biological targets is in major demand in the biotechnology industry today. This study considers the interaction of four surface-modified magnetic micro- and nanoparticles with selected DNA fragments. Different surface modifications of nanomaghemite precursors were investigated: MAN37 (silica-coated), MAN127 (polyvinylpyrrolidone-coated), MAN158 (phosphate-coated), and MAN164 (tripolyphosphate-coated). All particles were positive polycharged agglomerated monodispersed systems. Mean particle sizes were 0.48, 2.97, 2.93, and 3.67 μm for MAN37, MAN127, MAN164, and MAN158, respectively. DNA fragments exhibited negative zeta potential of −0.22 mV under binding conditions (high ionic strength, low pH, and dehydration). A decrease in zeta potential of particles upon exposure to DNA was observed with exception of MAN158 particles. The measured particle size of MAN164 particles increased by nearly twofold upon exposure to DNA. Quantitative PCR isolation of DNA with a high retrieval rate was observed by magnetic particles MAN127 and MAN164. Interaction between polycharged magnetic particles and DNA is mediated by various binding mechanisms such as hydrophobic and electrostatic interactions. Future development of DNA isolation technology requires an understanding of the physical and biochemical conditions of this process. PMID:27104527

  14. Joule heating effects on electromagnetohydrodynamic flow through a peristaltically induced micro-channel with different zeta potential and wall slip

    NASA Astrophysics Data System (ADS)

    Ranjit, N. K.; Shit, G. C.

    2017-09-01

    This paper aims to develop a mathematical model for magnetohydrodynamic flow of biofluids through a hydrophobic micro-channel with periodically contracting and expanding walls under the influence of an axially applied electric field. The velocity slip effects have been taken into account at the channel walls by employing different slip lengths due to hydrophobic gating. Different temperature jump factors have also been used to investigate the thermomechanical interactions at the fluid-solid interface. The electromagnetohydrodynamic flow in a microchannel is simplified under the framework of Debye-Hückel linearization approximation. We have derived the closed-form solutions for the linearized dimensionless boundary value problem under the assumptions of long wave length and low Reynolds number. The axial velocity, temperature, pressure distribution, stream function, wall shear stress and the Nusselt number have been appraised for diverse values of the parameters approaching into the problem. Our main focus is to determine the effects of different zeta potential on the axial velocity and temperature distribution under electromagnetic environment. This study puts forward an important observation that the different zeta potential plays an important role in controlling fluid velocity. The study further reveals that the temperature increases significantly with the Joule heating parameter and the Brinkman number (arises due to the dissipation of energy).

  15. Copernicus studies of interstellar material in the Perseus II complex. III - The line of sight to Zeta Persei

    NASA Technical Reports Server (NTRS)

    Snow, T. P., Jr.

    1977-01-01

    Ultraviolet spectrophotometric data obtained with Copernicus are used to analyze the distribution, composition, density, temperature, and kinematics of the interstellar material along the line of sight to Zeta Persei. The far-UV extinction curve for the star is evaluated along with the kinematics of the interstellar gas, observations of atomic and molecular hydrogen, curves of growth for neutral and ionized species, atomic abundances and depletions, ionization equilibria, and observations of CO and OH lines. The results show that there are apparently three clouds along the line of sight to Zeta Persei: a main cloud at approximately +13 km/s which contains most of the material and forms all the neutral and molecular lines as well as most of the ionic lines, a second component at +22 km/s which must contribute to the strong UV lines of most ions, and a third component at roughly +2 km/s which gives rise to a strong Si III line at 1206 A. It is also found that the UV extinction curve has a somewhat steep far-UV rise, indicating the presence of a substantial number of small grains, and that about 30% of the hydrogen nuclei over the entire line of sight are in molecular form.

  16. Zeta potential and Raman studies of PVP capped Bi2S3 nanoparticles synthesized by polyol method

    NASA Astrophysics Data System (ADS)

    Tarachand, Sathe, Vasant G.; Okram, Gunadhor S.

    2018-05-01

    Here we report the synthesis and characterisation of polyvinylpyrrolidone (PVP) capped Bi2S3 nanoparticles via one step catalyst-free polyol method. Raman spectroscopy, dynamic light scattering and zeta potential analysis were performed on it. Rietveld refinement of powder XRD of PVP capped samples confirmed the formation of single phase orthorhombic Bi2S3 for all PVP capped samples. The presence of eight obvious Raman modes further confirmed the formation of stoichiometric Bi2S3. Dynamic light scattering (DLS) studies show a clear increase in hydrodynamic diameter for samples made with increasing PVP concentration. Particle size obtained from DLS and XRD (using Scherrer's formula) combine with change in full width half maxima of Raman modes collectively suggest overall improvement in crystallinity and quality of product on introducing PVP. In zeta potential (ζ) measurement, steric hindrance of carbon chains plays very crucial role and a systematic reduction of ζ value is observed for samples made with decreasing PVP concentration. An isoelectric point is obtained for sample made with low PVP (1g). Present results are likely to open a window for its medical and catalytic applications.

  17. The Isolation of DNA by Polycharged Magnetic Particles: An Analysis of the Interaction by Zeta Potential and Particle Size.

    PubMed

    Haddad, Yazan; Xhaxhiu, Kledi; Kopel, Pavel; Hynek, David; Zitka, Ondrej; Adam, Vojtech

    2016-04-20

    Magnetic isolation of biological targets is in major demand in the biotechnology industry today. This study considers the interaction of four surface-modified magnetic micro- and nanoparticles with selected DNA fragments. Different surface modifications of nanomaghemite precursors were investigated: MAN37 (silica-coated), MAN127 (polyvinylpyrrolidone-coated), MAN158 (phosphate-coated), and MAN164 (tripolyphosphate-coated). All particles were positive polycharged agglomerated monodispersed systems. Mean particle sizes were 0.48, 2.97, 2.93, and 3.67 μm for MAN37, MAN127, MAN164, and MAN158, respectively. DNA fragments exhibited negative zeta potential of -0.22 mV under binding conditions (high ionic strength, low pH, and dehydration). A decrease in zeta potential of particles upon exposure to DNA was observed with exception of MAN158 particles. The measured particle size of MAN164 particles increased by nearly twofold upon exposure to DNA. Quantitative PCR isolation of DNA with a high retrieval rate was observed by magnetic particles MAN127 and MAN164. Interaction between polycharged magnetic particles and DNA is mediated by various binding mechanisms such as hydrophobic and electrostatic interactions. Future development of DNA isolation technology requires an understanding of the physical and biochemical conditions of this process.

  18. Fuzzy-PI-based centralised control of semi-isolated FP-SEPIC/ZETA BDC in a PV/battery hybrid system

    NASA Astrophysics Data System (ADS)

    Mahendran, Venmathi; Ramabadran, Ramaprabha

    2016-11-01

    Multiport converters with centralised controller have been most commonly used in stand-alone photovoltaic (PV)/battery hybrid system to supply the load smoothly without any disturbances. This study presents the performance analysis of four-port SEPIC/ZETA bidirectional converter (FP-SEPIC/ZETA BDC) using various types of centralised control schemes like Fuzzy tuned proportional integral controller (Fuzzy-PI), fuzzy logic controller (FLC) and conventional proportional integral (PI) controller. The proposed FP-SEPIC/ZETA BDC with various control strategy is derived for simultaneous power management of a PV source using distributed maximum power point tracking (DMPPT) algorithm, a rechargeable battery, and a load by means of centralised controller. The steady state and the dynamic response of the FP-SEPIC/ZETA BDC are analysed using three different types of controllers under line and load regulation. The Fuzzy-PI-based control scheme improves the dynamic response of the system when compared with the FLC and the conventional PI controller. The power balance between the ports is achieved by pseudorandom carrier modulation scheme. The response of the FP-SEPIC/ZETA BDC is also validated experimentally using hardware prototype model of 500 W system. The effectiveness of the control strategy is validated using simulation and experimental results.

  19. NPR design basis

    SciTech Connect

    Locke, G.L.

    1958-09-08

    The design basis is composed of requirements and conditions for the design of the reactor plant (composed of the reactor and heat dissipation system). Its intent is to insure that the final product meets the economic, safety, and technical objectives of the project. The design basis is dependent on the ground rules, objectives, technical criteria, and practical design considerations. This document is being issued with the understanding that these items are not yet firmly established in all respects, and therefore, the numbers put down here are subject to change. Consideration of the spectrum of probable changes that might be mademore » leads to the conclusion that the numbers here are close to the final ones and are satisfactory as a basis for the initial stages of design. Some numbers are omitted because of insufficient data at this time.« less

  20. Performance Basis for Airborne Separation

    NASA Technical Reports Server (NTRS)

    Wing, David J.

    2008-01-01

    Emerging applications of Airborne Separation Assistance System (ASAS) technologies make possible new and powerful methods in Air Traffic Management (ATM) that may significantly improve the system-level performance of operations in the future ATM system. These applications typically involve the aircraft managing certain components of its Four Dimensional (4D) trajectory within the degrees of freedom defined by a set of operational constraints negotiated with the Air Navigation Service Provider. It is hypothesized that reliable individual performance by many aircraft will translate into higher total system-level performance. To actually realize this improvement, the new capabilities must be attracted to high demand and complexity regions where high ATM performance is critical. Operational approval for use in such environments will require participating aircraft to be certified to rigorous and appropriate performance standards. Currently, no formal basis exists for defining these standards. This paper provides a context for defining the performance basis for 4D-ASAS operations. The trajectory constraints to be met by the aircraft are defined, categorized, and assessed for performance requirements. A proposed extension of the existing Required Navigation Performance (RNP) construct into a dynamic standard (Dynamic RNP) is outlined. Sample data is presented from an ongoing high-fidelity batch simulation series that is characterizing the performance of an advanced 4D-ASAS application. Data of this type will contribute to the evaluation and validation of the proposed performance basis.

  1. Economic communication model set

    NASA Astrophysics Data System (ADS)

    Zvereva, Olga M.; Berg, Dmitry B.

    2017-06-01

    This paper details findings from the research work targeted at economic communications investigation with agent-based models usage. The agent-based model set was engineered to simulate economic communications. Money in the form of internal and external currencies was introduced into the models to support exchanges in communications. Every model, being based on the general concept, has its own peculiarities in algorithm and input data set since it was engineered to solve the specific problem. Several and different origin data sets were used in experiments: theoretic sets were estimated on the basis of static Leontief's equilibrium equation and the real set was constructed on the basis of statistical data. While simulation experiments, communication process was observed in dynamics, and system macroparameters were estimated. This research approved that combination of an agent-based and mathematical model can cause a synergetic effect.

  2. A novel conductivity mechanism of highly disordered carbon systems based on an investigation of graph zeta function

    NASA Astrophysics Data System (ADS)

    Matsutani, Shigeki; Sato, Iwao

    2017-09-01

    In the previous report (Matsutani and Suzuki, 2000 [21]), by proposing the mechanism under which electric conductivity is caused by the activational hopping conduction with the Wigner surmise of the level statistics, the temperature-dependent of electronic conductivity of a highly disordered carbon system was evaluated including apparent metal-insulator transition. Since the system consists of small pieces of graphite, it was assumed that the reason why the level statistics appears is due to the behavior of the quantum chaos in each granular graphite. In this article, we revise the assumption and show another origin of the Wigner surmise, which is more natural for the carbon system based on a recent investigation of graph zeta function in graph theory. Our method can be applied to the statistical treatment of the electronic properties of the randomized molecular system in general.

  3. Variability in Bioreactivity Linked to Changes in Size and Zeta Potential of Diesel Exhaust Particles in Human Immune Cells

    PubMed Central

    Sarkar, Srijata; Zhang, Lin; Subramaniam, Prasad; Lee, Ki-Bum; Garfunkel, Eric; Strickland, Pamela A. Ohman.; Mainelis, Gediminas; Lioy, Paul J.; Tetley, Teresa D.; Chung, Kian Fan; Zhang, Junfeng; Ryan, Mary; Porter, Alex; Schwander, Stephan

    2014-01-01

    Acting as fuel combustion catalysts to increase fuel economy, cerium dioxide (ceria, CeO2) nanoparticles have been used in Europe as diesel fuel additives (Envirox™). We attempted to examine the effects of particles emitted from a diesel engine burning either diesel (diesel exhaust particles, DEP) or diesel doped with various concentrations of CeO2 (DEP-Env) on innate immune responses in THP-1 and primary human peripheral blood mononuclear cells (PBMC). Batches of DEP and DEP-Env were obtained on three separate occasions using identical collection and extraction protocols with the aim of determining the reproducibility of particles generated at different times. However, we observed significant differences in size and surface charge (zeta potential) of the DEP and DEP-Env across the three batches. We also observed that exposure of THP-1 cells and PBMC to identical concentrations of DEP and DEP-Env from the three batches resulted in statistically significant differences in bioreactivity as determined by IL-1β, TNF-α, IL-6, IFN-γ, and IL-12p40 mRNA (by qRT-PCR) and protein expression (by ELISPOT assays). Importantly, bioreactivity was noted in very tight ranges of DEP size (60 to 120 nm) and zeta potential (−37 to −41 mV). Thus, these physical properties of DEP and DEP-Env were found to be the primary determinants of the bioreactivity measured in this study. Our findings also point to the potential risk of over- or under- estimation of expected bioreactivity effects (and by inference of public health risks) from bulk DEP use without taking into account potential batch-to-batch variations in physical (and possibly chemical) properties. PMID:24825358

  4. Kinetic temperature in the interior of the zeta Ophiuchi cloud from Copernicus observations of interstellar C/sub 2/

    SciTech Connect

    Snow, T.P. Jr.

    1978-03-15

    The Copernicus ultraviolet telescope-spectrometer has been used to carry out sensitive scans of the D/sup 1/..sigma../sub u//sup +/-X/sup 1/..sigma../sup +/ (0-0) transition of C/sub 2/ at 2312 A in the spectrum of zeta Ophiuchi. An absorption feature was detected at the 4sigma level of significance at the position of the R(0) line, implying a column density of 1.22 x 10/sup 12/ cm/sup -2/ for the J=0 level. An upper limit on the R(2) line of 2.6 mA, yielding N(J=2) < or =1.66 x 10/sup 12/ cm/sup -2/ implies a rotational temperature of at most 22 K, with a high probabilitymore » that T/sub rot/< or =16 K. This represents the limit on the kinetic temperature of the ambient gas because radiative transitions between the rotational levels of this homonuclear molecule are forbidden. The total column density of C/sub 2/ is estimated to be at most 3.2 x 10/sup 12/, a factor of approx.4 below the abundance expected from a recent model calculation for the zeta Oph cloud. The discrepancy may be due to an incorrect branching ratio for the reaction CH)..-->..CH/sub 2/+H ..-->..+H/sub 2/, to the presence of greater depletion of carbon in the cloud core than assumed, to an underestimate of the photodissociation rate for C/sub 2/, or to an incorrect oscillator strength.« less

  5. Molecular structure, FT IR, NMR, UV, NBO and HOMO-LUMO of 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile by DFT/B3LYP and PBEPBE methods with LanL2DZ and 6-311++G(d,2p) basis sets.

    PubMed

    Khajehzadeh, Mostafa; Moghadam, Majid

    2017-06-05

    Structural and molecular properties of antidepressants 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile were examined using quantum mechanics of Density Functional Theory (DFT)/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets to study the therapeutic properties of the drug. For this, the structure of desired material was optimized by the computer calculation method and with the use of powerful Gaussian 09 software. Then the lowest energy value and the bond length, bond angle and dihedral angle between its constituent atoms in the crystal structure of the desired material were measured from the optimized values. Then the amount of positive and negative charges, polarizability and dipole moment of its atoms using Mulliken charge and Natural atomic charges, DFT/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets were determined and the results were compared with each other for individual atoms and by mentioned methods. Also the type of stretching vibrations and bending vibrations between the constituent atoms of the molecule were specified using mentioned computational methods and FT IR vibrational spectra. The experimental spectrum of this material was taken to determine the functional groups and the computational and experimental values were compared to each other and Nuclear Magnetic Resonance (NMR) was used to specify the isomer shift between the carbons and protons in the presence of polar and nonpolar solvents. Also Natural Bond Orbital (NBO) was used to determine the type of electron transfers in σ→σ∗ and π→π∗ and LP(1)→σ∗ and LP(2)→σ∗ and the amount of hardness and softness in molecule was determined using the difference between ionization energy and electron affinity energy in constituent atoms of that molecule in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and in the presence of solvents H 2 O, CH 3 CN and C 6 H 12

  6. Molecular structure, FT IR, NMR, UV, NBO and HOMO-LUMO of 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile by DFT/B3LYP and PBEPBE methods with LanL2DZ and 6-311 ++G(d,2p) basis sets

    NASA Astrophysics Data System (ADS)

    Khajehzadeh, Mostafa; Moghadam, Majid

    2017-06-01

    Structural and molecular properties of antidepressants 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile were examined using quantum mechanics of Density Functional Theory (DFT)/B3LYP and PBEPBE methods with 6-311 ++ G(d,2p) and LanL2DZ basis sets to study the therapeutic properties of the drug. For this, the structure of desired material was optimized by the computer calculation method and with the use of powerful Gaussian 09 software. Then the lowest energy value and the bond length, bond angle and dihedral angle between its constituent atoms in the crystal structure of the desired material were measured from the optimized values. Then the amount of positive and negative charges, polarizability and dipole moment of its atoms using Mulliken charge and Natural atomic charges, DFT/B3LYP and PBEPBE methods with 6-311 ++ G(d,2p) and LanL2DZ basis sets were determined and the results were compared with each other for individual atoms and by mentioned methods. Also the type of stretching vibrations and bending vibrations between the constituent atoms of the molecule were specified using mentioned computational methods and FT IR vibrational spectra. The experimental spectrum of this material was taken to determine the functional groups and the computational and experimental values were compared to each other and Nuclear Magnetic Resonance (NMR) was used to specify the isomer shift between the carbons and protons in the presence of polar and nonpolar solvents. Also Natural Bond Orbital (NBO) was used to determine the type of electron transfers in σ → σ ∗ and π → π ∗ and LP(1) → σ ∗ and LP(2) → σ ∗ and the amount of hardness and softness in molecule was determined using the difference between ionization energy and electron affinity energy in constituent atoms of that molecule in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and in the presence of solvents H2O, CH3CN

  7. The ng_ζ1 toxin of the gonococcal epsilon/zeta toxin/antitoxin system drains precursors for cell wall synthesis.

    PubMed

    Rocker, Andrea; Peschke, Madeleine; Kittilä, Tiia; Sakson, Roman; Brieke, Clara; Meinhart, Anton

    2018-04-27

    Bacterial toxin-antitoxin complexes are emerging as key players modulating bacterial physiology as activation of toxins induces stasis or programmed cell death by interference with vital cellular processes. Zeta toxins, which are prevalent in many bacterial genomes, were shown to interfere with cell wall formation by perturbing peptidoglycan synthesis in Gram-positive bacteria. Here, we characterize the epsilon/zeta toxin-antitoxin (TA) homologue from the Gram-negative pathogen Neisseria gonorrhoeae termed ng_ɛ1 / ng_ζ1. Contrary to previously studied streptococcal epsilon/zeta TA systems, ng_ɛ1 has an epsilon-unrelated fold and ng_ζ1 displays broader substrate specificity and phosphorylates multiple UDP-activated sugars that are precursors of peptidoglycan and lipopolysaccharide synthesis. Moreover, the phosphorylation site is different from the streptococcal zeta toxins, resulting in a different interference with cell wall synthesis. This difference most likely reflects adaptation to the individual cell wall composition of Gram-negative and Gram-positive organisms but also the distinct involvement of cell wall components in virulence.

  8. Expression of the growth factor pleiotrophin and its receptor protein tyrosine phosphatase beta/zeta in the serum, cartilage and subchondral bone of patients with osteoarthritis.

    PubMed

    Kaspiris, Angelos; Mikelis, Constantinos; Heroult, Melanie; Khaldi, Lubna; Grivas, Theodoros B; Kouvaras, Ioannis; Dangas, Spyridon; Vasiliadis, Elias; Lioté, Frédéric; Courty, José; Papadimitriou, Evangelia

    2013-07-01

    Pleiotrophin is a heparin-binding growth factor expressed in embryonic but not mature cartilage, suggesting a role in cartilage development. Elucidation of the molecular changes observed during the remodelling process in osteoarthritis is of paramount importance. This study aimed to investigate serum pleiotrophin levels and expression of pleiotrophin and its receptor protein tyrosine phosphatase beta/zeta in the cartilage and subchondral bone of osteoarthritis patients. Serum samples derived from 16 osteoarthritis patients and 18 healthy donors. Pleiotrophin and receptor protein tyrosine phosphatase beta/zeta in the cartilage and subchondral bone were studied in 29 patients who had undergone total knee or hip replacement for primary osteoarthritis and in 10 control patients without macroscopic osteoarthritis changes. Serum pleiotrophin levels and expression of pleiotrophin in chondrocytes and subchondral bone osteocytes significantly increased in osteoarthritis patients graded Ahlback II to III. Receptor protein tyrosine phosphatase beta/zeta was mainly detected in the subchondral bone osteocytes of patients with moderate osteoarthritis and as disease severity increased, in the osteocytes and bone lining cells of the distant trabeculae. These data render pleiotrophin and receptor protein tyrosine phosphatase beta/zeta promising candidates for further studies towards developing targeted therapeutic schemes for osteoarthritis. Copyright © 2012 Société française de rhumatologie. Published by Elsevier SAS. All rights reserved.

  9. A zeta potential value determines the aggregate's size of penta-substituted [60]fullerene derivatives in aqueous suspension whereas positive charge is required for toxicity against bacterial cells.

    PubMed

    Deryabin, Dmitry G; Efremova, Ludmila V; Vasilchenko, Alexey S; Saidakova, Evgeniya V; Sizova, Elena A; Troshin, Pavel A; Zhilenkov, Alexander V; Khakina, Ekaterina A; Khakina, Ekaterina E

    2015-08-08

    The cause-effect relationships between physicochemical properties of amphiphilic [60]fullerene derivatives and their toxicity against bacterial cells have not yet been clarified. In this study, we report how the differences in the chemical structure of organic addends in 10 originally synthesized penta-substituted [60]fullerene derivatives modulate their zeta potential and aggregate's size in salt-free and salt-added aqueous suspensions as well as how these physicochemical characteristics affect the bioenergetics of freshwater Escherichia coli and marine Photobacterium phosphoreum bacteria. Dynamic light scattering, laser Doppler micro-electrophoresis, agarose gel electrophoresis, atomic force microscopy, and bioluminescence inhibition assay were used to characterize the fullerene aggregation behavior in aqueous solution and their interaction with the bacterial cell surface, following zeta potential changes and toxic effects. Dynamic light scattering results indicated the formation of self-assembled [60]fullerene aggregates in aqueous suspensions. The measurement of the zeta potential of the particles revealed that they have different surface charges. The relationship between these physicochemical characteristics was presented as an exponential regression that correctly described the dependence of the aggregate's size of penta-substituted [60]fullerene derivatives in salt-free aqueous suspension from zeta potential value. The prevalence of DLVO-related effects was shown in salt-added aqueous suspension that decreased zeta potential values and affected the aggregation of [60]fullerene derivatives expressed differently for individual compounds. A bioluminescence inhibition assay demonstrated that the toxic effect of [60]fullerene derivatives against E. coli cells was strictly determined by their positive zeta potential charge value being weakened against P. phosphoreum cells in an aquatic system of high salinity. Atomic force microscopy data suggested that the

  10. 48 CFR 25.504-4 - Group award basis.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American Act applies and the acquisition cannot be set aside for small...

  11. 48 CFR 25.504-4 - Group award basis.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American Act applies and the acquisition cannot be set aside for small...

  12. 48 CFR 25.504-4 - Group award basis.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 1 2014-10-01 2014-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American statute applies and the acquisition cannot be set aside for...

  13. 48 CFR 25.504-4 - Group award basis.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 1 2012-10-01 2012-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American Act applies and the acquisition cannot be set aside for small...

  14. 48 CFR 25.504-4 - Group award basis.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Group award basis. 25.504... SOCIOECONOMIC PROGRAMS FOREIGN ACQUISITION Evaluating Foreign Offers-Supply Contracts 25.504-4 Group award basis... a group basis. Assume the Buy American Act applies and the acquisition cannot be set aside for small...

  15. HD 93521, zeta Ophiuchi, and the effects of rapid rotation on the atmospheres and winds of 09.5 V stars

    NASA Technical Reports Server (NTRS)

    Massa, Derck

    1995-01-01

    Both low- and high-resolution IUE spectra of the rapidly rotating 09.5 V stars HD 93521 and zeta Oph are used to develop a coherent picture of the effects of rapid rotation on the atmospheres and winds of late, main-sequence O stars. The observational consequences are by far the strongest on HD 93521, most likely because it is being viewed nearly equator-on. In particular, it is shown that HD 93521 (1) a much smaller UV optical flux ratio than expected, (2) UV photospheric lines indicative of a BO supergiant, (3) an abnormally strong N v wind doublet, and (4) wind profiles suggesting that its wind has latitudinally dependent properties. Because HD 93521 has a larger observed v sin i than zeta Oph and yet its H-alpha emission is no stronger than in zeta Oph, it is speculated that zeta Oph actually rotates as fast or faster than HD 93521, but has a smaller sin i. Because zeta Oph is significantly reddened, nothing can be determined about its intrinsic UV energy distribution. However, it is shown that its UV photospheric lines are a bit peculiar and that its C IV and N V wind doublets are abnormally strong and have unusual profiles. The C IV profile agrees with models of a rotationally distorted wind similar to the one in HD 93521, except viewed at an angle i approximately 60 deg-80 deg. The spectral peculiarities of both stars are attributed to the combined effects of gravity darkening of their atmospheres and rotational distortion of their winds. The differences between their spectra are interpreted as the result of being viewed at different inclination angles. Because of the gravity darkening, atmospheric analyses of either star based on single temperature and surface gravity model atmospheres are probably unreliable. Finally, I describe how different effects conspire to make the spectroscopic signatures of gravity darkening so pronounced at 09.5 V.

  16. Detection of GRB 060927 at zeta = 5.47: Implications for the Use of Gamma-Ray Bursts as Probes of the End of the Dark Ages

    NASA Technical Reports Server (NTRS)

    Ruiz-Velasco, A. E.; Swan, H.; Troja, E.; Malesani, D.; Fynbo, J. P. U.; Sterling, R. L. C.; Xu, D.; Aharonian, F.; Akerlof, C.; Andersen, M. I.; hide

    2007-01-01

    We report on follow-up observations of the gamma-ray burst GRB 060927 using the robotic ROTSE-IIIa telescope and a suite of larger aperture groundbased telescopes. An optical afterglow was detected 20 s after the burst, the earliest rest-frame detection of optical emission from any GRB. Spectroscopy performed with the VLT about 13 hours after the trigger shows a continuum break at lambda approx. equals 8070 A, produced by neutral hydrogen absorption at zeta = 5.6. We also detect an absorption line at 8158 A which we interpret as Si II lambda 1260 at zeta = 5.467. Hence, GRB 060927 is the second most distant GRB with a spectroscopically measured redshift. The shape of the red wing of the spectral break can be fitted by a damped Ly(alpha) profile with a column density with log(N(sub HI)/sq cm) = 22.50 +/- 0.15. We discuss the implications of this work for the use of GRBs as probes of the end of the dark ages and draw three main conclusions: i) GRB afterglows originating from zeta greater than or approx. equal to 6 should be relatively easy to detect from the ground, but rapid near-infrared monitoring is necessary to ensure that they are found; ii) The presence of large H I column densities in some GRBs host galaxies at zeta > 5 makes the use of GRBs to probe the reionization epoch via spectroscopy of the red damping wing challenging; iii) GRBs appear crucial to locate typical star-forming galaxies at zeta > 5 and therefore the type of galaxies responsible for the reionization of the universe.

  17. Neuronal Basis of Learning.

    DTIC Science & Technology

    1986-03-03

    First, antagonists such as scopolamine (as opposed to agonists such as oxotremorine ) enhance one-trial Pavlovian conditioning, but do not seem to...intraperitoneal injection of scopolamine 1 hr before training; another set received an injection of oxotremorine (middle pair of illustrations); and

  18. The Emotional and Moral Basis of Rationality

    ERIC Educational Resources Information Center

    Boostrom, Robert

    2013-01-01

    This chapter explores the basis of rationality, arguing that critical thinking tends to be taught in schools as a set of skills because of the failure to recognize that choosing to think critically depends on the prior development of stable sentiments or moral habits that nourish a rational self. Primary among these stable sentiments are the…

  19. The Biological Basis of Learning and Individuality.

    ERIC Educational Resources Information Center

    Kandel, Eric R.; Hawkins, Robert D.

    1992-01-01

    Describes the biological basis of learning and individuality. Presents an overview of recent discoveries that suggest learning engages a simple set of rules that modify the strength of connection between neurons in the brain. The changes are cited as playing an important role in making each individual unique. (MCO)

  20. Characterization and Expression Pattern Analysis of the T-Complex Protein-1 Zeta Subunit in Musca domestica L (Diptera).

    PubMed

    Zhao, Xuejun; Xiu, Jiangfan; Li, Yan; Ma, Huiling; Wu, Jianwei; Wang, Bo; Guo, Guo

    2017-07-01

    Chaperonins, belonging to the T-complex protein-1 (TCP-1) family, assist in the correct folding of nascent and misfolded proteins. It is well-known that in mammals, the zeta subunit of the TCP-1 complex (TCP-1ζ) plays a vital role in the folding and assembly of cytoskeleta proteins. This study reported for the first time the cloning, characterization and expression pattern analysis of the TCP-1ζ from Musca domestica, which was named as MdTCP-1ζ. The MdTCP-1ζ cDNA is 1,803 bp long with a 1,596 bp open reading frame that encodes a protein with 531 bp amino acids. The analysis of the transcriptional profile of MdTCP-1ζ using qRT-PCR revealed relatively high expression in the salivary glands and trachea at the tissues while among the developmental stages. The highest expression was observed only in the eggs suggesting that the MdTCP-1ζ may play a role in embryonic development. The expression of MdTCP-1ζ was also significantly induced after exposure to short-term heat shock and infection by Escherichia coli, Staphylococcus aureus, or Candida albicans. This suggested that MdTCP-1ζ may take part in the immune responses of housefly and perhaps contribute to the protection against cellular injury. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

  1. Electroosmotic flow in a rectangular channel with variable wall zeta-potential: comparison of numerical simulation with asymptotic theory.

    PubMed

    Datta, Subhra; Ghosal, Sandip; Patankar, Neelesh A

    2006-02-01

    Electroosmotic flow in a straight micro-channel of rectangular cross-section is computed numerically for several situations where the wall zeta-potential is not constant but has a specified spatial variation. The results of the computation are compared with an earlier published asymptotic theory based on the lubrication approximation: the assumption that any axial variations take place on a long length scale compared to a characteristic channel width. The computational results are found to be in excellent agreement with the theory even when the scale of axial variations is comparable to the channel width. In the opposite limit when the wavelength of fluctuations is much shorter than the channel width, the lubrication theory fails to describe the solution either qualitatively or quantitatively. In this short wave limit the solution is well described by Ajdari's theory for electroosmotic flow between infinite parallel plates (Ajdari, A., Phys. Rev. E 1996, 53, 4996-5005.) The infinitely thin electric double layer limit is assumed in the theory as well as in the simulation.

  2. Assembly dynamics and stability of the pneumococcal epsilon zeta antitoxin toxin (PezAT) system from Streptococcus pneumoniae.

    PubMed

    Mutschler, Hannes; Reinstein, Jochen; Meinhart, Anton

    2010-07-09

    The pneumococcal epsilon zeta antitoxin toxin (PezAT) system is a chromosomally encoded, class II toxin antitoxin system from the human pathogen Streptococcus pneumnoniae. Neutralization of the bacteriotoxic protein PezT is carried out by complex formation with its cognate antitoxin PezA. Here we study the stability of the inhibitory complex in vivo and in vitro. We found that toxin release is impeded in Escherichia coli and Bacillus subtilis due to the proteolytic resistance of PezA once bound to PezT. These findings are supported by in vitro experiments demonstrating a strong thermodynamic stabilization of both proteins upon binding. A detailed kinetic analysis of PezAT assembly revealed that these particular features of PezAT are based on a strong, electrostatically guided binding mechanism leading to a stable toxin antitoxin complex with femtomolar affinity. Our data show that PezAT complex formation is distinct to all other conventional toxin antitoxin modules and a controlled mode of toxin release is required for activation.

  3. The CD3-Zeta Chimeric Antigen Receptor Overcomes TCR Hypo-Responsiveness of Human Terminal Late-Stage T Cells

    PubMed Central

    Awerkiew, Sabine; Schmidt, Annette; Hombach, Andreas A.; Pfister, Herbert; Abken, Hinrich

    2012-01-01

    Adoptive therapy of malignant diseases with tumor-specific cytotoxic T cells showed remarkable efficacy in recent trials. Repetitive T cell receptor (TCR) engagement of target antigen, however, inevitably ends up in hypo-responsive cells with terminally differentiated KLRG-1+ CD57+ CD7− phenotype limiting their therapeutic efficacy. We here revealed that hypo-responsiveness of CMV-specific late-stage CD8+ T cells is due to reduced TCR synapse formation compared to younger cells. Membrane anchoring of TCR components contributes to T cell hypo-responsiveness since dislocation of galectin-3 from the synapse by swainsonine restored both TCR synapse formation and T cell response. Transgenic expression of a CD3-zeta signaling chimeric antigen receptor (CAR) recovered hypo-responsive T cells to full effector functions indicating that the defect is restricted to TCR membrane components while synapse formation of the transgenic CAR was not blocked. CAR engineered late-stage T cells released cytokines and mediated redirected cytotoxicity as efficiently as younger effector T cells. Our data provide a rationale for TCR independent, CAR mediated activation in the adoptive cell therapy to avoid hypo-responsiveness of late-stage T cells upon repetitive antigen encounter. PMID:22292024

  4. pH Effects on solubility, zeta potential, and correlation between antibacterial activity and molecular weight of chitosan.

    PubMed

    Chang, Shun-Hsien; Lin, Hong-Ting Victor; Wu, Guan-James; Tsai, Guo Jane

    2015-12-10

    Six chitosans with molecular weights (MWs) of 300, 156, 72.1, 29.2, 7.1, and 3.3 kDa were prepared by cellulase degradation of chitosan (300 kDa) and ultrafiltration techniques. We examined the correlation between activity against Escherichia coli and Staphylococcus aureus and chitosan MW, and provided the underlying explanation. In acidic pH conditions, the chitosan activity increased with increasing MW, irrespective of the temperature and bacteria tested. However, at neutral pH, chitosan activity increased as the MW decreased, and little activity was observed for chitosans with MW >29.2 kDa. At pH 5.0 and 6.0, chitosans exhibited good water solubility and zeta potential (ZP) decreased with the MW, whereas the solubility and ZP of the chitosans decreased with increasing MW at pH 7.0. Particularly, low solubility and negative ZP values were determined for chitosans with MW >29.2 kDa, which may explain the loss of their antibacterial activity at pH 7.0. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Does advancing male age influence the expression levels and localisation patterns of phospholipase C zeta (PLCζ) in human sperm?

    PubMed Central

    Yeste, Marc; Jones, Celine; Amdani, Siti Nornadhirah; Yelumalai, Suseela; Mounce, Ginny; da Silva, Sarah J. Martins; Child, Tim; Coward, Kevin

    2016-01-01

    Socio-economic factors have led to an increasing trend for couples to delay parenthood. However, advancing age exerts detrimental effects upon gametes which can have serious consequences upon embryo viability. While such effects are well documented for the oocyte, relatively little is known with regard to the sperm. One fundamental role of sperm is to activate the oocyte at fertilisation, a process initiated by phospholipase C zeta (PLCζ), a sperm-specific protein. While PLCζ deficiency can lead to oocyte activation deficiency and infertility, it is currently unknown whether the expression or function of PLCζ is compromised by advancing male age. Here, we evaluate sperm motility and the proportion of sperm expressing PLCζ in 71 males (22–54 years; 44 fertile controls and 27 infertile patients), along with total levels and localisation patterns of PLCζ within the sperm head. Three different statistical approaches were deployed with male age considered both as a categorical and a continuous factor. While progressive motility was negatively correlated with male age, all three statistical models concurred that no PLCζ–related parameter was associated with male age, suggesting that advancing male age is unlikely to cause problems in terms of the sperm’s fundamental ability to activate an oocyte. PMID:27270687

  6. HST-WFC3 Near-Infrared Spectroscopy of Quenched Galaxies at zeta approx 1.5 from the WISP Survey: Stellar Populations Properties

    NASA Technical Reports Server (NTRS)

    Bedregal, A. G.; Scarlata, C.; Henry, A. L.; Atek, H.; Rafelski, M.; Teplitz, H. I.; Dominguez, A.; Siana, B.; Colbert, J. W.; Malkan, M.; hide

    2013-01-01

    We combine Hubble Space Telescope (HST) G102 and G141 near-IR (NIR) grism spectroscopy with HST/WFC3- UVIS, HST/WFC3-IR, and Spitzer/IRAC [3.6 microns] photometry to assemble a sample of massive (log(Mstar/M solar mass) at approx 11.0) and quenched (specific star formation rate < 0.01 G/yr(exp -1) galaxies at zeta approx 1.5. Our sample of 41 galaxies is the largest with G102+G141 NIR spectroscopy for quenched sources at these redshifts. In contrast to the local universe, zeta approx 1.5 quenched galaxies in the high-mass range have a wide range of stellar population properties. We find that their spectral energy distributions (SEDs) are well fitted with exponentially decreasing star formation histories and short star formation timescales (tau less than or equal to 100 M/yr). Quenched galaxies also show a wide distribution in ages, between 1 and 4 G/yr. In the (u - r)0-versus-mass space quenched galaxies have a large spread in rest-frame color at a given mass. Most quenched galaxies populate the zeta appro. 1.5 red sequence (RS), but an important fraction of them (32%) have substantially bluer colors. Although with a large spread, we find that the quenched galaxies on the RS have older median ages (3.1 G/yr) than the quenched galaxies off the RS (1.5 G/yr). We also show that a rejuvenated SED cannot reproduce the observed stacked spectra of (the bluer) quenched galaxies off the RS. We derive the upper limit on the fraction of massive galaxies on the RS at zeta approx 1.5 to be <43%.We speculate that the young quenched galaxies off the RS are in a transition phase between vigorous star formation at zeta > 2 and the zeta approx 1.5 RS. According to their estimated ages, the time required for quenched galaxies off the RS to join their counterparts on the z approx. 1.5 RS is of the order of approx. 1G/yr.

  7. A practical radial basis function equalizer.

    PubMed

    Lee, J; Beach, C; Tepedelenlioglu, N

    1999-01-01

    A radial basis function (RBF) equalizer design process has been developed in which the number of basis function centers used is substantially fewer than conventionally required. The reduction of centers is accomplished in two-steps. First an algorithm is used to select a reduced set of centers that lie close to the decision boundary. Then the centers in this reduced set are grouped, and an average position is chosen to represent each group. Channel order and delay, which are determining factors in setting the initial number of centers, are estimated from regression analysis. In simulation studies, an RBF equalizer with more than 2000-to-1 reduction in centers performed as well as the RBF equalizer without reduction in centers, and better than a conventional linear equalizer.

  8. Text Sets.

    ERIC Educational Resources Information Center

    Giorgis, Cyndi; Johnson, Nancy J.

    2002-01-01

    Presents annotations of approximately 30 titles grouped in text sets. Defines a text set as five to ten books on a particular topic or theme. Discusses books on the following topics: living creatures; pirates; physical appearance; natural disasters; and the Irish potato famine. (SG)

  9. Basis Selection for Wavelet Regression

    NASA Technical Reports Server (NTRS)

    Wheeler, Kevin R.; Lau, Sonie (Technical Monitor)

    1998-01-01

    A wavelet basis selection procedure is presented for wavelet regression. Both the basis and the threshold are selected using cross-validation. The method includes the capability of incorporating prior knowledge on the smoothness (or shape of the basis functions) into the basis selection procedure. The results of the method are demonstrated on sampled functions widely used in the wavelet regression literature. The results of the method are contrasted with other published methods.

  10. First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems.

    PubMed

    Jaén-Luchoro, Daniel; Aliaga-Lozano, Francisco; Gomila, Rosa Maria; Gomila, Margarita; Salvà-Serra, Francisco; Lalucat, Jorge; Bennasar-Figueras, Antoni

    2017-01-01

    A putative type II toxin-antitoxin (TA) system was found in the clinical isolate Mycobacterium sp. MHSD3, a strain closely related to Mycobacterium chelonae. Further analyses of the protein sequences of the two genes revealed the presence of domains related to a TA system. BLAST analyses indicated the presence of closely related proteins in the genomes of other recently published M. chelonae strains. The functionality of both elements of the TA system was demonstrated when expressed in Escherichia coli cells, and the predicted structure of the toxin is very similar to those of well-known zeta-toxins, leading to the definition of a type II TA system similar to epsilon/zeta TA systems in strains that are closely related to M. chelonae.

  11. Toxicity and Metabolism of Zeta-Cypermethrin in Field-Collected and Laboratory Strains of the Neotropical Predator Chrysoperla externa Hagen (Neuroptera: Chrysopidae).

    PubMed

    Haramboure, M; Smagghe, G; Niu, J; Christiaens, O; Spanoghe, P; Alzogaray, R A

    2017-06-01

    Resistance to pesticides has been studied in several insect pests, but information on the natural enemies of pests-including the Neotropical predator Chrysoperla externa Hagen (Neuroptera: Chrysopidae), a major biological control agent in South America-is lacking. We report here a comparative study between a field-collected strain of C. externa subjected to monthly sprayings of pyrethroids and neonicotinoids and a laboratory strain without exposure to pesticides. The tolerance of both strains against zeta-cypermethrin was similar, and addition of the synergist piperonyl butoxide increased the toxicity by 30% in both strains. Gas-chromatography analyses and mixed-function-oxidase measurements indicated similar values in both strains and also confirmed the key role of oxidative metabolism in this species. Because C. externa has maintained a tolerance to zeta-cypermethrin without previous pesticide exposure, this species could potentially be mass-reared and released in fields in the presence of pesticide pressure.

  12. Protein kinase C zeta suppresses low- or high-grade colorectal cancer (CRC) phenotypes by interphase centrosome anchoring.

    PubMed

    Deevi, Ravi Kiran; Javadi, Arman; McClements, Jane; Vohhodina, Jekaterina; Savage, Kienan; Loughrey, Maurice Bernard; Evergren, Emma; Campbell, Frederick Charles

    2018-04-01

    Histological grading provides prognostic stratification of colorectal cancer (CRC) by scoring heterogeneous phenotypes. Features of aggressiveness include aberrant mitotic spindle configurations, chromosomal breakage, and bizarre multicellular morphology, but pathobiology is poorly understood. Protein kinase C zeta (PKCz) controls mitotic spindle dynamics, chromosome segregation, and multicellular patterns, but its role in CRC phenotype evolution remains unclear. Here, we show that PKCz couples genome segregation to multicellular morphology through control of interphase centrosome anchoring. PKCz regulates interdependent processes that control centrosome positioning. Among these, interaction between the cytoskeletal linker protein ezrin and its binding partner NHERF1 promotes the formation of a localized cue for anchoring interphase centrosomes to the cell cortex. Perturbation of these phenomena induced different outcomes in cells with single or extra centrosomes. Defective anchoring of a single centrosome promoted bipolar spindle misorientation, multi-lumen formation, and aberrant epithelial stratification. Collectively, these disturbances induce cribriform multicellular morphology that is typical of some categories of low-grade CRC. By contrast, defective anchoring of extra centrosomes promoted multipolar spindle formation, chromosomal instability (CIN), disruption of glandular morphology, and cell outgrowth across the extracellular matrix interface characteristic of aggressive, high-grade CRC. Because PKCz enhances apical NHERF1 intensity in 3D epithelial cultures, we used an immunohistochemical (IHC) assay of apical NHERF1 intensity as an indirect readout of PKCz activity in translational studies. We show that apical NHERF1 IHC intensity is inversely associated with multipolar spindle frequency and high-grade morphology in formalin-fixed human CRC samples. To conclude, defective PKCz control of interphase centrosome anchoring may underlie distinct categories of

  13. Cell surface groups of two picocyanobacteria strains studied by zeta potential investigations, potentiometric titration, and infrared spectroscopy.

    PubMed

    Dittrich, Maria; Sibler, Sabine

    2005-06-15

    In order to clarify the role of picocyanobacteria in aquatic biogeochemical processes (e.g., calcite precipitation), cell surface properties need to be investigated. An experimental study of the cell surface characteristics of two Synechococcus-type unicellular autotrophic picocyanobacterial strains was carried out. One strain was isolated from Lake Plon and contained phycocyanin, the other strain came from Lago Maggiore and was rich in phycoerythrin. Potentiometric titrations were conducted to determine the different types of sites present on the bacteria cell walls. Infrared spectroscopy allowed characterization of the various functional groups (RNH(2), RCOOH, ROH, RPO(2)) and investigations of zeta potential provided insight into the isoelectrical points of the strains. Titrations reveal three distinct sites on the bacterial surfaces of phycocyanin- and phycoerythrin-rich strains with pK values of 4.8+/-0.3/5.0+/-0.2, 6.6+/-0.2/6.7+/-0.4, and 8.8+/-0.1/8.7+/-0.2, corresponding to carboxyl, phosphate, and amine groups with surface densities of 2.6+/-0.4/7.4+/-1.6 x 10(-4), 1.9+/-0.5/4.4+/-0.8 x 10(-4), and 2.5+/-0.4/4.8+/-0.7 x 10(-4) mol/g of dry bacteria. The deprotonation constants are similar to those of bacterial strains and site densities are also within an order of magnitude of other strains. The phycoerythrin-rich strain had a higher number of binding sites than the phycocyanin-rich strain. The results showed that picocyanobacteria may adsorb either calcium cations or carbonate anions and therefore strongly influence the biogeochemical cycling of calcite in pelagic systems.

  14. Phosphorylated Protein Kinase C (Zeta/Lambda) Expression in Colorectal Adenocarcinoma and Its Correlation with Clinicopathologic Characteristics and Prognosis.

    PubMed

    Yeo, Min-Kyung; Kim, Ji Yeon; Seong, In-Ock; Kim, Jin-Man; Kim, Kyung-Hee

    2017-01-01

    Background: Protein kinase C zeta/lambda (PKCζ/λ) is a family of protein kinase enzymes that contributes to cell proliferation and regulation, which are important for cancer development. PKCζ/λ has been shown to be an important regulator of tumorigenesis in intestinal cancer. The phosphorylated form of PKCζ/λ, p-PKCζ/λ, is suggested as an active form of PKCζ/λ. However, p-PKCζ/λ expression and its clinicopathologic implication in colorectal adenocarcinoma (CRAC) are unclear. Methods: Seven whole-tissue sections of malignant polyps containing both non-neoplastic and neoplastic mucosa, 11 adenomas with low-grade dysplasia, and 173 CRACs were examined by immunohistochemistry and western blot assay for p-PKCζ/λ protein expression. The association of p-PKCζ/λ expression with clinicopathologic factors including patient survival was studied. Results: In non-neoplastic epithelia, p-PKCζ/λ showed a weak cytoplasmic immunostaining. Adenomas and CRACs demonstrated up-regulated p-PKCζ/λ detection. Cytoplasmic p-PKCζ/λ expression was higher in CRAC than in adenoma. In CRACs, p-PKCζ/λ expression was inversely correlated with pathologic TNM stage (I-II versus III-IV) and poor differentiation. Statistical correlations between low expression of p-PKCζ/λ with shortened overall survival and disease-free survival were seen (p=0.004 and p=0.034, respectively). Conclusions: P-PKCζ/λ overexpression is implicated in tumorigenesis but down-regulation was a poor prognostic factor in CRAC.

  15. Protein kinase C zeta suppresses low‐ or high‐grade colorectal cancer (CRC) phenotypes by interphase centrosome anchoring

    PubMed Central

    Deevi, Ravi Kiran; Javadi, Arman; McClements, Jane; Vohhodina, Jekaterina; Savage, Kienan; Loughrey, Maurice Bernard; Evergren, Emma

    2018-01-01

    Abstract Histological grading provides prognostic stratification of colorectal cancer (CRC) by scoring heterogeneous phenotypes. Features of aggressiveness include aberrant mitotic spindle configurations, chromosomal breakage, and bizarre multicellular morphology, but pathobiology is poorly understood. Protein kinase C zeta (PKCz) controls mitotic spindle dynamics, chromosome segregation, and multicellular patterns, but its role in CRC phenotype evolution remains unclear. Here, we show that PKCz couples genome segregation to multicellular morphology through control of interphase centrosome anchoring. PKCz regulates interdependent processes that control centrosome positioning. Among these, interaction between the cytoskeletal linker protein ezrin and its binding partner NHERF1 promotes the formation of a localized cue for anchoring interphase centrosomes to the cell cortex. Perturbation of these phenomena induced different outcomes in cells with single or extra centrosomes. Defective anchoring of a single centrosome promoted bipolar spindle misorientation, multi‐lumen formation, and aberrant epithelial stratification. Collectively, these disturbances induce cribriform multicellular morphology that is typical of some categories of low‐grade CRC. By contrast, defective anchoring of extra centrosomes promoted multipolar spindle formation, chromosomal instability (CIN), disruption of glandular morphology, and cell outgrowth across the extracellular matrix interface characteristic of aggressive, high‐grade CRC. Because PKCz enhances apical NHERF1 intensity in 3D epithelial cultures, we used an immunohistochemical (IHC) assay of apical NHERF1 intensity as an indirect readout of PKCz activity in translational studies. We show that apical NHERF1 IHC intensity is inversely associated with multipolar spindle frequency and high‐grade morphology in formalin‐fixed human CRC samples. To conclude, defective PKCz control of interphase centrosome anchoring may underlie

  16. Generation of nanobubbles by ceramic membrane filters: The dependence of bubble size and zeta potential on surface coating, pore size and injected gas pressure.

    PubMed

    Ahmed, Ahmed Khaled Abdella; Sun, Cuizhen; Hua, Likun; Zhang, Zhibin; Zhang, Yanhao; Zhang, Wen; Marhaba, Taha

    2018-07-01

    Generation of gaseous nanobubbles (NBs) by simple, efficient, and scalable methods is critical for industrialization and applications of nanobubbles. Traditional generation methods mainly rely on hydrodynamic, acoustic, particle, and optical cavitation. These generation processes render issues such as high energy consumption, non-flexibility, and complexity. This research investigated the use of tubular ceramic nanofiltration membranes to generate NBs in water with air, nitrogen and oxygen gases. This system injects pressurized gases through a tubular ceramic membrane with nanopores to create NBs. The effects of membrane pores size, surface energy, and the injected gas pressures on the bubble size and zeta potential were examined. The results show that the gas injection pressure had considerable effects on the bubble size, zeta potential, pH, and dissolved oxygen of the produced NBs. For example, increasing the injection air pressure from 69 kPa to 414 kPa, the air bubble size was reduced from 600 to 340 nm respectively. Membrane pores size and surface energy also had significant effects on sizes and zeta potentials of NBs. The results presented here aim to fill out the gaps of fundamental knowledge about NBs and development of efficient generation methods. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Design and assembly of ternary Pt/Re/SnO2 NPs by controlling the zeta potential of individual Pt, Re, and SnO2 NPs

    NASA Astrophysics Data System (ADS)

    Drzymała, Elżbieta; Gruzeł, Grzegorz; Pajor-Świerzy, Anna; Depciuch, Joanna; Socha, Robert; Kowal, Andrzej; Warszyński, Piotr; Parlinska-Wojtan, Magdalena

    2018-05-01

    In this study Pt, Re, and SnO2 nanoparticles (NPs) were combined in a controlled manner into binary and ternary combinations for a possible application for ethanol oxidation. For this purpose, zeta potentials as a function of the pH of the individual NPs solutions were measured. In order to successfully combine the NPs into Pt/SnO2 and Re/SnO2 NPs, the solutions were mixed together at a pH guaranteeing opposite zeta potentials of the metal and oxide NPs. The individually synthesized NPs and their binary/ternary combinations were characterized by Fourier transform infrared spectroscopy (FTIR) and scanning transmission electron microscopy (STEM) combined with energy dispersive X-ray spectroscopy (EDS) analysis. FTIR and XPS spectroscopy showed that the individually synthesized Pt and Re NPs are metallic and the Sn component was oxidized to SnO2. STEM showed that all NPs are well crystallized and the sizes of the Pt, Re, and SnO2 NPs were 2.2, 1.0, and 3.4 nm, respectively. Moreover, EDS analysis confirmed the successful formation of binary Pt/SnO2 and Re/SnO2 NP, as well as ternary Pt/Re/SnO2 NP combinations. This study shows that by controlling the zeta potential of individual metal and oxide NPs, it is possible to assemble them into binary and ternary combinations. [Figure not available: see fulltext.

  18. Functional Role of Tyr12 in the Catalytic Activity of Novel Zeta-like Glutathione S-transferase from Acidovorax sp. KKS102.

    PubMed

    Shehu, Dayyabu; Alias, Zazali

    2018-05-19

    Glutathione S-transferases (GSTs) are a family of enzymes that function in the detoxification of variety of electrophilic substrates. In the present work, we report a novel zeta-like GST (designated as KKSG9) from the biphenyl/polychlorobiphenyl degrading organism Acidovorax sp. KKS102. KKSG9 possessed low sequence similarity but similar biochemical properties to zeta class GSTs. Functional analysis showed that the enzyme exhibits wider substrate specificity compared to most zeta class GSTs by reacting with 1-chloro-2,4-dinitrobenzene (CDNB), p-nitrobenzyl chloride (NBC), ethacrynic acid (EA), hydrogen peroxide, and cumene hydroperoxide. The enzyme also displayed dehalogenation function against dichloroacetate, permethrin, and dieldrin. The functional role of Tyr12 was also investigated by site-directed mutagenesis. The mutant (Y12C) displayed low catalytic activity and dehalogenation function against all the substrates when compared with the wild type. Kinetic analysis using NBC and GSH as substrates showed that the mutant (Y12C) displayed a higher affinity for NBC when compared with the wild type, however, no significant change in GSH affinity was observed. These findings suggest that the presence of tyrosine residue in the motif might represent an evolutionary trend toward improving the catalytic activity of the enzyme. The enzyme as well could be useful in the bioremediation of various types of organochlorine pollutants.

  19. Characterization of gold nanoparticles with different hydrophilic coatings via capillary electrophoresis and Taylor dispersion analysis. Part I: determination of the zeta potential employing a modified analytic approximation.

    PubMed

    Pyell, Ute; Jalil, Alaa H; Pfeiffer, Christian; Pelaz, Beatriz; Parak, Wolfgang J

    2015-07-15

    Taking gold nanoparticles with different hydrophilic coatings as an example, it is investigated whether capillary electrophoresis in combination with Taylor dispersion analysis allows for the precise determination of mean electrophoretic mobilities, electrophoretic mobility distributions, and zeta potentials in a matrix of exactly known composition and the calibration-free determination of number-weighted mean hydrodynamic radii. Our experimental data confirm that the calculation of the zeta potential for colloidal nanoparticles with ζ>25 mV requires to take the relaxation effect into account. Because of the requirement to avoid particle-wall interactions, a solution of disodiumtetraborate decahydrate (borax) in deionized water had been selected as suitable electrolyte. Measurements of the electrophoretic mobility at different ionic strength and application of the analytic approximation developed by Ohshima show that in the present case of a buffered solution with a weak electrolyte co-ion and a strong electrolyte counterion, the effective ionic drag coefficient should be approximated with the ionic drag coefficient of the counterion. The obtained results are in good agreement with theoretical expectations regarding the dependence of the zeta potential and the electrokinetic surface charge density on the ionic strength. We also show that Taylor dispersion analysis (besides estimation of the number-weighted mean hydrodynamic radius) provides additional information on the type and width of the number-weighted particle distribution. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Goal setting.

    PubMed

    Levin, Roger P

    2003-11-01

    I would not tell any individual what his or her goals should be or what the picture of one's life should look like. I strongly believe in human potential, and I love to see people achieve more of the things that are important to them. The Goal Curves exercise is probably one of the most powerful methodologies used to help individuals get the most out of their lives while enjoying every day; this exercise leads to much greater individual success. However, for it to be effective, one needs to develop his or her goals and then review and act on them on a regular basis.

  1. Zeta potential response of human erythrocyte membranes to the modulators of Gardos channel activity under low rate β-radiation.

    PubMed

    Zhirnov, V V; Iakovenko, I N; Voitsitskiy, V M; Khyzhnyak, S V; Zubrikova-Chugainova, O G; Gorobetz, V A

    2015-12-01

    Study of human erythrocyte DP response under modification by activators and blockers of the functional state of Ca2+-dependent K+ channels under low rate β-radiation. Erythrocytes were isolated from the donor blood. The zeta potential was computed from the value of the cell electrophoretic mobility. The investigated drugs preliminary introduced in cellular suspensions, and then aliquote of 90Sr(NO3)2 solution to get the final activity concentration of 44,4kBq⋅l-1. The radioisotope radiation of 90Sr/90Y (RR, 15 μGy⋅h-1) increases an absolute value of erythrocyte membranes DP (DPab), and its action is reversible. It specifies the effect is mediated by non-ionizing part of the RR. Dibutyril-cAMP dose-independent increases DPab of erythrocyte membranes in the concentration range of 1-100 мкМ, but RR does not amplify this effect. Anaprilin increases dose-independent DPab in concentrations 10 and 100 μМ. The effect of maximal concentration of anaprilin (100 μМ) decreases by RR. Clotrimazol increases DPab of erythrocyte membranes in the concentration range of 0,1-10 μМ relatively control, while its maximal concentration - decreases, and the minimal level does not reliably influence on this index The action of сlotrimazol on DP in concentrations of 10-100 μМ is abolished by RR, and is not changed in the range of 0,1-1,0 μМ. Nitrendipine raises DPab of erythrocyte membranes in all of range of concentrations, and RR amplifies the effect of the drug. 1. There is a threshold of the biological action on cells for the ionizing component of radioisotope radiation determined by efficiency of operation their antioxidant system.2. At dose rates below a threshold, the action of ionizing radiation is mediated by its non-ionizing component, and is reversible, and therefore is determined only in the field of radiation. V. V. Zhirnov, I. N. Iakovenko, V.M. Voitsitskiy, S. V. Khyzhnyak, О. G. Zubrikova-Chugainova, V.A. Gorobetz.

  2. Zebrafish pronephros tubulogenesis and epithelial identity maintenance are reliant on the polarity proteins Prkc iota and zeta.

    PubMed

    Gerlach, Gary F; Wingert, Rebecca A

    2014-12-15

    The zebrafish pronephros provides an excellent in vivo system to study the mechanisms of vertebrate nephron development. When and how renal progenitors in the zebrafish embryo undergo tubulogenesis to form nephrons is poorly understood, but is known to involve a mesenchymal to epithelial transition (MET) and the acquisition of polarity. Here, we determined the precise timing of these events in pronephros tubulogenesis. As the ternary polarity complex is an essential regulator of epithelial cell polarity across tissues, we performed gene knockdown studies to assess the roles of the related factors atypical protein kinase C iota and zeta (prkcι, prkcζ). We found that prkcι and prkcζ serve partially redundant functions to establish pronephros tubule epithelium polarity. Further, the loss of prkcι or the combined knockdown of prkcι/ζ disrupted proximal tubule morphogenesis and podocyte migration due to cardiac defects that prevented normal fluid flow to the kidney. Surprisingly, tubule cells in prkcι/ζ morphants displayed ectopic expression of the transcription factor pax2a and the podocyte-associated genes wt1a, wt1b, and podxl, suggesting that prkcι/ζ are needed to maintain renal epithelial identity. Knockdown of genes essential for cardiac contractility and vascular flow to the kidney, such as tnnt2a, or elimination of pronephros fluid output through knockdown of the intraflagellar transport gene ift88, was not associated with ectopic pronephros gene expression, thus suggesting a unique role for prkcι/ζ in maintaining tubule epithelial identity separate from the consequence of disruptions to renal fluid flow. Interestingly, knockdown of pax2a, but not wt1a, was sufficient to rescue ectopic tubule gene expression in prkcι/ζ morphants. These data suggest a model in which the redundant activities of prkcι and prkcζ are essential to establish tubule epithelial polarity and also serve to maintain proper epithelial cell type identity in the tubule by

  3. Zebrafish pronephros tubulogenesis and epithelial identity maintenance are reliant on the polarity proteins Prkc iota and zeta

    PubMed Central

    Gerlach, Gary F.; Wingert, Rebecca A.

    2014-01-01

    The zebrafish pronephros provides an excellent in vivo system to study the mechanisms of vertebrate nephron development. When and how renal progenitors in the zebrafish embryo undergo tubulogenesis to form nephrons is poorly understood, but is known to involve a mesenchymal to epithelial transition (MET) and the acquisition of polarity. Here, we determined the precise timing of these events in pronephros tubulogenesis. As the ternary polarity complex is an essential regulator of epithelial cell polarity across tissues, we performed gene knockdown studies to assess the roles of the related factors atypical protein kinase C iota and zeta (prkcι, prkcζ). We found that prkcι and prkcζ serve partially redundant functions to establish pronephros tubule epithelium polarity. Further, the loss of prkcι or the combined knockdown of prkcι/ζ disrupted proximal tubule morphogenesis and podocyte migration due to cardiac defects that prevented normal fluid flow to the kidney. Surprisingly, tubule cells in prkcι/ζ morphants displayed ectopic expression of the transcription factor pax2a and the podocyte-associated genes wt1a, wt1b, and podxl, suggesting that prkcι/ζ are needed to maintain renal epithelial identity. Knockdown of genes essential for cardiac contractility and vascular flow to the kidney, such as tnnt2a, or elimination of pronephros fluid output through knockdown of the intraflagellar transport gene ift88, was not associated with ectopic pronephros gene expression, thus suggesting a unique role for prkcι/ζ in maintaining tubule epithelial identity separate from the consequence of disruptions to renal fluid flow. Interestingly, knockdown of pax2a, but not wt1a, was sufficient to rescue ectopic tubule gene expression in prkcι/ζ morphants. These data suggest a model in which the redundant activities of prkcι and prkcζ are essential to establish tubule epithelial polarity and also serve to maintain proper epithelial cell type identity in the tubule by

  4. Zeta-Proteobacteria dominate the formation of microbial mats in low-temperature hydrothermal vents at Loihi Seamount

    NASA Astrophysics Data System (ADS)

    Rassa, A. C.; McAllister, S. M.; Safran, S. A.; Moyer, C. L.

    2007-12-01

    Loihi Seamount is Hawaii's youngest volcano and one of the earth's most active. Loihi is located 30 km SE of the big island of Hawaii and rises over 3000m above the sea floor and summits at 1100m below sea level. An eruption in 1996 of Loihi led to the formation of Pele's Pit, a 300 meter deep caldera. The current observations have revealed diffuse hydrothermal venting causing low to intermediate temperatures (10 to 65°C). The elevated temperatures, coupled with high concentrations of Fe(II) (ranging from 50 to 750 μM) support conditions allowing for extensive microbial mat formation. The focus of this study was to identify the colonizing populations of bacteria generated by the microbial mats at Loihi Seamount. Twenty-six microbial growth chambers were deployed and recovered after placement in the flow of hydrothermal vents for 3 to 8 days from within Loihi's caldera. Genomic DNA was extracted from samples and analyzed by Terminal-Restriction Fragment Length Polymorphism (T-RFLP) using eight restriction enzyme treatments to generate fingerprints from bacterial amplicons of small subunit rRNA genes (SSU rDNAs). Pearson product-moment coupled with UPGMA cluster analysis of these T-RFLP fingerprints showed that these communities bifurcated into two primary clusters. The first (Group 1) had an average vent effluent temperature of 44°C, and the second (Group 2) had an average vent effluent temperature of 64°C. Representative samples from within the two clusters (or groups) were chosen for further clone library and sequencing analysis. These libraries revealing a dominance of the recently discovered zeta- Proteobacteria in the lower temperature group (Group 1) indicating that they were the dominant colonizers of the microbial mats. These microaerophilic, obligately lithotrophic, Fe-oxidizing bacteria are most closely related to Mariprofundus ferrooxydans. The higher temperature group (Group 2) was dominated by epsilon- Proteobacteria primarily of the genus

  5. Evaluating excited state atomic polarizabilities of chromophores† †Electronic supplementary information (ESI) available: Basis set dependence, definition of bond charges, Romberg differentiation, python script to calculate atomic polarizabilities, influence of the cavity radius, atomic polarizabilities of coumarin 153, all tables in atomic units. See DOI: 10.1039/c7cp08549d

    PubMed Central

    Heid, Esther

    2018-01-01

    Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomic charge transfer and polarizability terms, and variation in the presence of an electric field has been used to evaluate atomic polarizabilities. On excitation, MQ undergoes very site-specific changes in polarizability while C153 shows significantly less variation. We also conclude that MQ cannot be adequately described by standard atomic polarizabilities based on atomic number and hybridization state. Changes in the molecular polarizability of MQ (on excitation) are not representative of the local site-specific changes in atomic polarizability, thus the overall molecular polarizability ratio does not provide a good approximation for local atom-specific polarizability changes on excitation. Accurate excited state force fields are needed for computer simulation of solvation dynamics. The chromophores considered in this study are often used as molecular probes. The methods and data reported here can be used for the construction of polarizable ground and excited state force fields. Atomic and molecular polarizabilities (ground and excited states) have been evaluated over a range of functionals and basis sets. Different mechanisms for including solvation effects have been examined; using a polarizable continuum model, explicit solvation and via sampling of clusters extracted from a MD simulation. A range of different solvents have also been considered. PMID:29542743

  6. 47 CFR 4.1 - Scope, basis and purpose.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Scope, basis and purpose. 4.1 Section 4.1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL DISRUPTIONS TO COMMUNICATIONS General § 4.1 Scope, basis and purpose. In this part, the Federal Communications Commission is setting forth requirements...

  7. 42 CFR § 512.1 - Basis and scope.

    Code of Federal Regulations, 2010 CFR

    2017-10-01

    ...) HEALTH CARE INFRASTRUCTURE AND MODEL PROGRAMS EPISODE PAYMENT MODEL General Provisions § 512.1 Basis and scope. (a) Basis. This part implements the test of episode payment models under section 1115A of the Act... sets forth the following: (1) The participants in each episode payment model. (2) The episodes being...

  8. 42 CFR 457.700 - Basis, scope, and applicability.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Strategic Planning, Reporting, and Evaluation § 457.700 Basis, scope, and applicability. (a) Statutory basis... strategic planning, reports, and program budgets; and (2) Section 2108 of the Act, which sets forth... strategic planning, monitoring, reporting and evaluation under title XXI. (c) Applicability. The...

  9. 47 CFR 4.1 - Scope, basis and purpose.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Scope, basis and purpose. 4.1 Section 4.1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL DISRUPTIONS TO COMMUNICATIONS General § 4.1 Scope, basis and purpose. In this part, the Federal Communications Commission is setting forth requirements...

  10. 42 CFR 457.700 - Basis, scope, and applicability.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Strategic Planning, Reporting, and Evaluation § 457.700 Basis, scope, and applicability. (a) Statutory basis... strategic planning, reports, and program budgets; and (2) Section 2108 of the Act, which sets forth... strategic planning, monitoring, reporting and evaluation under title XXI. (c) Applicability. The...

  11. Zeta Potential Measurements on Solid Surfaces for in Vitro Biomaterials Testing: Surface Charge, Reactivity Upon Contact With Fluids and Protein Absorption

    PubMed Central

    Ferraris, Sara; Cazzola, Martina; Peretti, Veronica; Stella, Barbara; Spriano, Silvia

    2018-01-01

    Surface properties of biomaterials (e.g., roughness, chemical composition, charge, wettability, and hydroxylation degree) are key features to understand and control the complex interface phenomena that happens upon contact with physiological fluids. Numerous physico-chemical techniques can be used in order to investigate in depth these crucial material features. Among them, zeta potential measurements are widely used for the characterization of colloidal suspensions, but actually poorly explored in the study of solid surfaces, even if they can give significant information about surface charge in function of pH and indirectly about surface functional groups and reactivity. The aim of the present research is application of zeta potential measurements of solid surfaces for the in vitro testing of biomaterials. In particular, bare and surface modified Ti6Al4V samples have been compared in order to evaluate their isoelectric points (IEPs), surface charge at physiological pH, in vitro bioactivity [in simulated body fluid (SBF)] and protein absorption. Zeta potential titration was demonstrated as a suitable technique for the surface characterization of surface treated Ti6Al4V substrates. Significant shift of the isoelectric point was recorded after a chemical surface treatment (because of the exposition of hydroxyl groups), SBF soaking (because of apatite precipitation IEP moves close to apatite one) and protein absorption (IEP moves close to protein ones). Moreover, the shape of the curve gives information about exposed functional groups (e.g., a plateau in the basic range appears due to the exposition of acidic OH groups and in the acidic range due to exposition of basic NH2 groups). PMID:29868575

  12. SETS. Set Equation Transformation System

    SciTech Connect

    Worrell, R.B.

    1992-01-13

    SETS is used for symbolic manipulation of Boolean equations, particularly the reduction of equations by the application of Boolean identities. It is a flexible and efficient tool for performing probabilistic risk analysis (PRA), vital area analysis, and common cause analysis. The equation manipulation capabilities of SETS can also be used to analyze noncoherent fault trees and determine prime implicants of Boolean functions, to verify circuit design implementation, to determine minimum cost fire protection requirements for nuclear reactor plants, to obtain solutions to combinatorial optimization problems with Boolean constraints, and to determine the susceptibility of a facility to unauthorized access throughmore » nullification of sensors in its protection system.« less

  13. Doubly stochastic radial basis function methods

    NASA Astrophysics Data System (ADS)

    Yang, Fenglian; Yan, Liang; Ling, Leevan

    2018-06-01

    We propose a doubly stochastic radial basis function (DSRBF) method for function recoveries. Instead of a constant, we treat the RBF shape parameters as stochastic variables whose distribution were determined by a stochastic leave-one-out cross validation (LOOCV) estimation. A careful operation count is provided in order to determine the ranges of all the parameters in our methods. The overhead cost for setting up the proposed DSRBF method is O (n2) for function recovery problems with n basis. Numerical experiments confirm that the proposed method not only outperforms constant shape parameter formulation (in terms of accuracy with comparable computational cost) but also the optimal LOOCV formulation (in terms of both accuracy and computational cost).

  14. The ClpXP protease is responsible for the degradation of the Epsilon antidote to the Zeta toxin of the streptococcal pSM19035 plasmid.

    PubMed

    Brzozowska, Iwona; Zielenkiewicz, Urszula

    2014-03-14

    Most bacterial genomes contain different types of toxin-antitoxin (TA) systems. The ω-ε-ζ proteinaceous type II TA cassette from the streptococcal pSM19035 plasmid is a member of the ε/ζ family, which is commonly found in multiresistance plasmids and chromosomes of various human pathogens. Regulation of type II TA systems relies on the proteolysis of antitoxin proteins. Under normal conditions, the Epsilon antidote neutralizes the Zeta toxin through the formation of a tight complex. In this study, we show, using both in vivo and in vitro analyses, that the ClpXP protease is responsible for Epsilon antitoxin degradation. Using in vivo studies, we examined the stability of the plasmids with active or inactive ω-ε-ζ TA cassettes in B. subtilis mutants that were defective for different proteases. Using in vitro assays, the degradation of purified His6-Epsilon by the His6-LonBs, ClpPBs, and ClpXBs proteases from B. subtilis was analyzed. Additionally, we showed that purified Zeta toxin protects the Epsilon protein from rapid ClpXP-catalyzed degradation.

  15. Synthesis of the RGO/Al2O3 core-shell nanocomposite flakes and characterization of their unique electrostatic properties using zeta potential measurements

    NASA Astrophysics Data System (ADS)

    Jastrzębska, A. M.; Karcz, J.; Letmanowski, R.; Zabost, D.; Ciecierska, E.; Zdunek, J.; Karwowska, E.; Siekierski, M.; Olszyna, A.; Kunicki, A.

    2016-01-01

    The aim of this study was to describe the influence of the modification of electrostatic properties of RGO/Al2O3 core-shell nanocomposite flakes. The amount of crystalline form of aluminum oxide was very small. It existed mostly in amorphous phase in the form of covalently bonded to GO surface. The morphological, structural and physicochemical investigations results showed that spherical Al2O3 nanoparticles (ca. 41 nm) in gamma phase completely covered the surface of curly-shaped RGO flakes and acted as a spreader between individual flakes. The high BET specific surface area of the analyzed composite (119.71 m2/g) together with very low open porosity (0.479 cm3/g) indicated that RGO/Al2O3 nanocomposite flakes showed low tendency to agglomeration. The zeta potential curves obtained for RGO/Al2O3 core-shell nanocomposite flakes were differing from curves obtained for GO and Al2O3 suspensions in distilled water and neutral environment. The specific electrostatic properties of the core-shell system of RGO/Al2O3 flakes had an influence on its surface charge (zeta potential) which was measured by applying an external electric field. The FTIR and Raman investigations results also confirmed that the Cdbnd O species were not taking part in the surface amphoteric reactions resulting in the formation of electrostatic surface charge.

  16. Characterization of the startup transient electrokinetic flow in rectangular channels of arbitrary dimensions, zeta potential distribution, and time-varying pressure gradient.

    PubMed

    Miller, Andrew; Villegas, Arturo; Diez, F Javier

    2015-03-01

    The solution to the startup transient EOF in an arbitrary rectangular microchannel is derived analytically and validated experimentally. This full 2D transient solution describes the evolution of the flow through five distinct periods until reaching a final steady state. The derived analytical velocity solution is validated experimentally for different channel sizes and aspect ratios under time-varying pressure gradients. The experiments used a time resolved micro particle image velocimetry technique to calculate the startup transient velocity profiles. The measurements captured the effect of time-varying pressure gradient fields derived in the analytical solutions. This is tested by using small reservoirs at both ends of the channel which allowed a time-varying pressure gradient to develop with a time scale on the order of the transient EOF. Results showed that under these common conditions, the effect of the pressure build up in the reservoirs on the temporal development of the transient startup EOF in the channels cannot be neglected. The measurements also captured the analytical predictions for channel walls made of different materials (i.e., zeta potentials). This was tested in channels that had three PDMS and one quartz wall, resulting in a flow with an asymmetric velocity profile due to variations in the zeta potential between the walls. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. DNA polymerase zeta cooperates with polymerases kappa and iota in translesion DNA synthesis across pyrimidine photodimers in cells from XPV patients.

    PubMed

    Ziv, Omer; Geacintov, Nicholas; Nakajima, Satoshi; Yasui, Akira; Livneh, Zvi

    2009-07-14

    Human cells tolerate UV-induced cyclobutane pyrimidine dimers (CPD) by translesion DNA synthesis (TLS), carried out by DNA polymerase eta, the POLH gene product. A deficiency in DNA polymerase eta due to germ-line mutations in POLH causes the hereditary disease xeroderma pigmentosum variant (XPV), which is characterized by sunlight sensitivity and extreme predisposition to sunlight-induced skin cancer. XPV cells are UV hypermutable due to the activity of mutagenic TLS across CPD, which explains the cancer predisposition of the patients. However, the identity of the backup polymerase that carries out this mutagenic TLS was unclear. Here, we show that DNA polymerase zeta cooperates with DNA polymerases kappa and iota to carry out error-prone TLS across a TT CPD. Moreover, DNA polymerases zeta and kappa, but not iota, protect XPV cells against UV cytotoxicity, independently of nucleotide excision repair. This presents an extreme example of benefit-risk balance in the activity of TLS polymerases, which provide protection against UV cytotoxicity at the cost of increased mutagenic load.

  18. Total levels, localization patterns, and proportions of sperm exhibiting phospholipase C zeta are significantly correlated with fertilization rates after intracytoplasmic sperm injection.

    PubMed

    Yelumalai, Suseela; Yeste, Marc; Jones, Celine; Amdani, Siti N; Kashir, Junaid; Mounce, Ginny; Da Silva, Sarah J Martins; Barratt, Christopher L; McVeigh, Enda; Coward, Kevin

    2015-09-01

    To study the relationship of total levels, localization patterns, and proportions of sperm exhibiting phospholipase C zeta, with fertilization rates after in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI). Laboratory study; controls vs. patients after IVF (n = 27) or ICSI (n = 17) treatment. Fertility center. A total of 44 semen samples, subjected to either IVF or ICSI treatment. Oocyte collection, ICSI or IVF, determination of sperm concentration and motility, and immunocytochemical analyses of phospholipase C zeta (PLCζ). None. Percentages of sperm exhibiting PLCζ. Significant positive correlation between ICSI fertilization rates and total levels, localization patterns, and the proportion (percentage) of sperm exhibiting PLCζ. Total levels, localization patterns, and the proportion of sperm exhibiting PLCζ are correlated with fertilization rates for ICSI, but not for IVF. Evaluating total levels, localization patterns, and proportions of PLCζ may represent a useful diagnostic tool for clinical purposes in men for whom IVF is not advised or has previously failed. This clinical study further supports the fundamental role of PLCζ in the oocyte activation process. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  19. Predicting the influence of liposomal lipid composition on liposome size, zeta potential and liposome-induced dendritic cell maturation using a design of experiments approach.

    PubMed

    Soema, Peter C; Willems, Geert-Jan; Jiskoot, Wim; Amorij, Jean-Pierre; Kersten, Gideon F

    2015-08-01

    In this study, the effect of liposomal lipid composition on the physicochemical characteristics and adjuvanticity of liposomes was investigated. Using a design of experiments (DoE) approach, peptide-containing liposomes containing various lipids (EPC, DOPE, DOTAP and DC-Chol) and peptide concentrations were formulated. Liposome size and zeta potential were determined for each formulation. Moreover, the adjuvanticity of the liposomes was assessed in an in vitro dendritic cell (DC) model, by quantifying the expression of DC maturation markers CD40, CD80, CD83 and CD86. The acquired data of these liposome characteristics were successfully fitted with regression models, and response contour plots were generated for each response factor. These models were applied to predict a lipid composition that resulted in a liposome with a target zeta potential. Subsequently, the expression of the DC maturation factors for this lipid composition was predicted and tested in vitro; the acquired maturation responses corresponded well with the predicted ones. These results show that a DoE approach can be used to screen various lipids and lipid compositions, and to predict their impact on liposome size, charge and adjuvanticity. Using such an approach may accelerate the formulation development of liposomal vaccine adjuvants. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  20. Microencapsulation of β-Carotene Based on Casein/Guar Gum Blend Using Zeta Potential-Yield Stress Phenomenon: an Approach to Enhance Photo-stability and Retention of Functionality.

    PubMed

    Thakur, Deepika; Jain, Ashay; Ghoshal, Gargi; Shivhare, U S; Katare, O P

    2017-07-01

    β-Carotene, abundant majorly in carrot, pink guava yams, spinach, kale, sweet potato, and palm oil, is an important nutrient for human health due to its scavenging action upon reactive free radicals wherever produced in the body. Inclusion of liposoluble β-carotene in foods and food ingredients is a challenging aspect due to its labile nature and low absorption from natural sources. This fact has led to the application of encapsulation of β-carotene to improve stability and bioavailability. The present work was aimed to fabricate microcapsules (MCs) of β-carotene oily dispersion using the complex coacervation technique with casein (CA) and guar gum (GG) blend. The ratio of CA:GG was found to be 1:0.5 (w/v) when optimized on the basis of zeta potential-yield stress phenomenon. These possessed a higher percentage yield (71.34 ± 0.55%), lower particle size (176.47 ± 4.65 μm), higher encapsulation efficiency (65.95 ± 5.33%), and in general, a uniform surface morphology was observed with particles showing optimized release behavior. Prepared MCs manifested effective and controlled release (up to 98%) following zero-order kinetics which was adequately explained by the Korseymer-Peppas model. The stability of the freeze-dried MCs was established in simulated gastrointestinal fluids (SGF, SIF) for 8 h. Antioxidant activity of the MCs was studied and revealed the retention of the functional architecture of β-carotene in freeze-dried MCs. Minimal photolytic degradation upon encapsulation of β-carotene addressed the challenge regarding photo-stability of β-carotene as confirmed via mass spectroscopy.

  1. [Basis for designing a medical course curriculum].

    PubMed

    Villarreal, R; Bojalil, L F; Mercer, H

    1977-01-01

    This article sets forth the reasons for the structure given to the Division of Biology and Health on the Xochimilco campus of Metropolitan Autonomous University in Mexico: to adjust the university to the process of social change going forward in the country and gear the university to the problems of the present by avoiding the rigidity of its structure. The basic aspects of curriculum design are cited against a background of an historical analysis of the socioeconomic structure of education and health. The principles underlying the curriculum and the course work are then described on the basis of that analysis.

  2. Differential regulation of p65 and c-Rel NF-kappaB transactivating activity by Cot, protein kinase C zeta and NIK protein kinases in CD3/CD28 activated T cells.

    PubMed

    Sánchez-Valdepeñas, Carmen; Punzón, Carmen; San-Antonio, Belén; Martin, Angel G; Fresno, Manuel

    2007-03-01

    It has been shown that phosphorylation of p65/RelA and c-Rel plays a role in the regulation of transcriptional activity of NF-kappaB independent on IkappaB degradation. In this study, we show that anti CD3/CD28 activation induces the transactivation activity of both p65/RelA and c-Rel in T cells using Gal4 dependent assays. Moreover, protein kinase C (PKC)zeta, Cot kinase and NF-kappaB-inducing kinase (NIK) seem to be involved in those processes in a different manner. Thus, transfection of dominant negative forms of Cot and PKCzeta inhibits CD3/CD28 induction of Gal4-p65 transactivation, whereas the kinase inactive versions of the 3 kinases inhibit induction of Gal4-c-Rel. Cot induction of Gal4-c-Rel transactivating activity seems to be mediated sequentially through PKCzeta and NIK activation, since dominant negative form of NIK blocks Cot and PKCzeta induction, whereas kinase inactive PKCzeta only blocks Cot activity. In contrast, the contribution of NIK to the transactivation function of p65/RelA seems to be negligible and more importantly NIK-KD did not inhibit induction by Cot and PKCzeta. Besides, the enhancing effect of Cot on Gal4-p65 was not decreased in mouse embryo fibroblasts from NIK deficient aly/aly mice in contrast with a greatest reduction on Gal4-c-Rel. By using Ser to Ala mutants in p65 and c-Rel transactivation domains, PKCzeta and NIK activities seem to be dependent of a restricted set of Ser in both proteins. In contrast, the enhancing effect of Cot seems to be less dependent of a particular set of Ser residues being partially abrogated by mutation of several Ser residues.

  3. Comprehensive Survey of miRNA-mRNA Interactions Reveals That Ccr7 and Cd247 (CD3 zeta) are Posttranscriptionally Controlled in Pancreas Infiltrating T Lymphocytes of Non-Obese Diabetic (NOD) Mice.

    PubMed

    Fornari, Thais A; Donate, Paula B; Assis, Amanda F; Macedo, Claudia; Sakamoto-Hojo, Elza T; Donadi, Eduardo A; Passos, Geraldo A

    2015-01-01

    In autoimmune type 1 diabetes mellitus (T1D), auto-reactive clones of CD4+ and CD8+ T lymphocytes in the periphery evolve into pancreas-infiltrating T lymphocytes (PILs), which destroy insulin-producing beta-cells through inflammatory insulitis. Previously, we demonstrated that, during the development of T1D in non-obese diabetic (NOD) mice, a set of immune/inflammatory reactivity genes were differentially expressed in T lymphocytes. However, the posttranscriptional control involving miRNA interactions that occur during the evolution of thymocytes into PILs remains unknown. In this study, we postulated that miRNAs are differentially expressed during this period and that these miRNAs can interact with mRNAs involved in auto-reactivity during the progression of insulitis. To test this hypothesis, we used NOD mice to perform, for the first time, a comprehensive survey of miRNA and mRNA expression as thymocytes mature into peripheral CD3+ T lymphocytes and, subsequently, into PILs. Reconstruction of miRNA-mRNA interaction networks for target prediction revealed the participation of a large set of miRNAs that regulate mRNA targets related to apoptosis, cell adhesion, cellular regulation, cellular component organization, cellular processes, development and the immune system, among others. The interactions between miR-202-3p and the Ccr7 chemokine receptor mRNA or Cd247 (Cd3 zeta chain) mRNA found in PILs are highlighted because these interactions can contribute to a better understanding of how the lack of immune homeostasis and the emergence of autoimmunity (e.g., T1D) can be associated with the decreased activity of Ccr7 or Cd247, as previously observed in NOD mice. We demonstrate that these mRNAs are controlled at the posttranscriptional level in PILs.

  4. Comprehensive Survey of miRNA-mRNA Interactions Reveals That Ccr7 and Cd247 (CD3 zeta) are Posttranscriptionally Controlled in Pancreas Infiltrating T Lymphocytes of Non-Obese Diabetic (NOD) Mice

    PubMed Central

    Macedo, Claudia; Sakamoto-Hojo, Elza T.; Donadi, Eduardo A.; Passos, Geraldo A.

    2015-01-01

    In autoimmune type 1 diabetes mellitus (T1D), auto-reactive clones of CD4+ and CD8+ T lymphocytes in the periphery evolve into pancreas-infiltrating T lymphocytes (PILs), which destroy insulin-producing beta-cells through inflammatory insulitis. Previously, we demonstrated that, during the development of T1D in non-obese diabetic (NOD) mice, a set of immune/inflammatory reactivity genes were differentially expressed in T lymphocytes. However, the posttranscriptional control involving miRNA interactions that occur during the evolution of thymocytes into PILs remains unknown. In this study, we postulated that miRNAs are differentially expressed during this period and that these miRNAs can interact with mRNAs involved in auto-reactivity during the progression of insulitis. To test this hypothesis, we used NOD mice to perform, for the first time, a comprehensive survey of miRNA and mRNA expression as thymocytes mature into peripheral CD3+ T lymphocytes and, subsequently, into PILs. Reconstruction of miRNA-mRNA interaction networks for target prediction revealed the participation of a large set of miRNAs that regulate mRNA targets related to apoptosis, cell adhesion, cellular regulation, cellular component organization, cellular processes, development and the immune system, among others. The interactions between miR-202-3p and the Ccr7 chemokine receptor mRNA or Cd247 (Cd3 zeta chain) mRNA found in PILs are highlighted because these interactions can contribute to a better understanding of how the lack of immune homeostasis and the emergence of autoimmunity (e.g., T1D) can be associated with the decreased activity of Ccr7 or Cd247, as previously observed in NOD mice. We demonstrate that these mRNAs are controlled at the posttranscriptional level in PILs. PMID:26606254

  5. Applications of zeta functions and other spectral functions in mathematics and physics: a special issue in honour of Stuart Dowker's 75th birthday Applications of zeta functions and other spectral functions in mathematics and physics: a special issue in honour of Stuart Dowker's 75th birthday

    NASA Astrophysics Data System (ADS)

    Dowker, Fay; Elizalde, Emilio; Kirsten, Klaus

    2012-09-01

    . Chapter 5 is devoted to the image and inversion methods and I must have read this closely as there are lots of marginal notes...' The second principle can be read off from the following quote: 'After reading Eddington circa 1960 it was clear to me (and others of course) there is a strong analogy (at least) between gravitation and electromagnetism ... (His work has very strongly influenced me.) So I played a game of asking for the gravitational analogues of existing electromagnetic concepts. The basic analogue is between field strength/charge and curvature/spin... [in that] ...spin, in general relativity, plays the passive role that charge plays in electromagnetism in the sense that it is the spin-curvature coupling that knocks a particle off a geodesic.' It is quite amazing how much of Stuart's work can be traced back to these principles. This is briefly explained in the following by describing some of his most important works. His most cited work [7] fits this bill and can be seen as doing what Julian Schwinger did in [8], for a constant electromagnetic field in the gravitational setting. In more detail he noticed Schulman's work on propagators on the three sphere [9], which he extended to Lie groups; see [10, 11]. He then noticed that having exact propagators, work like Schwinger's could be done and de Sitter space was a natural 'curved' candidate. The paper is best known for the mathematical technique introduced, namely for the zeta function method much used since for the computation of singular quantum field theoretic quantities like effective actions and the Casimir energy. The motivation for introducing this scheme goes back to reading an article of I M Gel'fand about some number theory problem involving zeta functions, image sums, propagators etc. How could an object occurring with other objects physicists were using all the time not be useful? It turned out to be very useful, although in this paper the method was only introduced but actually not used! This is

  6. Grobner Basis Representations of Sudoku

    ERIC Educational Resources Information Center

    Taalman, Laura; Arnold, Elizabeth; Lucas, Stephen

    2010-01-01

    This paper uses Grobner bases to explore the inherent structure of Sudoku puzzles and boards. In particular, we develop three different ways of representing the constraints of Sudoku puzzles with a system of polynomial equations. In one case, we explicitly show how a Grobner basis can be used to obtain a more meaningful representation of the…

  7. GASB's Basis of Accounting Project.

    ERIC Educational Resources Information Center

    Kovlak, Daniel L.

    1986-01-01

    In July 1984, the Governmental Accounting Standards Board began its "Measurement Focus/Basis of Accounting" project, which addresses measurement issues and revenue and expenditure recognition problems involving governmental funds. This article explains the project's background, alternatives discussed by the board, and tentative…

  8. A Molecular Basis of Cancer.

    ERIC Educational Resources Information Center

    Weinberg, Robert A.

    1983-01-01

    Discusses the molecular basis of cancer, focusing on genetics of the disease. Indicates that human cancers are initiated by oncogenes (altered versions of normal genes) and that in one case the critical alteration is a single point mutation that changes one amino acid in the protein encoded by the gene. (JN)

  9. Mixtures of latex particles and the surfactant of opposite charge used as interface stabilizers--influence of particle contact angle, zeta potential, flocculation and shear energy.

    PubMed

    Deleurence, Rémi; Parneix, Caroline; Monteux, Cécile

    2014-09-28

    We investigate the stabilization of air-water interfaces by mixtures of negatively charged latex particles (sulfate polystyrene) and cationic surfactants (alkyl trimethylammonium bromides). First we report results concerning the binding of surfactant molecules to the latex particles. As the surfactant concentration increases, the charge of the particles reverses, from negative to positive, because CnTAB first binds electrostatically to the latex particles and then through hydrophobic interaction with the monolayer already adsorbed on the particles as well as directly with the hydrophobic surface of the latex. Over a large range of surfactant concentrations around the charge inversion, a strong flocculation is observed and 100 μm large aggregates form in the suspension. Unlike previous studies published on mixtures of inorganic particles with oppositely charged surfactants, we show that we can vary the sign of the zeta potential of the particles without changing the contact angle of the particles over a large range of surfactant concentrations. Indeed, the latex particles that we study are more hydrophobic than inorganic particles, hence adding moderate concentrations of the surfactant results in a weak variation of the contact angle while the charge of the particles can be reversed. This enables decoupling of the effect of zeta potential and contact angle on the interfacial properties of the mixtures. Our study shows that the contact angle and the charge of the particles are not sufficient parameters to control the foam properties, and the key-parameters are the flocculation state and the shear energy applied to produce the foam. Indeed, flocculated samples, whatever the sign of the zeta potential, enable production of a stable armour at the interface. The large aggregates do not adsorb spontaneously at the interface because of their large size, however when a large shear energy is used to produce the foam very stable foam is obtained, where particles are trapped

  10. Probabilistic Open Set Recognition

    NASA Astrophysics Data System (ADS)

    Jain, Lalit Prithviraj

    support vector machines. Building from the success of statistical EVT based recognition methods such as PI-SVM and W-SVM on the open set problem, we present a new general supervised learning algorithm for multi-class classification and multi-class open set recognition called the Extreme Value Local Basis (EVLB). The design of this algorithm is motivated by the observation that extrema from known negative class distributions are the closest negative points to any positive sample during training, and thus should be used to define the parameters of a probabilistic decision model. In the EVLB, the kernel distribution for each positive training sample is estimated via an EVT distribution fit over the distances to the separating hyperplane between positive training sample and closest negative samples, with a subset of the overall positive training data retained to form a probabilistic decision boundary. Using this subset as a frame of reference, the probability of a sample at test time decreases as it moves away from the positive class. Possessing this property, the EVLB is well-suited to open set recognition problems where samples from unknown or novel classes are encountered at test. Our experimental evaluation shows that the EVLB provides a substantial improvement in scalability compared to standard radial basis function kernel machines, as well as P I-SVM and W-SVM, with improved accuracy in many cases. We evaluate our algorithm on open set variations of the standard visual learning benchmarks, as well as with an open subset of classes from Caltech 256 and ImageNet. Our experiments show that PI-SVM, WSVM and EVLB provide significant advances over the previous state-of-the-art solutions for the same tasks.

  11. Quantum Sets and Clifford Algebras

    NASA Astrophysics Data System (ADS)

    Finkelstein, David

    1982-06-01

    The mathematical language presently used for quantum physics is a high-level language. As a lowest-level or basic language I construct a quantum set theory in three stages: (1) Classical set theory, formulated as a Clifford algebra of “ S numbers” generated by a single monadic operation, “bracing,” Br = {…}. (2) Indefinite set theory, a modification of set theory dealing with the modal logical concept of possibility. (3) Quantum set theory. The quantum set is constructed from the null set by the familiar quantum techniques of tensor product and antisymmetrization. There are both a Clifford and a Grassmann algebra with sets as basis elements. Rank and cardinality operators are analogous to Schroedinger coordinates of the theory, in that they are multiplication or “ Q-type” operators. “ P-type” operators analogous to Schroedinger momenta, in that they transform the Q-type quantities, are bracing (Br), Clifford multiplication by a set X, and the creator of X, represented by Grassmann multiplication c( X) by the set X. Br and its adjoint Br* form a Bose-Einstein canonical pair, and c( X) and its adjoint c( X)* form a Fermi-Dirac or anticanonical pair. Many coefficient number systems can be employed in this quantization. I use the integers for a discrete quantum theory, with the usual complex quantum theory as limit. Quantum set theory may be applied to a quantum time space and a quantum automaton.

  12. Elucidation of the mechanisms of action of Bacteriophage K/nano-emulsion formulations against S. aureus via measurement of particle size and zeta potential.

    PubMed

    Esteban, Patricia Perez; Jenkins, A Toby A; Arnot, Tom C

    2016-03-01

    In earlier work we have demonstrated the effect that nano-emulsions have on bacterial growth, and most importantly the enhanced bacteriophage infectivity against Staphylococcus aureus in planktonic culture when phage are carried in nano-emulsions. However, the mechanisms of enhancement of the bacteriophage killing effect are not specifically understood. This work focuses on the investigation of the possible interactions between emulsion droplets and bacterial cells, between emulsion droplets and bacteriophages, and finally interactions between all three components: nano-emulsion droplets, bacteria, and bacteriophages. The first approach consists of simple calculations to determine the spatial distribution of the components, based on measurements of particle size. It was found that nano-emulsion droplets are much more numerous than bacteria or bacteriophage, and due to their size and surface area they must be covering the surface of both cells and bacteriophage particles. Stabilisation of bacteriophages due to electrostatic forces and interaction with nano-emulsion droplets is suspected, since bacteriophages may be protected against inactivation due to 'charge shielding'. Zeta potential was measured for the individual components in the system, and for all of them combined. It was concluded that the presence of nano-emulsions could be reducing electrostatic repulsion between bacterial cells and bacteriophage, both of which are very negatively 'charged'. Moreover, nano-emulsions lead to more favourable interaction between bacteriophages and bacteria, enhancing the anti-microbial or killing effect. These findings are relevant since the physicochemical properties of nano-emulsions (i.e. particle size distribution and zeta potential) are key in determining the efficacy of the formulation against infection in the context of responsive burn wound dressings-which is the main target for this work. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  13. Generalized zeta function representation of groups and 2-dimensional topological Yang-Mills theory: The example of GL(2, #Mathematical Double-Struck Capital F#{sub q}) and PGL(2, #Mathematical Double-Struck Capital F#{sub q})

    SciTech Connect

    Roche, Ph., E-mail: philippe.roche@univ-montp2.fr

    We recall the relation between zeta function representation of groups and two-dimensional topological Yang-Mills theory through Mednikh formula. We prove various generalisations of Mednikh formulas and define generalization of zeta function representations of groups. We compute some of these functions in the case of the finite group GL(2, #Mathematical Double-Struck Capital F#{sub q}) and PGL(2, #Mathematical Double-Struck Capital F#{sub q}). We recall the table characters of these groups for any q, compute the Frobenius-Schur indicator of their irreducible representations, and give the explicit structure of their fusion rings.

  14. The structure of a zeta class glutathione S-transferase from Arabidopsis thaliana: characterisation of a GST with novel active-site architecture and a putative role in tyrosine catabolism.

    PubMed

    Thom, R; Dixon, D P; Edwards, R; Cole, D J; Lapthorn, A J

    2001-05-18

    The cis-trans isomerisation of maleylacetoacetate to fumarylacetoacetate is the penultimate step in the tyrosine/phenylalanine catabolic pathway and has recently been shown to be catalysed by glutathione S-transferase enzymes belonging to the zeta class. Given this primary metabolic role it is unsurprising that zeta class glutathione S-transferases are well conserved over a considerable period of evolution, being found in vertebrates, plants, insects and fungi. The structure of this glutathione S-transferase, cloned from Arabidopsis thaliana, has been solved by single isomorphous replacement with anomalous scattering and refined to a final crystallographic R-factor of 19.6% using data from 25.0 A to 1.65 A. The zeta class enzyme adopts the canonical glutathione S-transferase fold and forms a homodimer with each subunit consisting of 221 residues. In agreement with structures of glutathione S-transferases from the theta and phi classes, a serine residue (Ser17) is present in the active site, at a position that would allow it to stabilise the thiolate anion of glutathione. Site-directed mutagenesis of this residue confirms its importance in catalysis. In addition, the role of a highly conserved cysteine residue (Cys19) present in the active site of the zeta class glutathione S-transferase enzymes is discussed. Copyright 2001 Academic Press.

  15. 10 CFR 830.202 - Safety basis.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 4 2011-01-01 2011-01-01 false Safety basis. 830.202 Section 830.202 Energy DEPARTMENT OF ENERGY NUCLEAR SAFETY MANAGEMENT Safety Basis Requirements § 830.202 Safety basis. (a) The contractor responsible for a hazard category 1, 2, or 3 DOE nuclear facility must establish and maintain the safety basis...

  16. 10 CFR 830.202 - Safety basis.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Safety basis. 830.202 Section 830.202 Energy DEPARTMENT OF ENERGY NUCLEAR SAFETY MANAGEMENT Safety Basis Requirements § 830.202 Safety basis. (a) The contractor responsible for a hazard category 1, 2, or 3 DOE nuclear facility must establish and maintain the safety basis...

  17. [Neurobiological basis of depressive disorders].

    PubMed

    Stoppel, C; Bielau, H; Bogerts, B; Northoff, G

    2006-12-01

    Depressive disorders belong to the most frequent diseases worldwide showing a lifetime prevalence of up to 20%. Moreover they are one of the leading causes for the amount of years lived with disability. Increasing knowledge about the pathological mechanisms underlying depressive syndromes is obtained by using modern neurobiological research-techniques. Thereby some older theories that have been the basis of emotion-research for decades--like the monoamine hypothesis--have been strengthened. In addition new aspects of the pathological processes underlying depressive disturbances have been unraveled. In this review established models and recent findings will be discussed, to bridge various research-fields, ranging from genetics, epigenetics and morphological changes to the functional consequences of depression. Finally therapeutic implications that could be derived from these results will be presented, showing up putative possibilities for diagnosis and treatment of depressive syndromes.

  18. FLAMMABLE GAS TECHNICAL BASIS DOCUMENT

    SciTech Connect

    KRIPPS, L.J.

    2005-02-18

    This document describes the qualitative evaluation of frequency and consequences for double shell tank (DST) and single shell tank (SST) representative flammable gas accidents and associated hazardous conditions without controls. The evaluation indicated that safety-significant SSCs and/or TSRS were required to prevent or mitigate flammable gas accidents. Discussion on the resulting control decisions is included. This technical basis document was developed to support of the Tank Farms Documented Safety Analysis (DSA) and describes the risk binning process for the flammable gas representative accidents and associated represented hazardous conditions. The purpose of the risk binning process is to determine the needmore » for safety-significant structures, systems, and components (SSC) and technical safety requirement (TSR)-level controls for a given representative accident or represented hazardous condition based on an evaluation of the event frequency and consequence.« less

  19. Internal dosimetry technical basis manual

    SciTech Connect

    Not Available

    1990-12-20

    The internal dosimetry program at the Savannah River Site (SRS) consists of radiation protection programs and activities used to detect and evaluate intakes of radioactive material by radiation workers. Examples of such programs are: air monitoring; surface contamination monitoring; personal contamination surveys; radiobioassay; and dose assessment. The objectives of the internal dosimetry program are to demonstrate that the workplace is under control and that workers are not being exposed to radioactive material, and to detect and assess inadvertent intakes in the workplace. The Savannah River Site Internal Dosimetry Technical Basis Manual (TBM) is intended to provide a technical and philosophicalmore » discussion of the radiobioassay and dose assessment aspects of the internal dosimetry program. Detailed information on air, surface, and personal contamination surveillance programs is not given in this manual except for how these programs interface with routine and special bioassay programs.« less

  20. The Chemical Basis of Pharmacology

    PubMed Central

    2010-01-01

    Molecular biology now dominates pharmacology so thoroughly that it is difficult to recall that only a generation ago the field was very different. To understand drug action today, we characterize the targets through which they act and new drug leads are discovered on the basis of target structure and function. Until the mid-1980s the information often flowed in reverse: investigators began with organic molecules and sought targets, relating receptors not by sequence or structure but by their ligands. Recently, investigators have returned to this chemical view of biology, bringing to it systematic and quantitative methods of relating targets by their ligands. This has allowed the discovery of new targets for established drugs, suggested the bases for their side effects, and predicted the molecular targets underlying phenotypic screens. The bases for these new methods, some of their successes and liabilities, and new opportunities for their use are described. PMID:21058655

  1. The neurological basis of occupation.

    PubMed

    Gutman, Sharon A; Schindler, Victoria P

    2007-01-01

    The purpose of the present paper was to survey the literature about the neurological basis of human activity and its relationship to occupation and health. Activities related to neurological function were organized into three categories: those that activate the brain's reward system; those that promote the relaxation response; and those that preserve cognitive function into old age. The results from the literature review correlating neurological evidence and activities showed that purposeful and meaningful activities could counter the effects of stress-related diseases and reduce the risk for dementia. Specifically, it was found that music, drawing, meditation, reading, arts and crafts, and home repairs, for example, can stimulate the neurogical system and enhance health and well-being, Prospective research studies are needed to examine the effects of purposeful activities on reducing stress and slowing the rate of cognitive decline.

  2. Identification and clarification of the role of key active site residues in bacterial glutathione S-transferase zeta/maleylpyruvate isomerase

    SciTech Connect

    Fang, Ti; Li, De-Feng; Zhou, Ning-Yi, E-mail: n.zhou@pentium.whiov.ac.cn

    2011-07-08

    Highlights: {yields} Application of site-directed mutagenesis to probe the active site residues of glutathione-dependent maleylpyruvate isomerase. {yields} Two conserved residues, Arg8 and Arg176, in zeta class glutathione S-transferases are critical for maleylpyruvate orientation and enolization. {yields} Arg109, found exclusively in NagL, participates in k{sub cat} regulation. {yields} The T11A mutant exhibited a significantly decreased K{sub m} value for glutathione with little impact on maleylpyruvate kinetics. {yields} The Thr11 residue appears to have significance in the evolution of glutathione S-transferase classes. -- Abstract: The maleylpyruvate isomerase NagL from Ralstonia sp. strain U2, which has been structurally characterized previously, catalyzes the isomerizationmore » of maleylpyruvate to fumarylpyruvate. It belongs to the class zeta glutathione S-transferases (GSTZs), part of the cytosolic GST family (cGSTs). In this study, site-directed mutagenesis was conducted to probe the functions of 13 putative active site residues. Steady-state kinetic information for mutants in the reduced glutathione (GSH) binding site, suggested that (a) Gln64 and Asp102 interact directly with the glutamyl moiety of glutathione, (b) Gln49 and Gln64 are involved in a potential electron-sharing network that influences the ionization of the GSH thiol. The information also suggests that (c) His38, Asn108 and Arg109 interact with the GSH glycine moiety, (d) His104 has a role in the ionization of the GSH sulfur and the stabilization of the maleyl terminal carboxyl group in the reaction intermediate and (e) Arg110 influences the electron distribution in the active site and therefore the ionization of the GSH thiolate. Kinetic data for mutants altered in the substrate-binding site imply that (a) Arg8 and Arg176 are critical for maleylpyruvate orientation and enolization, and (b) Arg109 (exclusive to NagL) participates in k{sub cat} regulation. Surprisingly, the T11A mutant

  3. A numerical fragment basis approach to SCF calculations.

    NASA Astrophysics Data System (ADS)

    Hinde, Robert J.

    1997-11-01

    The counterpoise method is often used to correct for basis set superposition error in calculations of the electronic structure of bimolecular systems. One drawback of this approach is the need to specify a ``reference state'' for the system; for reactive systems, the choice of an unambiguous reference state may be difficult. An example is the reaction F^- + HCl arrow HF + Cl^-. Two obvious reference states for this reaction are F^- + HCl and HF + Cl^-; however, different counterpoise-corrected interaction energies are obtained using these two reference states. We outline a method for performing SCF calculations which employs numerical basis functions; this method attempts to eliminate basis set superposition errors in an a priori fashion. We test the proposed method on two one-dimensional, three-center systems and discuss the possibility of extending our approach to include electron correlation effects.

  4. 42 CFR 412.400 - Basis and scope of subpart.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Inpatient Hospital Services of Inpatient Psychiatric Facilities § 412.400 Basis and scope of subpart. (a... psychiatric facilities. (b) Scope. This subpart sets forth the framework for the prospective payment system for the inpatient hospital services of inpatient psychiatric facilities, including the methodology...

  5. 42 CFR 421.300 - Basis, applicability, and scope.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 3 2011-10-01 2011-10-01 false Basis, applicability, and scope. 421.300 Section 421.300 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... organizational conflicts of interest. (5) Prescribes responsibilities. (6) Sets forth limitations on contractor...

  6. 40 CFR 35.162 - Basis for allotment.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... STATE AND LOCAL ASSISTANCE Environmental Program Grants Water Pollution Control (section 106) § 35.162 Basis for allotment. (a) Allotments. Each fiscal year funds appropriated for Water Pollution Control... for States under the Water Pollution Control grant program will be set aside for allotment to eligible...

  7. 42 CFR 493.1 - Basis and scope.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... AND CERTIFICATION LABORATORY REQUIREMENTS General Provisions § 493.1 Basis and scope. This part sets forth the conditions that all laboratories must meet to be certified to perform testing on human specimens under the Clinical Laboratory Improvement Amendments of 1988 (CLIA). It implements sections 1861...

  8. 42 CFR 493.1 - Basis and scope.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... AND CERTIFICATION LABORATORY REQUIREMENTS General Provisions § 493.1 Basis and scope. This part sets forth the conditions that all laboratories must meet to be certified to perform testing on human specimens under the Clinical Laboratory Improvement Amendments of 1988 (CLIA). It implements sections 1861...

  9. 45 CFR 402.30 - Basis of awards.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false Basis of awards. 402.30 Section 402.30 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN... award constitutes the authority to draw and expend funds for the purposes set forth in the Act and this...

  10. The basis function approach for modeling autocorrelation in ecological data

    USGS Publications Warehouse

    Hefley, Trevor J.; Broms, Kristin M.; Brost, Brian M.; Buderman, Frances E.; Kay, Shannon L.; Scharf, Henry; Tipton, John; Williams, Perry J.; Hooten, Mevin B.

    2017-01-01

    Analyzing ecological data often requires modeling the autocorrelation created by spatial and temporal processes. Many seemingly disparate statistical methods used to account for autocorrelation can be expressed as regression models that include basis functions. Basis functions also enable ecologists to modify a wide range of existing ecological models in order to account for autocorrelation, which can improve inference and predictive accuracy. Furthermore, understanding the properties of basis functions is essential for evaluating the fit of spatial or time-series models, detecting a hidden form of collinearity, and analyzing large data sets. We present important concepts and properties related to basis functions and illustrate several tools and techniques ecologists can use when modeling autocorrelation in ecological data.

  11. The basis function approach for modeling autocorrelation in ecological data.

    PubMed

    Hefley, Trevor J; Broms, Kristin M; Brost, Brian M; Buderman, Frances E; Kay, Shannon L; Scharf, Henry R; Tipton, John R; Williams, Perry J; Hooten, Mevin B

    2017-03-01

    Analyzing ecological data often requires modeling the autocorrelation created by spatial and temporal processes. Many seemingly disparate statistical methods used to account for autocorrelation can be expressed as regression models that include basis functions. Basis functions also enable ecologists to modify a wide range of existing ecological models in order to account for autocorrelation, which can improve inference and predictive accuracy. Furthermore, understanding the properties of basis functions is essential for evaluating the fit of spatial or time-series models, detecting a hidden form of collinearity, and analyzing large data sets. We present important concepts and properties related to basis functions and illustrate several tools and techniques ecologists can use when modeling autocorrelation in ecological data. © 2016 by the Ecological Society of America.

  12. Triplication of a four-gene set during evolution of the goat beta-globin locus produced three genes now expressed differentially during development.

    PubMed Central

    Townes, T M; Fitzgerald, M C; Lingrel, J B

    1984-01-01

    Distinct hemoglobins are synthesized in goats at different stages of development, similar to humans. Embryonic hemoglobins (zeta 2 epsilon 2 and alpha 2 epsilon 2) are synthesized initially and are followed sequentially by fetal (alpha 2 beta F2), preadult (alpha 2 beta C2), and adult (alpha 2 beta A2) hemoglobins. To help understand the basis of these switches, the genes of the beta-globin locus have been cloned and their linkage arrangement has been determined by the isolation of lambda phage carrying overlapping inserts of genomic goat DNA. The locus extends over 120 kilobase pairs and consists of 12 genes arranged in the following order: epsilon I-epsilon II-psi beta X-beta C-epsilon III-epsilon IV-psi beta Z-beta A-epsilon V-epsilon VI-psi beta Y-beta F. Comparison of the nucleotide sequence of the 12 genes shows that the locus is organized into three homologous four-gene sets that presumably evolved by the triplication of an ancestral set of four genes (epsilon-epsilon-psi beta-beta). Interestingly, the three genes (beta C, beta A, and beta F) located at the ends of the four-gene sets are expressed at different stages of development. Therefore, the goat beta F-, beta C-, and beta A-globin genes appear to have evolved by a mechanism that includes the triplication of 40-50 kilobase pairs of DNA and the recruitment of newly formed genes for expression in fetal, preadult, and adult life. PMID:6593719

  13. Comparison of localized basis and plane-wave basis for density-functional calculations of organic molecules on metals

    NASA Astrophysics Data System (ADS)

    Lee, Kyuho; Yu, Jaejun; Morikawa, Yoshitada

    2007-01-01

    Localized pseudoatomic orbitals (PAOs) are mainly optimized and tested for the strong chemical bonds within molecules and solids with their proven accuracy and efficiency, but are prone to significant basis set superposition error (BSSE) for weakly interacting systems. Here we test the accuracy of PAO basis in comparison with the BSSE-free plane-wave basis for the physisorption of pentacene molecule on Au (001) by calculating the binding energy, adsorption height, and energy level alignment. We show that both the large cutoff radius for localized PAOs and the counter-poise correction for BSSE are necessary to obtain well-converged physical properties. Thereby obtained results are as accurate as the plane-wave basis results. The comparison with experiment is given as well.

  14. Effect of contact angle, zeta potential and particles size on the in vitro studies of Al2O3 and SiO2 nanoparticles.

    PubMed

    Karunakaran, Gopalu; Suriyaprabha, Rangaraj; Rajendran, Venkatachalam; Kannan, Narayanasamy

    2015-02-01

    Currently, nanometal oxides find their role in different biological applications such as tissue engineering, implant and bone replacement materials. Owing to the increased use of nanoparticles, it is necessary to understand their release and toxicity in the biological system. In this regard, three independent studies such as in vitro cytotoxicity, antioxidant activity and biocompatibility of nano- and micrometal oxide particles such as alumina (Al2O3) and silica (SiO2) are evaluated. It is evident from cell viability study that nanoAl2O3 and SiO2 particles are less toxic when compared with microAl2O3 and SiO2 to NIH 3T3 cell lines up to 200 µg/ml. Antioxidant properties of micro- and nanoAl2O3 in terms of radical scavenging percentage for micro- and nanoAl2O3 are 59.1% and 72.1%, respectively, at 100 mg. Similarly, the radical scavenging percentage of nano- and bulk SiO2 are 81.0% and 67.2%, respectively. The present study reveals that the cellular behaviour, interaction and biocompatibility of metal oxides differ with dose, particle size, contact angle and zeta potential. The present study opens up a new strategy to analyse in vitro nanotoxicity.

  15. Essential role of protein kinase C zeta in transducing a motility signal induced by superoxide and a chemotactic peptide, fMLP.

    PubMed

    Kuribayashi, Kageaki; Nakamura, Kiminori; Tanaka, Maki; Sato, Tsutomu; Kato, Junji; Sasaki, Katsunori; Takimoto, Rishu; Kogawa, Katsuhisa; Terui, Takeshi; Takayama, Tetsuji; Onuma, Takayuki; Matsunaga, Takuya; Niitsu, Yoshiro

    2007-03-26

    Under various pathological conditions, including infection, malignancy, and autoimmune diseases, tissues are incessantly exposed to reactive oxygen species produced by infiltrating inflammatory cells. We show augmentation of motility associated with morphological changes of human squamous carcinoma SASH1 cells, human peripheral monocytes (hPMs), and murine macrophage-like cell line J774.1 by superoxide stimulation. We also disclose that motility of hPMs and J774.1 induced by a chemotactic peptide (N-formyl-methionyl-leucyl-phenylalanine [fMLP]) was inhibited by superoxide dismutase or N-acetylcystein, indicating stimulation of motility by superoxide generated by fMLP stimulation. In these cells, protein kinase C (PKC) zeta was activated to phosphorylate RhoGDI-1, which liberated RhoGTPases, leading to their activation. These events were inhibited by dominant-negative PKCzeta in SASH1 cells, myristoylated PKCzeta peptides in hPMs and J774.1, or a specific inhibitor of RhoGTPase in SASH1, hPMs, and J774.1. These results suggest a new approach for manipulation of inflammation as well as tumor cell invasion by targeting this novel signaling pathway.

  16. The preparation, surface structure, zeta potential, surface charge density and photocatalytic activity of TiO2 nanostructures of different shapes

    NASA Astrophysics Data System (ADS)

    Grover, Inderpreet Singh; Singh, Satnam; Pal, Bonamali

    2013-09-01

    Titania based nanocatalysts such as sodium titanates of different morphology having superior surface properties are getting wide importance in photocatalysis research. Despite having sodium (Na) contents and its high temperature synthesis (that generally deteriorate the photoreactivity), these Na-titanates often exhibit better photoactivity than P25-TiO2 catalyst. Hence, this work demonstrated the influence of crystal structure, BET surface area, surface charge, zeta potential (ζ) and metal loading on the photocatalytic activity of as-prepared sodium titanate nanotube (TNT) and titania nanorod (TNR). Straw like hollow orthorhombic-TNT (Na2Ti2O5·H2O) particles (W = 9-12 nm and L = 82-115 nm) and rice like pure anatase-TNR particles (W = 8-13 nm and L = 81-134 nm) are obtained by the hydrothermal treatment of P25-TiO2 with NaOH, which in fact, altered the net surface charge of TNT and TNR particles. The observed ζ = -2.82 (P25-TiO2), -13.5 (TNT) and -22.5 mV (TNR) are significantly altered by the Ag and Cu deposition. It has been found here that TNT displayed best photocatalytic activity for the imidacloprid insecticide (C9H10ClN5O2) degradation to CO2 formation under UV irradiation because of its largest surface area 176 m2 g-1 among the catalysts studied.

  17. Aprotinin stimulates angiogenesis and human endothelial cell migration through the growth factor pleiotrophin and its receptor protein tyrosine phosphatase beta/zeta.

    PubMed

    Koutsioumpa, Marina; Hatziapostolou, Maria; Mikelis, Constantinos; Koolwijk, Pieter; Papadimitriou, Evangelia

    2009-01-14

    Pleiotrophin is an 18 kDa secreted polypeptide growth factor with direct pro-angiogenic and tumorigenic properties. Pleiotrophin is a substrate for proteolytic enzymes, such as plasmin, leading to proteolytic fragments with distinct activities on endothelial cell activation in vitro or angiogenesis in vivo. Aprotinin is a naturally occurring broad spectrum protease inhibitor, used widely in cardiac surgery due to its ability to inhibit plasmin and reduce perioperative bleeding. Since we have seen that aprotinin inhibits proteolysis of pleiotrophin by plasmin, the aim of the present study was to evaluate the possible role of pleiotrophin in the effects of aprotinin on angiogenesis and human endothelial cell migration. Our data demonstrate that aprotinin, in a concentration-dependent manner, is angiogenic in the chicken embryo chorioallantoic membrane assay in vivo and induces human endothelial cell migration in vitro. Aprotinin inhibits pleiotrophin proteolysis and induces expression and secretion of pleiotrophin through an AP-1-dependent transcriptional activation of the pleiotrophin gene, and pleiotrophin seems to mediate the stimulatory effects of aprotinin on cell migration through its receptor protein tyrosine phosphatase beta/zeta. The stimulatory effect of aprotinin on pleiotrophin expression and cell migration may explain, at least partly, the problems observed with the clinical use of aprotinin.

  18. Density-functional theory of spherical electric double layers and zeta potentials of colloidal particles in restricted-primitive-model electrolyte solutions.

    PubMed

    Yu, Yang-Xin; Wu, Jianzhong; Gao, Guang-Hua

    2004-04-15

    A density-functional theory is proposed to describe the density profiles of small ions around an isolated colloidal particle in the framework of the restricted primitive model where the small ions have uniform size and the solvent is represented by a dielectric continuum. The excess Helmholtz energy functional is derived from a modified fundamental measure theory for the hard-sphere repulsion and a quadratic functional Taylor expansion for the electrostatic interactions. The theoretical predictions are in good agreement with the results from Monte Carlo simulations and from previous investigations using integral-equation theory for the ionic density profiles and the zeta potentials of spherical particles at a variety of solution conditions. Like the integral-equation approaches, the density-functional theory is able to capture the oscillatory density profiles of small ions and the charge inversion (overcharging) phenomena for particles with elevated charge density. In particular, our density-functional theory predicts the formation of a second counterion layer near the surface of highly charged spherical particle. Conversely, the nonlinear Poisson-Boltzmann theory and its variations are unable to represent the oscillatory behavior of small ion distributions and charge inversion. Finally, our density-functional theory predicts charge inversion even in a 1:1 electrolyte solution as long as the salt concentration is sufficiently high. (c) 2004 American Institute of Physics.

  19. Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO).

    PubMed

    Alborghetti, Marcos Rodrigo; Furlan, Ariane da Silva; da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

    2013-01-01

    Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.

  20. Structural Analysis of Intermolecular Interactions in the Kinesin Adaptor Complex Fasciculation and Elongation Protein Zeta 1/ Short Coiled-Coil Protein (FEZ1/SCOCO)

    PubMed Central

    da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L.; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

    2013-01-01

    Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth. PMID:24116125

  1. The genetic basis of gout.

    PubMed

    Merriman, Tony R; Choi, Hyon K; Dalbeth, Nicola

    2014-05-01

    Gout results from deposition of monosodium urate (MSU) crystals. Elevated serum urate concentrations (hyperuricemia) are not sufficient for the development of disease. Genome-wide association studies (GWAS) have identified 28 loci controlling serum urate levels. The largest genetic effects are seen in genes involved in the renal excretion of uric acid, with others being involved in glycolysis. Whereas much is understood about the genetic control of serum urate levels, little is known about the genetic control of inflammatory responses to MSU crystals. Extending knowledge in this area depends on recruitment of large, clinically ascertained gout sample sets suitable for GWAS. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. The anatomical basis for wrinkles.

    PubMed

    Pessa, Joel E; Nguyen, Hang; John, George B; Scherer, Philipp E

    2014-02-01

    Light and electron microscopy have not identified a distinct anatomical structure associated with either skin wrinkles or creases, and a histological difference between wrinkled and adjacent skin has not been identified. The authors investigate whether facial wrinkles are related to underlying lymphatic vessels and perilymphatic fat. Lymphatic vessels with a specialized tube of perilymphatic fat were identified beneath palmar creases. Sections of skin, adipose tissue, and muscle were harvested from each of 13 cadavers. Three sites were investigated: the transverse forehead crease, lateral orbicularis oculi wrinkle (crow's feet), and the nasojugal crease. The tissue was paraffin embedded and processed. Two-step indirect immunohistochemistry was performed, and images were examined using laser confocal microscopy. Measurements were taken with software. Every wrinkle examined was found above and within ±1 mm of a major lymphatic vessel and its surrounding tube of adipose tissue. The results satisfied our null hypothesis and were statistically significant. Lymphatic vessels were identified by positive immunofluorescence as well as histological criteria. These findings have been further validated by fluorochrome tracer studies. An anatomical basis for wrinkles was identified among the specimens studied. Lymphatic vessels, along with the surrounding distinct perilymphatic fat, traveled directly beneath wrinkles and creases. Lymphatic dysregulation leads to inflammation, scarring, and fibrosis, but inadvertent injection of these vessels can be avoided with anatomical knowledge.

  3. Molecular basis of atopic dermatitis.

    PubMed

    Bonness, Sonja; Bieber, Thomas

    2007-10-01

    Atopic dermatitis is a common chronic inflammatory skin disease and there are numerous publications on this topic. This review will focus on developments in understanding the molecular basis of atopic dermatitis while considering the genetic background, skin barrier impairment, immune system deviation and microbial superinfections. Atopic dermatitis is a complex genetic disease in which gene-gene and gene-environment interactions play a key role. Surprisingly some genetic regions of interest were found to be overlapping with loci identified to play a role in another very common inflammatory skin disease, psoriasis, while no overlap has so far been observed with asthma. Impairment of the skin barrier followed by antigens trespassing seems to play an important role, favouring sensitization via transepidermal penetration which is the focus of current investigations. Superinfections by pathogens such as Staphylococcus aureus due to a weak innate defence seem to be significant in atopic dermatitis as they elicit a strong inflammatory response. Atopic dermatitis is a chronic inflammatory skin disease with a high incidence in school children and adults. Disease pathogenesis is complex and the background is multifactorial, making the underlying predispositions elusive. Understanding new pathogenic pathways may lead to the development of new drugs with enhanced benefit for the patient.

  4. The Interpolation Theory of Radial Basis Functions

    NASA Astrophysics Data System (ADS)

    Baxter, Brad

    2010-06-01

    In this dissertation, it is first shown that, when the radial basis function is a p-norm and 1 < p < 2, interpolation is always possible when the points are all different and there are at least two of them. We then show that interpolation is not always possible when p > 2. Specifically, for every p > 2, we construct a set of different points in some Rd for which the interpolation matrix is singular. The greater part of this work investigates the sensitivity of radial basis function interpolants to changes in the function values at the interpolation points. Our early results show that it is possible to recast the work of Ball, Narcowich and Ward in the language of distributional Fourier transforms in an elegant way. We then use this language to study the interpolation matrices generated by subsets of regular grids. In particular, we are able to extend the classical theory of Toeplitz operators to calculate sharp bounds on the spectra of such matrices. Applying our understanding of these spectra, we construct preconditioners for the conjugate gradient solution of the interpolation equations. Our main result is that the number of steps required to achieve solution of the linear system to within a required tolerance can be independent of the number of interpolation points. The Toeplitz structure allows us to use fast Fourier transform techniques, which imp lies that the total number of operations is a multiple of n log n, where n is the number of interpolation points. Finally, we use some of our methods to study the behaviour of the multiquadric when its shape parameter increases to infinity. We find a surprising link with the sinus cardinalis or sinc function of Whittaker. Consequently, it can be highly useful to use a large shape parameter when approximating band-limited functions.

  5. Positive basis for surface skein algebras

    PubMed Central

    Thurston, Dylan Paul

    2014-01-01

    We show that the twisted SL2 skein algebra of a surface has a natural basis (the bracelets basis) that is positive, in the sense that the structure constants for multiplication are positive integers. PMID:24982193

  6. Gaussian basis functions for highly oscillatory scattering wavefunctions

    NASA Astrophysics Data System (ADS)

    Mant, B. P.; Law, M. M.

    2018-04-01

    We have applied a basis set of distributed Gaussian functions within the S-matrix version of the Kohn variational method to scattering problems involving deep potential energy wells. The Gaussian positions and widths are tailored to the potential using the procedure of Bačić and Light (1986 J. Chem. Phys. 85 4594) which has previously been applied to bound-state problems. The placement procedure is shown to be very efficient and gives scattering wavefunctions and observables in agreement with direct numerical solutions. We demonstrate the basis function placement method with applications to hydrogen atom–hydrogen atom scattering and antihydrogen atom–hydrogen atom scattering.

  7. The effect of diffuse basis functions on valence bond structural weights

    NASA Astrophysics Data System (ADS)

    Galbraith, John Morrison; James, Andrew M.; Nemes, Coleen T.

    2014-03-01

    Structural weights and bond dissociation energies have been determined for H-F, H-X, and F-X molecules (-X = -OH, -NH2, and -CH3) at the valence bond self-consistent field (VBSCF) and breathing orbital valence bond (BOVB) levels of theory with the aug-cc-pVDZ and 6-31++G(d,p) basis sets. At the BOVB level, the aug-cc-pVDZ basis set yields a counterintuitive ordering of ionic structural weights when the initial heavy atom s-type basis functions are included. For H-F, H-OH, and F-X, the ordering follows chemical intuition when these basis functions are not included. These counterintuitive weights are shown to be a result of the diffuse polarisation function on one VB fragment being spatially located, in part, on the other VB fragment. Except in the case of F-CH3, this problem is corrected with the 6-31++G(d,p) basis set. The initial heavy atom s-type functions are shown to make an important contribution to the VB orbitals and bond dissociation energies and, therefore, should not be excluded. It is recommended to not use diffuse basis sets in valence bond calculations unless absolutely necessary. If diffuse basis sets are needed, the 6-31++G(d,p) basis set should be used with caution and the structural weights checked against VBSCF values which have been shown to follow the expected ordering in all cases.

  8. UpSet: Visualization of Intersecting Sets

    PubMed Central

    Lex, Alexander; Gehlenborg, Nils; Strobelt, Hendrik; Vuillemot, Romain; Pfister, Hanspeter

    2016-01-01

    Understanding relationships between sets is an important analysis task that has received widespread attention in the visualization community. The major challenge in this context is the combinatorial explosion of the number of set intersections if the number of sets exceeds a trivial threshold. In this paper we introduce UpSet, a novel visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections. UpSet is focused on creating task-driven aggregates, communicating the size and properties of aggregates and intersections, and a duality between the visualization of the elements in a dataset and their set membership. UpSet visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes. Sorting according to various measures enables a task-driven analysis of relevant intersections and aggregates. The elements represented in the sets and their associated attributes are visualized in a separate view. Queries based on containment in specific intersections, aggregates or driven by attribute filters are propagated between both views. We also introduce several advanced visual encodings and interaction methods to overcome the problems of varying scales and to address scalability. UpSet is web-based and open source. We demonstrate its general utility in multiple use cases from various domains. PMID:26356912

  9. Transcript levels of the soluble sperm factor protein phospholipase C zeta 1 (PLCζ1) increase through induced spermatogenesis in European eel.

    PubMed

    Morini, Marina; Peñaranda, David S; Vílchez, María C; Gallego, Víctor; Nourizadeh-Lillabadi, Rasoul; Asturiano, Juan F; Weltzien, Finn-Arne; Pérez, Luz

    2015-09-01

    Activation at fertilization of the vertebrate egg is triggered by Ca(2+) waves. Recent studies suggest the phospholipase C zeta (PLCζ), a sperm-specific protein, triggers egg activation by an IP3-mediated Ca(2+) release and allow Ca(2+) waves at fertilization. In the present study we cloned, characterized, and phylogenetically positioned the European eel PLCζ (PLCζ1). It is 1521 bp long, with 10 exons encoding an open reading frame of 506 amino acids. The amino acid sequence contains an EF-hand domain, X and Y catalytic domains, and a carboxy-terminal C2 domain, all typical of other PLCζ orthologous. The tissue distribution was studied, and the gene expression was determined in testis during induced sexual maturation at three different thermal regimes. Also, brain and pituitary expression was studied through sex maturation at constant temperature. plcζ1 was expressed in brain of male and female, in testis but not in ovaries. By first time in vertebrates, it is reported plcζ1 expression in the pituitary gland. Testis plcζ1 expression increased through spermatogenesis under all the thermal regimes, but being significantly elevated at lower temperatures. It was very low when testis contained only spermatogonia or spermatocytes, while maximum expression was found during spermiogenesis. These results support the hypothesis for an eel sperm-specific PLCζ1 inducing egg activation, similarly to mammals and some teleosts, but different from some other teleost species, which express this protein in ovaries, but not in testes. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Genome-wide association study identifies phospholipase C zeta 1 (PLCz1) as a stallion fertility locus in Hanoverian warmblood horses.

    PubMed

    Schrimpf, Rahel; Dierks, Claudia; Martinsson, Gunilla; Sieme, Harald; Distl, Ottmar

    2014-01-01

    A consistently high level of stallion fertility plays an economically important role in modern horse breeding. We performed a genome-wide association study for estimated breeding values of the paternal component of the pregnancy rate per estrus cycle (EBV-PAT) in Hanoverian stallions. A total of 228 Hanoverian stallions were genotyped using the Equine SNP50 Beadchip. The most significant association was found on horse chromosome 6 for a single nucleotide polymorphism (SNP) within phospholipase C zeta 1 (PLCz1). In the close neighbourhood to PLCz1 is located CAPZA3 (capping protein (actin filament) muscle Z-line, alpha 3). The gene PLCz1 encodes a protein essential for spermatogenesis and oocyte activation through sperm induced Ca2+-oscillation during fertilization. We derived equine gene models for PLCz1 and CAPZA3 based on cDNA and genomic DNA sequences. The equine PLCz1 had four different transcripts of which two contained a premature termination codon. Sequencing all exons and their flanking sequences using genomic DNA samples from 19 Hanoverian stallions revealed 47 polymorphisms within PLCz1 and one SNP within CAPZA3. Validation of these 48 polymorphisms in 237 Hanoverian stallions identified three intronic SNPs within PLCz1 as significantly associated with EBV-PAT. Bioinformatic analysis suggested regulatory effects for these SNPs via transcription factor binding sites or microRNAs. In conclusion, non-coding polymorphisms within PLCz1 were identified as conferring stallion fertility and PLCz1 as candidate locus for male fertility in Hanoverian warmblood. CAPZA3 could be eliminated as candidate gene for fertility in Hanoverian stallions.

  11. Zeta Inhibitory Peptide Disrupts Electrostatic Interactions That Maintain Atypical Protein Kinase C in Its Active Conformation on the Scaffold p62.

    PubMed

    Tsai, Li-Chun Lisa; Xie, Lei; Dore, Kim; Xie, Li; Del Rio, Jason C; King, Charles C; Martinez-Ariza, Guillermo; Hulme, Christopher; Malinow, Roberto; Bourne, Philip E; Newton, Alexandra C

    2015-09-04

    Atypical protein kinase C (aPKC) enzymes signal on protein scaffolds, yet how they are maintained in an active conformation on scaffolds is unclear. A myristoylated peptide based on the autoinhibitory pseudosubstrate fragment of the atypical PKCζ, zeta inhibitory peptide (ZIP), has been extensively used to inhibit aPKC activity; however, we have previously shown that ZIP does not inhibit the catalytic activity of aPKC isozymes in cells (Wu-Zhang, A. X., Schramm, C. L., Nabavi, S., Malinow, R., and Newton, A. C. (2012) J. Biol. Chem. 287, 12879-12885). Here we sought to identify a bona fide target of ZIP and, in so doing, unveiled a novel mechanism by which aPKCs are maintained in an active conformation on a protein scaffold. Specifically, we used protein-protein interaction network analysis, structural modeling, and protein-protein docking to predict that ZIP binds an acidic surface on the Phox and Bem1 (PB1) domain of p62, an interaction validated by peptide array analysis. Using a genetically encoded reporter for PKC activity fused to the p62 scaffold, we show that ZIP inhibits the activity of wild-type aPKC, but not a construct lacking the pseudosubstrate. These data support a model in which the pseudosubstrate of aPKCs is tethered to the acidic surface on p62, locking aPKC in an open, signaling-competent conformation. ZIP competes for binding to the acidic surface, resulting in displacement of the pseudosubstrate of aPKC and re-engagement in the substrate-binding cavity. This study not only identifies a cellular target for ZIP, but also unveils a novel mechanism by which scaffolded aPKC is maintained in an active conformation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Phospholipase C-zeta deficiency as a cause for repetitive oocyte fertilization failure during ovarian stimulation for in vitro fertilization with ICSI: a case report.

    PubMed

    Chithiwala, Zahabiya H; Lee, Hoi Chang; Hill, David L; Jellerette-Nolan, Teru; Fissore, Rafael; Grow, Daniel; Dumesic, Daniel A

    2015-09-01

    The purpose of this study is to describe impaired oocyte fertilization from phospholipase C-zeta (PLC-ζ) deficiency in normal-appearing sperm that was successfully treated using calcium (Ca(2+)) ionophore with intracytoplasmic sperm injection (ICSI) of oocytes matured in vitro. An infertile couple undergoing in vitro fertilization (IVF) experienced failed oocyte fertilization following ICSI with normal-appearing sperm. A semen sample collected from the patient was used to assess the expression of sperm PLC- ζ protein by Western blot analysis and immunofluorescence and PLC-ζ bioactivity by an in vitro model of Ca(2+) release. A second IVF cycle was performed using Ca(2+) ionophore with ICSI to enhance Ca(2+)-induced oocyte activation of oocytes matured in vitro. Sperm PLC-ζ protein deficiency was demonstrated by Western blot analysis and immunofluorescence and confirmed by reduced PLC-ζ bioactivity using an in vitro model of Ca(2+) release. Nevertheless, with this sperm and supplementation of Ca(2+) ionophore following ICSI, fertilization of four of six oocytes matured in vitro was obtained. In addition, four embryos underwent cleavage and two of them reached the blastocyst stage. Transfer of these blastocysts into the uterus led to a single pregnancy and live birth. Deficiency of PLC-ζ in normal-appearing human sperm is associated with impaired Ca(2+)-dependent oocyte activation during ICSI. Under this condition, use of Ca(2+) ionophore following ICSI of oocytes matured in vitro improves embryo developmental competence, possibly through the activation of Ca(2+)-dependent mechanisms governing fertilization and preimplantation embryogenesis.

  13. Environmental Enrichment Increases Glucocorticoid Receptors and Decreases GluA2 and Protein Kinase M Zeta (PKMζ) Trafficking During Chronic Stress: A Protective Mechanism?

    PubMed Central

    Zanca, Roseanna M.; Braren, Stephen H.; Maloney, Brigid; Schrott, Lisa M.; Luine, Victoria N.; Serrano, Peter A.

    2015-01-01

    Environmental enrichment (EE) housing paradigms have long been shown beneficial for brain function involving neural growth and activity, learning and memory capacity, and for developing stress resiliency. The expression of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subunit GluA2, which is important for synaptic plasticity and memory, is increased with corticosterone (CORT), undermining synaptic plasticity and memory. Thus, we determined the effect of EE and stress on modulating GluA2 expression in Sprague-Dawley male rats. Several markers were evaluated which include: plasma CORT, the glucocorticoid receptor (GR), GluA2, and the atypical protein kinase M zeta (PKMζ). For 1 week standard-(ST) or EE-housed animals were treated with one of the following four conditions: (1) no stress; (2) acute stress (forced swim test, FST; on day 7); (3) chronic restraint stress (6 h/day for 7 days); and (4) chronic + acute stress (restraint stress 6 h/day for 7 days + FST on day 7). Hippocampi were collected on day 7. Our results show that EE animals had reduced time immobile on the FST across all conditions. After chronic + acute stress EE animals showed increased GR levels with no change in synaptic GluA2/PKMζ. ST-housed animals showed the reverse pattern with decreased GR levels and a significant increase in synaptic GluA2/PKMζ. These results suggest that EE produces an adaptive response to chronic stress allowing for increased GR levels, which lowers neuronal excitability reducing GluA2/PKMζ trafficking. We discuss this EE adaptive response to stress as a potential underlying mechanism that is protective for retaining synaptic plasticity and memory function. PMID:26617502

  14. Effects of mechanical loading on the expression of pleiotrophin and its receptor protein tyrosine phosphatase beta/zeta in a rat spinal deformity model.

    PubMed

    Kaspiris, Angelos; Chronopoulos, Efstathios; Grivas, Theodoros B; Vasiliadis, Elias; Khaldi, Lubna; Lamprou, Margarita; Lelovas, Pavlos P; Papaioannou, Nikolaos; Dontas, Ismene A; Papadimitriou, Evangelia

    2016-02-01

    Mechanical loading of the spine is a major causative factor of degenerative changes and causes molecular and structural changes in the intervertebral disc (IVD) and the vertebrae end plate (EP). Pleiotrophin (PTN) is a growth factor with a putative role in bone remodeling through its receptor protein tyrosine phosphatase beta/zeta (RPTPβ/ζ). The present study investigates the effects of strain on PTN and RPTPβ/ζ protein expression in vivo. Tails of eight weeks old Sprague-Dawley rats were subjected to mechanical loading using a mini Ilizarov external apparatus. Rat tails untreated (control) or after 0 degrees of compression and 10°, 30° and 50° of angulation (groups 0, I, II and III respectively) were studied. PTN and RPTPβ/ζ expression were evaluated using immunohistochemistry and Western blot analysis. In the control group, PTN was mostly expressed by the EP hypertrophic chondrocytes. In groups 0 to II, PTN expression was increased in the chondrocytes of hypertrophic and proliferating zones, as well as in osteocytes and osteoblast-like cells of the ossification zone. In group III, only limited PTN expression was observed in osteocytes. RPTPβ/ζ expression was increased mainly in group 0, but also in group I, in all types of cells. Low intensity RPTPβ/ζ immunostaining was observed in groups II and III. Collectively, PTN and RPTPβ/ζ are expressed in spinal deformities caused by mechanical loading, and their expression depends on the type and severity of the applied strain. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Genome-Wide Association Study Identifies Phospholipase C zeta 1 (PLCz1) as a Stallion Fertility Locus in Hanoverian Warmblood Horses

    PubMed Central

    Schrimpf, Rahel; Dierks, Claudia; Martinsson, Gunilla; Sieme, Harald; Distl, Ottmar

    2014-01-01

    A consistently high level of stallion fertility plays an economically important role in modern horse breeding. We performed a genome-wide association study for estimated breeding values of the paternal component of the pregnancy rate per estrus cycle (EBV-PAT) in Hanoverian stallions. A total of 228 Hanoverian stallions were genotyped using the Equine SNP50 Beadchip. The most significant association was found on horse chromosome 6 for a single nucleotide polymorphism (SNP) within phospholipase C zeta 1 (PLCz1). In the close neighbourhood to PLCz1 is located CAPZA3 (capping protein (actin filament) muscle Z-line, alpha 3). The gene PLCz1 encodes a protein essential for spermatogenesis and oocyte activation through sperm induced Ca2+-oscillation during fertilization. We derived equine gene models for PLCz1 and CAPZA3 based on cDNA and genomic DNA sequences. The equine PLCz1 had four different transcripts of which two contained a premature termination codon. Sequencing all exons and their flanking sequences using genomic DNA samples from 19 Hanoverian stallions revealed 47 polymorphisms within PLCz1 and one SNP within CAPZA3. Validation of these 48 polymorphisms in 237 Hanoverian stallions identified three intronic SNPs within PLCz1 as significantly associated with EBV-PAT. Bioinformatic analysis suggested regulatory effects for these SNPs via transcription factor binding sites or microRNAs. In conclusion, non-coding polymorphisms within PLCz1 were identified as conferring stallion fertility and PLCz1 as candidate locus for male fertility in Hanoverian warmblood. CAPZA3 could be eliminated as candidate gene for fertility in Hanoverian stallions. PMID:25354211

  16. The system neurophysiological basis of backward inhibition.

    PubMed

    Zhang, Rui; Stock, Ann-Kathrin; Fischer, Rico; Beste, Christian

    2016-12-01

    Task switching is regularly required in our everyday life. To succeed in switching, it is important to inhibit the most recently performed task and instead activate the currently relevant task. The process that inhibits a recently performed task when a new task is to be performed is referred to as 'backward inhibition' (BI). While the BI effect has been subject to intense research in cognitive psychology, little is known about the neuronal mechanisms that are related to the BI effect and those that relate to differences in the magnitude of the BI effect. In the current study, we examined the system neurophysiological basis of BI processes using event-related potentials (ERPs) and sLORETA by also taking inter-individual differences in the magnitude of the BI into account. The results suggest that BI processes and inter-individual differences in them strongly depend upon attentional selection mechanisms (reflected by N1-ERP modulations in the current task/trial) mediated via networks consisting of extrastriate occipital areas, the temporo-parietal junction and the inferior frontal gyrus. Other processes and mechanisms related to conflict monitoring, response selection, or the updating, organization and implementation of a new task-set (i.e. N2 and P3 processes) were not shown to be modulated by BI processes and differences in their magnitude, as evoked with a common BI paradigm.

  17. Electromagnetic Basis of Metabolism and Heredity

    NASA Technical Reports Server (NTRS)

    Freund, Friedemann; Stolc, Viktor

    2016-01-01

    Living organisms control their cellular biological clocks to maintain functional oscillation of the redox cycle, also called the "metabolic cycle" or "respiratory cycle". Organization of cellular processes requires parallel processing on a synchronized time-base. These clocks coordinate the timing of all biochemical processes in the cell, including energy production, DNA replication, and RNA transcription. When this universal time keeping function is perturbed by exogenous induction of reactive oxygen species (ROS), the rate of metabolism changes. This causes oxidative stress, aging and mutations. Therefore, good temporal coordination of the redox cycle not only actively prevents chemical conflict between the reductive and oxidative partial reactions; it also maintains genome integrity and lifespan. Moreover, this universal biochemical rhythm can be disrupted by ROS induction in vivo. This in turn can be achieved by blocking the electron transport chain either endogenously or exogenously by various metabolites, e.g. hydrogen sulfide (H2S), highly diffusible drugs, and carbon monoxide (CO). Alternatively, the electron transport in vivo can be attenuated via a coherent or interfering transfer of energy from exogenous ultralow frequency (ULF) and extremely low frequency (ELF) electromagnetic (EM) fields, suggesting that-on Earth-such ambient fields are an omnipresent (and probably crucially important) factor for the time-setting basis of universal biochemical reactions in living cells. Our work demonstrated previously un-described evidence for quantum effects in biology by electromagnetic coupling below thermal noise at the universal electron transport chain (ETC) in vivo.

  18. Lysine N[superscript zeta]-Decarboxylation Switch and Activation of the [beta]-Lactam Sensor Domain of BlaR1 Protein of Methicillin-resistant Staphylococcus aureus

    SciTech Connect

    Borbulevych, Oleg; Kumarasiri, Malika; Wilson, Brian

    The integral membrane protein BlaR1 of methicillin-resistant Staphylococcus aureus senses the presence of {beta}-lactam antibiotics in the milieu and transduces the information to the cytoplasm, where the biochemical events that unleash induction of antibiotic resistance mechanisms take place. We report herein by two-dimensional and three-dimensional NMR experiments of the sensor domain of BlaR1 in solution and by determination of an x-ray structure for the apo protein that Lys-392 of the antibiotic-binding site is posttranslationally modified by N{sup {zeta}}-carboxylation. Additional crystallographic and NMR data reveal that on acylation of Ser-389 by antibiotics, Lys-392 experiences N{sup {zeta}}-decarboxylation. This unique process, termed themore » lysine N{sup {zeta}}-decarboxylation switch, arrests the sensor domain in the activated ('on') state, necessary for signal transduction and all the subsequent biochemical processes. We present structural information on how this receptor activation process takes place, imparting longevity to the antibiotic-receptor complex that is needed for the induction of the antibiotic-resistant phenotype in methicillin-resistant S. aureus.« less

  19. Initial evaluation of discrete orthogonal basis reconstruction of ECT images

    SciTech Connect

    Moody, E.B.; Donohue, K.D.

    1996-12-31

    Discrete orthogonal basis restoration (DOBR) is a linear, non-iterative, and robust method for solving inverse problems for systems characterized by shift-variant transfer functions. This simulation study evaluates the feasibility of using DOBR for reconstructing emission computed tomographic (ECT) images. The imaging system model uses typical SPECT parameters and incorporates the effects of attenuation, spatially-variant PSF, and Poisson noise in the projection process. Sample reconstructions and statistical error analyses for a class of digital phantoms compare the DOBR performance for Hartley and Walsh basis functions. Test results confirm that DOBR with either basis set produces images with good statistical properties. Nomore » problems were encountered with reconstruction instability. The flexibility of the DOBR method and its consistent performance warrants further investigation of DOBR as a means of ECT image reconstruction.« less

  20. Neural-like computing with populations of superparamagnetic basis functions.

    PubMed

    Mizrahi, Alice; Hirtzlin, Tifenn; Fukushima, Akio; Kubota, Hitoshi; Yuasa, Shinji; Grollier, Julie; Querlioz, Damien

    2018-04-18

    In neuroscience, population coding theory demonstrates that neural assemblies can achieve fault-tolerant information processing. Mapped to nanoelectronics, this strategy could allow for reliable computing with scaled-down, noisy, imperfect devices. Doing so requires that the population components form a set of basis functions in terms of their response functions to inputs, offering a physical substrate for computing. Such a population can be implemented with CMOS technology, but the corresponding circuits have high area or energy requirements. Here, we show that nanoscale magnetic tunnel junctions can instead be assembled to meet these requirements. We demonstrate experimentally that a population of nine junctions can implement a basis set of functions, providing the data to achieve, for example, the generation of cursive letters. We design hybrid magnetic-CMOS systems based on interlinked populations of junctions and show that they can learn to realize non-linear variability-resilient transformations with a low imprint area and low power.

  1. Basis for paraxial surface-plasmon-polariton packets

    NASA Astrophysics Data System (ADS)

    Martinez-Herrero, Rosario; Manjavacas, Alejandro

    2016-12-01

    We present a theoretical framework for the study of surface-plasmon polariton (SPP) packets propagating along a lossy metal-dielectric interface within the paraxial approximation. Using a rigorous formulation based on the plane-wave spectrum formalism, we introduce a set of modes that constitute a complete basis set for the solutions of Maxwell's equations for a metal-dielectric interface in the paraxial approximation. The use of this set of modes allows us to fully analyze the evolution of the transversal structure of SPP packets beyond the single plane-wave approximation. As a paradigmatic example, we analyze the case of a Gaussian SPP mode, for which, exploiting the analogy with paraxial optical beams, we introduce a set of parameters that characterize its propagation.

  2. Comparison of ZetaPlus 60S and nitrocellulose membrane filters for the simultaneous concentration of F-RNA coliphages, porcine teschovirus and porcine adenovirus from river water.

    PubMed

    Jones, T H; Muehlhauser, V; Thériault, G

    2014-09-01

    Increasing attention is being paid to the impact of agricultural activities on water quality to understand the impact on public health. F-RNA coliphages have been proposed as viral indicators of fecal contamination while porcine teschovirus (PTV) and porcine adenovirus (PAdV) are proposed indicators of fecal contamination of swine origin. Viruses and coliphages are present in water in very low concentrations and must be concentrated to permit their detection. There is little information comparing the effectiveness of the methods for concentrating F-RNA coliphages with concentration methods for other viruses and vice versa. The objective of this study was to compare 5 current published methods for recovering F-RNA coliphages, PTV and PAdV from river water samples concentrated by electronegative nitrocellulose membrane filters (methods A and B) or electropositive Zeta Plus 60S filters (methods C-E). Method A is used routinely for the detection of coliphages (Méndez et al., 2004) and method C (Brassard et al., 2005) is the official method in Health Canada's compendium for the detection of viruses in bottled mineral or spring water. When river water was inoculated with stocks of F-RNA MS2, PAdV, and PTV to final concentrations of 1×10(6) PFU/100 mL, 1×10(5) gc/100 mL and 3×10(5) gc/100 mL, respectively, a significantly higher recovery for each virus was consistently obtained for method A with recoveries of 52% for MS2, 95% for PAdV, and 1.5% for PTV. When method A was compared with method C for the detection of F-coliphages, PAdV and PTV in river water samples, viruses were detected with higher frequencies and at higher mean numbers with method A than with method C. With method A, F-coliphages were detected in 11/12 samples (5-154 PFU/100 mL), PTV in 12/12 samples (397-10,951 gc/100 mL), PAdV in 1/12 samples (15 gc/100 mL), and F-RNA GIII in 1/12 samples (750 gc/100 mL) while F-RNA genotypes I, II, and IV were not detected by qRT-PCR. Crown Copyright © 2014

  3. Experimental Basis for IED Particle Model

    NASA Astrophysics Data System (ADS)

    Zheng-Johansson, J.

    2009-03-01

    The internally electrodynamic (IED) particle model is built on three experimental facts: a) electric charges present in all matter particles, b) an accelerated charge generates electromagnetic (EM) waves by Maxwell's equations and Planck energy equation, and c) source motion gives Doppler effect. A set of well-kwon basic particle equations have been predicted based on first-principles solutions for IED particle (e.g. J Phys CS128, 012019, 2008); the equations are long experimentally validated. A critical review of the key experiments suggests that the IED process underlies these equations not just sufficiently but also necessarily. E.g.: 1) A free IED electron solution is a plane wave ψ= Ce^i(kdX-φT) requisite for producing the diffraction fringe in a Davisson-Germer experiment, and of also all basic point-like attributes facilitated by a linear momentum kd and the model structure. It needs not further be a wave packet which produces not a diffraction fringe. 2)The radial partial EM waves, hence the total ψ, of an IED electron will, on both EM theory and experiment basis -not by assumption, enter two slits at the same time, as is requisite for an electron to interfere with itself as shown in double slit experiments. 3) On annihilation, an electron converts (from mass m) to a radiation energy φ without an acceleration which is externally observable and yet requisite by EM theory. So a charge oscillation of frequency φ and its EM waves must regularly present internal of a normal electron, whence the IED model.

  4. Experimental Basis for IED Particle Model

    NASA Astrophysics Data System (ADS)

    Zheng-Johansson, J.

    2009-05-01

    The internally electrodynamic (IED) particle model is built on three experimental facts: a) electric charges present in all matter particles, b) an accelerated charge generates electromagnetic (EM) waves by Maxwell's equations and Planck energy equation, and c) source motion gives Doppler effect. A set of well-kwon basic particle equations have been predicted based on first-principles solutions for IED particle (e.g. arxiv:0812.3951, J Phys CS128, 012019, 2008); the equations are long experimentally validated. A critical review of the key experiments suggests that the IED process underlies these equations not just sufficiently but also necessarily. E.g.: 1) A free IED electron solution is a plane wave ψ= Ce^i(kdX-φT) requisite for producing the diffraction fringe in a Davisson-Germer experiment, and of also all basic point-like attributes facilitated by a linear momentum kd and the model structure. It needs not further be a wave packet which produces not a diffraction fringe. 2)The radial partial EM waves, hence the total ψ, of an IED electron will, on both EM theory and experiment basis -not by assumption, enter two slits at the same time, as is requisite for an electron to interfere with itself as shown in double slit experiments. 3) On annihilation, an electron converts (from mass m) to a radiation energy φ without an acceleration which is externally observable and yet requisite by EM theory. So a charge oscillation of frequency φ and its EM waves must regularly present internal of a normal electron, whence the IED model.

  5. 27ps DFT Molecular Dynamics Simulation of a-maltose: A Reduced Basis Set Study.

    USDA-ARS?s Scientific Manuscript database

    DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose, requiring up to three or more weeks on a fast 16-processor computer to obtain just 5ps of constant energy dynamics. In a recent publication [1] forces for dynamics were generated from B3LY...

  6. 27ps DFTMD Simulations of Maltose using a Reduced Basis Set

    USDA-ARS?s Scientific Manuscript database

    The disaccharide, a-maltose, has been studied using constant energy density functional molecular dynamics (DFTMD) at the B3LYP/6-31+G*/4-31G+COSMO (solvent) level of theory. Maltose is of particular interest as the variation in glycosidic dihedral angles has been found to be dependent upon the star...

  7. Contracted or uncontracted polarization functions? Comment on Dunning's correlation-consistent basis sets

    NASA Astrophysics Data System (ADS)

    Hashimoto, Tomohiro; Hirao, Kimihiko; Tatewaki, Hiroshi

    1997-07-01

    For the sake of computational economy, the polarization functions given by Dunning are contracted by multiconfigurational SCF calculations for H, B, C, N, O, F and Ne atoms. For the first-row atoms, B through Ne, the generated contracted polarization functions are ( 2 d/1 d) and ( 3 d/2 d) and for H they are ( 2 p/1 p), ( 3 p/1 p), and ( 3 p/2 p) where the numbers before and after the slash are the numbers of uncontracted and contracted polarization functions. Numerical examples on some diatomic molecules and benzene illustrate a large improvement in going from ( 1 d/1 dto ( 2 d/1 d) for various molecular properties.

  8. How to select basis sets and computational methods for carbohydrate modeling

    USDA-ARS?s Scientific Manuscript database

    In the last decade there have been significant improvements in computer hardware but also in development of quantum mechanical methods. This makes it more feasible to study large carbohydrate molecules via quantum mechanical methods whereas in the past studies of carbohydrates were restricted to em...