WorldWideScience

Sample records for binding energy

  1. Skyrmions with low binding energies

    Directory of Open Access Journals (Sweden)

    Mike Gillard

    2015-06-01

    Full Text Available Nuclear binding energies are investigated in two variants of the Skyrme model: the first replaces the usual Skyrme term with a term that is sixth order in derivatives, and the second includes a potential that is quartic in the pion fields. Solitons in the first model are shown to deviate significantly from ansätze previously assumed in the literature. The binding energies obtained in both models are lower than those obtained from the standard Skyrme model, and those obtained in the second model are close to the experimental values.

  2. Skyrmions with low binding energies

    Energy Technology Data Exchange (ETDEWEB)

    Gillard, Mike, E-mail: m.n.gillard@leeds.ac.uk; Harland, Derek, E-mail: d.g.harland@leeds.ac.uk; Speight, Martin, E-mail: speight@maths.leeds.ac.uk

    2015-06-15

    Nuclear binding energies are investigated in two variants of the Skyrme model: the first replaces the usual Skyrme term with a term that is sixth order in derivatives, and the second includes a potential that is quartic in the pion fields. Solitons in the first model are shown to deviate significantly from ansätze previously assumed in the literature. The binding energies obtained in both models are lower than those obtained from the standard Skyrme model, and those obtained in the second model are close to the experimental values.

  3. Gravitational Binding Energy in Charged Cylindrical Symmetry

    CERN Document Server

    Sharif, M

    2014-01-01

    We consider static cylindrically symmetric charged gravitating object with perfect fluid and investigate the gravitational binding energy. It is found that only the localized part of the mass function provides the gravitational binding energy, whereas the non-localized part generated by the electric coupling does not contribute for such energy.

  4. Exciton Binding Energy of Monolayer WS2

    OpenAIRE

    Bairen Zhu; Xi Chen; Xiaodong Cui

    2015-01-01

    The optical properties of monolayer transition metal dichalcogenides (TMDC) feature prominent excitonic natures. Here we report an experimental approach toward measuring the exciton binding energy of monolayer WS2 with linear differential transmission spectroscopy and two-photon photoluminescence excitation spectroscopy (TP-PLE). TP-PLE measurements show the exciton binding energy of 0.71eV around K valley in the Brillouin zone. The trion binding energy of 34meV, two-photon absorption cross s...

  5. Predicting binding free energies in solution

    CERN Document Server

    Jensen, Jan H

    2015-01-01

    Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I summarize some of the many factors that could easily contribute 1-3 kcal/mol errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well-represented by continuum models. While the paper is primarily a synthesis of previously published work there are two new results: the adaptation of Legendre transformed free energies to electronic structure theory and a use of water clusters that maximizes error cancellation in binding free energies computed using explicit solvent molecules. While I focus on binding free energies in aqueous solution the approach also a...

  6. Binding Energy and Equilibrium of Compact Objects

    Directory of Open Access Journals (Sweden)

    Germano M.

    2014-04-01

    Full Text Available The theoretical analysis of the existence of a limit mass for compact astronomic ob- jects requires the solution of the Einstein’s equations of g eneral relativity together with an appropriate equation of state. Analytical solutions exi st in some special cases like the spherically symmetric static object without energy sou rces that is here considered. Solutions, i.e. the spacetime metrics, can have a singular m athematical form (the so called Schwarzschild metric due to Hilbert or a nonsingula r form (original work of Schwarzschild. The former predicts a limit mass and, conse quently, the existence of black holes above this limit. Here it is shown that, the origi nal Schwarzschild met- ric permits compact objects, without mass limit, having rea sonable values for central density and pressure. The lack of a limit mass is also demonst rated analytically just imposing reasonable conditions on the energy-matter densi ty, of positivity and decreas- ing with radius. Finally the ratio between proper mass and to tal mass tends to 2 for high values of mass so that the binding energy reaches the lim it m (total mass seen by a distant observer. As it is known the negative binding energ y reduces the gravitational mass of the object; the limit of m for the binding energy provides a mechanism for stable equilibrium of any amount of mass to contrast the gravitatio nal collapse.

  7. Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

    Science.gov (United States)

    Mentes, Ahmet; Deng, Nan-Jie; Vijayan, R S K; Xia, Junchao; Gallicchio, Emilio; Levy, Ronald M

    2016-05-10

    Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy Distribution Analysis Method (BEDAM), to reduce energy barriers along torsional degrees of freedom and accelerate sampling of intramolecular degrees of freedom relevant to protein-ligand binding. The method is tested on a standard benchmark (T4 Lysozyme/L99A/p-xylene complex) and on a library of HIV-1 integrase complexes derived from the SAMPL4 blind challenge. We applied the torsional flattening strategy to 26 of the 53 known binders to the HIV Integrase LEDGF site found to have a binding energy landscape funneled toward the crystal structure. We show that our approach samples the conformational space more efficiently than the original method without flattening when starting from a poorly docked pose with incorrect ligand dihedral angle conformations. In these unfavorable cases convergence to a binding pose within 2-3 Å from the crystallographic pose is obtained within a few nanoseconds of the Hamiltonian replica exchange simulation. We found that torsional flattening is insufficient in cases where trapping is due to factors other than torsional energy, such as the formation of incorrect intramolecular hydrogen bonds and stacking. Work is in progress to generalize the approach to handle these cases and thereby make it more widely applicable. PMID:27070865

  8. Systematic Calculations of Total Atomic Binding Energies

    International Nuclear Information System (INIS)

    We have calculated total atomic binding energies of 3- to 91-electron ions of all atoms with Z=3 to 118, in the Dirac-Fock model, for applications to atomic mass determination from highly-charged ions. In this process we have determined the ground-state configuration of many ions for which it was not known. We also provide total electronic correlation including Breit correlation for iso-electronic series of beryllium, neon, magnesium and argon, using the multiconfiguration Dirac-Fock approach.

  9. Effect of Nuclear Binding Energy to K Factor

    Institute of Scientific and Technical Information of China (English)

    HOU Zhao-Yu; GUO Ai-Qiang

    2007-01-01

    We modify the square of virtual photon four-momentum by using nuclear binding energy formula,and calculate the effect of nuclear binding energy to K factor and Compton subprocess and annihilate subprocess in A-A collision Drell-Yan process.The outcome indicates that the effect of nuclear binding energy to K factor is obvious in little x region and it would disappear gradually as x increases.

  10. Relativistic Nuclear Energy Density Functionals: adjusting parameters to binding energies

    CERN Document Server

    Niksic, T; Ring, P

    2008-01-01

    We study a particular class of relativistic nuclear energy density functionals in which only nucleon degrees of freedom are explicitly used in the construction of effective interaction terms. Short-distance (high-momentum) correlations, as well as intermediate and long-range dynamics, are encoded in the medium (nucleon density) dependence of the strength functionals of an effective interaction Lagrangian. Guided by the density dependence of microscopic nucleon self-energies in nuclear matter, a phenomenological ansatz for the density-dependent coupling functionals is accurately determined in self-consistent mean-field calculations of binding energies of a large set of axially deformed nuclei. The relationship between the nuclear matter volume, surface and symmetry energies, and the corresponding predictions for nuclear masses is analyzed in detail. The resulting best-fit parametrization of the nuclear energy density functional is further tested in calculations of properties of spherical and deformed medium-he...

  11. Experimental Binding Energies in Supramolecular Complexes.

    Science.gov (United States)

    Biedermann, Frank; Schneider, Hans-Jörg

    2016-05-11

    On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information. PMID:27136957

  12. Binding energy calculations using the molecular orbital wave function

    International Nuclear Information System (INIS)

    The molecular orbital wave function is used in describing the 4 N-nuclei internal wave function. Using the variational technique the binding energies of the nuclei 12C, 16O, 20Ne and 24Mg are calculated using different Skyrm interaction parameters. Both v.m.s. radii and binding energies obtained in this work are comparable with the corresponding experimental values. (author)

  13. Extrapolations of nuclear binding energies from new linear mass relations

    DEFF Research Database (Denmark)

    Hove, D.; Jensen, A. S.; Riisager, K.

    2013-01-01

    We present a method to extrapolate nuclear binding energies from known values for neighboring nuclei. We select four specific mass relations constructed to eliminate smooth variation of the binding energy as function nucleon numbers. The fast odd-even variations are avoided by comparing nuclei...

  14. Binding-energy distribution and dephasing of localized biexcitons

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher; Umlauff, M.;

    1997-01-01

    We report on the binding energy and dephasing of localized biexciton states in narrow ZnSe multiple quantum wells. The measured binding-energy distribution of the localized biexcitons shows a width of 2.2 meV centered at 8.5 meV, and is fairly independent of the exciton localization energy. In four......-wave mixing, the biexciton photon echo decays fast and nonexponentially. This behavior results from the inhomogeneous broadening of the biexciton binding energy, as we show by a comparison with an analytical model calculation. The fast decay is thus not related to a fast microscopic biexciton dephasing....

  15. Influence of binding energies of electrons on nuclear mass predictions

    Science.gov (United States)

    Tang, Jing; Niu, Zhong-Ming; Guo, Jian-You

    2016-07-01

    Nuclear mass contains a wealth of nuclear structure information, and has been widely employed to extract the nuclear effective interactions. The known nuclear mass is usually extracted from the experimental atomic mass by subtracting the masses of electrons and adding the binding energy of electrons in the atom. However, the binding energies of electrons are sometimes neglected in extracting the known nuclear masses. The influence of binding energies of electrons on nuclear mass predictions are carefully investigated in this work. If the binding energies of electrons are directly subtracted from the theoretical mass predictions, the rms deviations of nuclear mass predictions with respect to the known data are increased by about 200 keV for nuclei with Z, N ⩾ 8. Furthermore, by using the Coulomb energies between protons to absorb the binding energies of electrons, their influence on the rms deviations is significantly reduced to only about 10 keV for nuclei with Z, N ⩾ 8. However, the binding energies of electrons are still important for the heavy nuclei, about 150 keV for nuclei around Z = 100 and up to about 500 keV for nuclei around Z = 120. Therefore, it is necessary to consider the binding energies of electrons to reliably predict the masses of heavy nuclei at an accuracy of hundreds of keV. Supported by National Natural Science Foundation of China (11205004)

  16. Atomic Mass and Nuclear Binding Energy for Fe-52 (Iron)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume A `Nuclei with Z = 1 - 54' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Fe-52 (Iron, atomic number Z = 26, mass number A = 52).

  17. Neutron Skin size dependence of the nuclear binding energy

    OpenAIRE

    van der Lee, S. J.; Mekjian, A. Z.

    2011-01-01

    The nuclear binding energy is studied using a finite temperature density functional theory. A Skyrme interaction is used in this work. Volume, surface, and symmetry energy contributions to the binding energy are investigated. The case of neutron skin is considered in detail. The neutron skin modifies the mass $A$ dependence of various terms and $I$ dependence of the skin thickness is proportional to $I$ for the case of same central density.

  18. Atomic Mass and Nuclear Binding Energy for Sr-71 (Strontium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume A `Nuclei with Z = 1 - 54' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Sr-71 (Strontium, atomic number Z = 38, mass number A = 71).

  19. Nuclear binding energies from a BPS Skyrme model

    OpenAIRE

    Adam, C.; Naya, C.; Sanchez-Guillen, J.(Departamento de Física de Partículas, Universidad de Santiago de Compostela and Instituto Galego de Física de Altas Enerxias (IGFAE), Santiago de Compostela, E-15782, Spain); Wereszczynski, A.

    2013-01-01

    Recently, within the space of generalized Skyrme models, a BPS submodel was identified which reproduces some bulk properties of nuclear matter already on a classical level and, as such, constitutes a promising field theory candidate for the detailed and reliable description of nuclei and hadrons. Here we extend and further develop these investigations by applying the model to the calculation of nuclear binding energies. Concretely, we calculate these binding energies by including the classica...

  20. Atomic Mass and Nuclear Binding Energy for Bh-318 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-318 (Bohrium, atomic number Z = 107, mass number A = 318).

  1. Atomic Mass and Nuclear Binding Energy for Bh-356 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-356 (Bohrium, atomic number Z = 107, mass number A = 356).

  2. Atomic Mass and Nuclear Binding Energy for Bh-322 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-322 (Bohrium, atomic number Z = 107, mass number A = 322).

  3. Atomic Mass and Nuclear Binding Energy for Bh-351 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-351 (Bohrium, atomic number Z = 107, mass number A = 351).

  4. Atomic Mass and Nuclear Binding Energy for Bh-310 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-310 (Bohrium, atomic number Z = 107, mass number A = 310).

  5. Atomic Mass and Nuclear Binding Energy for Bh-336 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-336 (Bohrium, atomic number Z = 107, mass number A = 336).

  6. Atomic Mass and Nuclear Binding Energy for Bh-299 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-299 (Bohrium, atomic number Z = 107, mass number A = 299).

  7. Atomic Mass and Nuclear Binding Energy for Bh-288 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-288 (Bohrium, atomic number Z = 107, mass number A = 288).

  8. Atomic Mass and Nuclear Binding Energy for Bh-359 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-359 (Bohrium, atomic number Z = 107, mass number A = 359).

  9. Atomic Mass and Nuclear Binding Energy for Bh-343 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-343 (Bohrium, atomic number Z = 107, mass number A = 343).

  10. Atomic Mass and Nuclear Binding Energy for Bh-304 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-304 (Bohrium, atomic number Z = 107, mass number A = 304).

  11. Atomic Mass and Nuclear Binding Energy for Bh-280 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-280 (Bohrium, atomic number Z = 107, mass number A = 280).

  12. Atomic Mass and Nuclear Binding Energy for Bh-349 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-349 (Bohrium, atomic number Z = 107, mass number A = 349).

  13. Atomic Mass and Nuclear Binding Energy for Bh-325 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-325 (Bohrium, atomic number Z = 107, mass number A = 325).

  14. Atomic Mass and Nuclear Binding Energy for Bh-332 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-332 (Bohrium, atomic number Z = 107, mass number A = 332).

  15. Atomic Mass and Nuclear Binding Energy for Bh-306 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-306 (Bohrium, atomic number Z = 107, mass number A = 306).

  16. Atomic Mass and Nuclear Binding Energy for Bh-324 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-324 (Bohrium, atomic number Z = 107, mass number A = 324).

  17. Atomic Mass and Nuclear Binding Energy for Bh-293 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-293 (Bohrium, atomic number Z = 107, mass number A = 293).

  18. Atomic Mass and Nuclear Binding Energy for Bh-327 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-327 (Bohrium, atomic number Z = 107, mass number A = 327).

  19. Atomic Mass and Nuclear Binding Energy for Bh-350 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-350 (Bohrium, atomic number Z = 107, mass number A = 350).

  20. Atomic Mass and Nuclear Binding Energy for Bh-308 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-308 (Bohrium, atomic number Z = 107, mass number A = 308).

  1. Atomic Mass and Nuclear Binding Energy for Bh-358 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-358 (Bohrium, atomic number Z = 107, mass number A = 358).

  2. Atomic Mass and Nuclear Binding Energy for Bh-321 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-321 (Bohrium, atomic number Z = 107, mass number A = 321).

  3. Atomic Mass and Nuclear Binding Energy for Bh-345 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-345 (Bohrium, atomic number Z = 107, mass number A = 345).

  4. Atomic Mass and Nuclear Binding Energy for Bh-286 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-286 (Bohrium, atomic number Z = 107, mass number A = 286).

  5. Atomic Mass and Nuclear Binding Energy for Bh-307 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-307 (Bohrium, atomic number Z = 107, mass number A = 307).

  6. Atomic Mass and Nuclear Binding Energy for Bh-303 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-303 (Bohrium, atomic number Z = 107, mass number A = 303).

  7. Atomic Mass and Nuclear Binding Energy for Bh-312 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-312 (Bohrium, atomic number Z = 107, mass number A = 312).

  8. Atomic Mass and Nuclear Binding Energy for Bh-294 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-294 (Bohrium, atomic number Z = 107, mass number A = 294).

  9. Atomic Mass and Nuclear Binding Energy for Bh-326 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-326 (Bohrium, atomic number Z = 107, mass number A = 326).

  10. Atomic Mass and Nuclear Binding Energy for Bh-273 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-273 (Bohrium, atomic number Z = 107, mass number A = 273).

  11. Atomic Mass and Nuclear Binding Energy for Bh-284 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-284 (Bohrium, atomic number Z = 107, mass number A = 284).

  12. Atomic Mass and Nuclear Binding Energy for Bh-315 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-315 (Bohrium, atomic number Z = 107, mass number A = 315).

  13. Atomic Mass and Nuclear Binding Energy for Bh-328 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-328 (Bohrium, atomic number Z = 107, mass number A = 328).

  14. Atomic Mass and Nuclear Binding Energy for Bh-311 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-311 (Bohrium, atomic number Z = 107, mass number A = 311).

  15. Atomic Mass and Nuclear Binding Energy for Bh-353 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-353 (Bohrium, atomic number Z = 107, mass number A = 353).

  16. Atomic Mass and Nuclear Binding Energy for Bh-348 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-348 (Bohrium, atomic number Z = 107, mass number A = 348).

  17. Atomic Mass and Nuclear Binding Energy for Bh-360 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-360 (Bohrium, atomic number Z = 107, mass number A = 360).

  18. Atomic Mass and Nuclear Binding Energy for Bh-347 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-347 (Bohrium, atomic number Z = 107, mass number A = 347).

  19. Atomic Mass and Nuclear Binding Energy for Bh-277 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-277 (Bohrium, atomic number Z = 107, mass number A = 277).

  20. Atomic Mass and Nuclear Binding Energy for Bh-309 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-309 (Bohrium, atomic number Z = 107, mass number A = 309).

  1. Atomic Mass and Nuclear Binding Energy for Bh-340 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-340 (Bohrium, atomic number Z = 107, mass number A = 340).

  2. Atomic Mass and Nuclear Binding Energy for Bh-285 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-285 (Bohrium, atomic number Z = 107, mass number A = 285).

  3. Atomic Mass and Nuclear Binding Energy for Bh-341 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-341 (Bohrium, atomic number Z = 107, mass number A = 341).

  4. Atomic Mass and Nuclear Binding Energy for Bh-283 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-283 (Bohrium, atomic number Z = 107, mass number A = 283).

  5. Atomic Mass and Nuclear Binding Energy for Bh-305 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-305 (Bohrium, atomic number Z = 107, mass number A = 305).

  6. Atomic Mass and Nuclear Binding Energy for Bh-331 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-331 (Bohrium, atomic number Z = 107, mass number A = 331).

  7. Atomic Mass and Nuclear Binding Energy for Bh-342 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-342 (Bohrium, atomic number Z = 107, mass number A = 342).

  8. Atomic Mass and Nuclear Binding Energy for Bh-300 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-300 (Bohrium, atomic number Z = 107, mass number A = 300).

  9. Atomic Mass and Nuclear Binding Energy for Bh-330 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-330 (Bohrium, atomic number Z = 107, mass number A = 330).

  10. Atomic Mass and Nuclear Binding Energy for Bh-296 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-296 (Bohrium, atomic number Z = 107, mass number A = 296).

  11. Atomic Mass and Nuclear Binding Energy for Bh-338 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-338 (Bohrium, atomic number Z = 107, mass number A = 338).

  12. Atomic Mass and Nuclear Binding Energy for Bh-270 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-270 (Bohrium, atomic number Z = 107, mass number A = 270).

  13. Atomic Mass and Nuclear Binding Energy for Bh-320 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-320 (Bohrium, atomic number Z = 107, mass number A = 320).

  14. Atomic Mass and Nuclear Binding Energy for Bh-346 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-346 (Bohrium, atomic number Z = 107, mass number A = 346).

  15. Atomic Mass and Nuclear Binding Energy for Bh-274 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-274 (Bohrium, atomic number Z = 107, mass number A = 274).

  16. Atomic Mass and Nuclear Binding Energy for Bh-357 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-357 (Bohrium, atomic number Z = 107, mass number A = 357).

  17. Atomic Mass and Nuclear Binding Energy for Bh-319 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-319 (Bohrium, atomic number Z = 107, mass number A = 319).

  18. Atomic Mass and Nuclear Binding Energy for Bh-337 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-337 (Bohrium, atomic number Z = 107, mass number A = 337).

  19. Atomic Mass and Nuclear Binding Energy for Bh-329 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-329 (Bohrium, atomic number Z = 107, mass number A = 329).

  20. Atomic Mass and Nuclear Binding Energy for Bh-276 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-276 (Bohrium, atomic number Z = 107, mass number A = 276).

  1. Atomic Mass and Nuclear Binding Energy for Bh-335 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-335 (Bohrium, atomic number Z = 107, mass number A = 335).

  2. Atomic Mass and Nuclear Binding Energy for Bh-314 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-314 (Bohrium, atomic number Z = 107, mass number A = 314).

  3. Atomic Mass and Nuclear Binding Energy for Bh-281 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-281 (Bohrium, atomic number Z = 107, mass number A = 281).

  4. Atomic Mass and Nuclear Binding Energy for Bh-282 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-282 (Bohrium, atomic number Z = 107, mass number A = 282).

  5. Atomic Mass and Nuclear Binding Energy for Bh-339 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-339 (Bohrium, atomic number Z = 107, mass number A = 339).

  6. Atomic Mass and Nuclear Binding Energy for Bh-275 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-275 (Bohrium, atomic number Z = 107, mass number A = 275).

  7. Atomic Mass and Nuclear Binding Energy for Bh-289 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-289 (Bohrium, atomic number Z = 107, mass number A = 289).

  8. Atomic Mass and Nuclear Binding Energy for Bh-316 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-316 (Bohrium, atomic number Z = 107, mass number A = 316).

  9. Atomic Mass and Nuclear Binding Energy for Bh-354 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-354 (Bohrium, atomic number Z = 107, mass number A = 354).

  10. Atomic Mass and Nuclear Binding Energy for Bh-355 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-355 (Bohrium, atomic number Z = 107, mass number A = 355).

  11. Atomic Mass and Nuclear Binding Energy for Bh-295 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-295 (Bohrium, atomic number Z = 107, mass number A = 295).

  12. Atomic Mass and Nuclear Binding Energy for Bh-272 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-272 (Bohrium, atomic number Z = 107, mass number A = 272).

  13. Atomic Mass and Nuclear Binding Energy for Bh-334 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-334 (Bohrium, atomic number Z = 107, mass number A = 334).

  14. Atomic Mass and Nuclear Binding Energy for Bh-279 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-279 (Bohrium, atomic number Z = 107, mass number A = 279).

  15. Atomic Mass and Nuclear Binding Energy for Bh-323 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-323 (Bohrium, atomic number Z = 107, mass number A = 323).

  16. Atomic Mass and Nuclear Binding Energy for Bh-352 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-352 (Bohrium, atomic number Z = 107, mass number A = 352).

  17. Atomic Mass and Nuclear Binding Energy for Bh-298 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-298 (Bohrium, atomic number Z = 107, mass number A = 298).

  18. Atomic Mass and Nuclear Binding Energy for Bh-317 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-317 (Bohrium, atomic number Z = 107, mass number A = 317).

  19. Atomic Mass and Nuclear Binding Energy for Bh-344 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-344 (Bohrium, atomic number Z = 107, mass number A = 344).

  20. Atomic Mass and Nuclear Binding Energy for Bh-302 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-302 (Bohrium, atomic number Z = 107, mass number A = 302).

  1. Atomic Mass and Nuclear Binding Energy for Bh-292 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-292 (Bohrium, atomic number Z = 107, mass number A = 292).

  2. Atomic Mass and Nuclear Binding Energy for Bh-287 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-287 (Bohrium, atomic number Z = 107, mass number A = 287).

  3. Atomic Mass and Nuclear Binding Energy for Bh-301 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-301 (Bohrium, atomic number Z = 107, mass number A = 301).

  4. Atomic Mass and Nuclear Binding Energy for Bh-291 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-291 (Bohrium, atomic number Z = 107, mass number A = 291).

  5. Atomic Mass and Nuclear Binding Energy for Bh-278 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-278 (Bohrium, atomic number Z = 107, mass number A = 278).

  6. Atomic Mass and Nuclear Binding Energy for Bh-290 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-290 (Bohrium, atomic number Z = 107, mass number A = 290).

  7. Atomic Mass and Nuclear Binding Energy for Bh-333 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-333 (Bohrium, atomic number Z = 107, mass number A = 333).

  8. Atomic Mass and Nuclear Binding Energy for Bh-268 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-268 (Bohrium, atomic number Z = 107, mass number A = 268).

  9. Atomic Mass and Nuclear Binding Energy for Bh-313 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-313 (Bohrium, atomic number Z = 107, mass number A = 313).

  10. Atomic Mass and Nuclear Binding Energy for Bh-271 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-271 (Bohrium, atomic number Z = 107, mass number A = 271).

  11. Atomic Mass and Nuclear Binding Energy for Bh-269 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-269 (Bohrium, atomic number Z = 107, mass number A = 269).

  12. Atomic Mass and Nuclear Binding Energy for Bh-297 (Bohrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Bh-297 (Bohrium, atomic number Z = 107, mass number A = 297).

  13. Accurate nuclear radii and binding energies from a chiral interaction

    CERN Document Server

    Ekstrom, A; Wendt, K A; Hagen, G; Papenbrock, T; Carlsson, B D; Forssen, C; Hjorth-Jensen, M; Navratil, P; Nazarewicz, W

    2015-01-01

    The accurate reproduction of nuclear radii and binding energies is a long-standing challenge in nuclear theory. To address this problem two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective 3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.

  14. The Binding Energy Parameter for Common Envelope Evolution

    CERN Document Server

    Wang, Cheng; Li, Xiang-Dong

    2016-01-01

    The binding energy parameter $\\lambda$ plays a vital role in common envelope evolution. Though it is well known that $\\lambda$ takes different values for stars with different masses and varies during stellar evolution, it has been erroneously adopted as a constant in most of the population synthesis calculations. We have systematically calculated the values of $\\lambda$ for stars of masses $1-60\\,M_{\\odot}$ by use of an updated stellar evolution code, taking into account contribution from both gravitational energy and internal energy to the binding energy of the envelope. We adopt the criterion for the core-envelope boundary advocated by \\citet{Ivanova2011}. A new kind of $\\lambda$ with the enthalpy prescription is also investigated. We present fitting formulae for the calculated values of various kinds of $\\lambda$, which can be used in future population synthesis studies.

  15. The binding energy parameter for common envelope evolution

    Science.gov (United States)

    Wang, Chen; Jia, Kun; Li, Xiang-Dong

    2016-08-01

    The binding energy parameter λ plays a vital role in common envelope evolution. Though it is well known that λ takes different values for stars with different masses and varies during stellar evolution, it has been erroneously adopted as a constant in most population synthesis calculations. We have systematically calculated the values of λ for stars of masses 1 – 60 M ⊙ by use of an updated stellar evolution code, taking into account the contribution from both gravitational energy and internal energy to the binding energy of the envelope. We adopt the criterion for the core-envelope boundary advocated by Ivanova. A new kind of λ with an enthalpy prescription is also investigated. We present fitting formulae for the calculated values of various kinds of λ, which can be used in future population synthesis studies.

  16. Hydrogen-impurity binding energy in vanadium and niobium

    OpenAIRE

    Mokrani, A.; Demangeat, C.

    1989-01-01

    H-H and H-substitutional impurity interaction energy are estimated by the Green operator method developed in the tight binding approximation. This electronic (or chemical) energy is split in four terms : i) the bound states (introduced by the hydrogen) contribution, ii) the band structure contribution, iii) the electron-electron interaction without charge transfer and iv) the charge transfer (between matrix and impurity) contribution. The calculations are done for the transition metal matrix ...

  17. Binding energy and stability of heavy and superheavy nuclei

    OpenAIRE

    Kolesnikov, N.N.

    2012-01-01

    Three different ways for description of binding energy of superheavy nuclei are discussed. First, one can consider superheavy nuclei as a part of a whole system of nuclei for which a global mass formula is found. Another way is the detailed local description of energy of superheavy nuclei taking into account the effects of shells and subshells. The third way of description, applied for nuclei in the region limited by principal magic numbers, is attached to the beta-stability line.

  18. A new phenomenological formula for ground-state binding energies

    International Nuclear Information System (INIS)

    A phenomenological formula based on liquid drop model has been proposed for ground-state binding energies of nuclei. The effect due to bunching of single particle levels has been incorporated through a term resembling the one-body Hamiltonian. The effect of n–p interaction has been included through a function of valence nucleons. A total of 50 parameters has been used in the present calculation. The root mean square (r.m.s.) deviation for the binding energy values for 2140 nuclei comes out to be 0.376 MeV, and that for 1091 alpha decay energies is 0.284 MeV. The correspondence with the conventional liquid drop model is discussed. (author)

  19. Impurity binding energy for -doped quantum well structures

    Indian Academy of Sciences (India)

    V Tulupenko; C A Duque; R Demediuk; O Fomina; V Akimov; V Belykh; T Dmitrichenko; V Poroshin

    2014-10-01

    The binding energy of an impurity delta layer situated either in the centre or at the edge of a quantum well (QW) is theoretically considered for the example of -type Si0.8Ge0.2/Si/Si0.8Ge0.2 QW doped with phosphorus. Calculations are made for the case of not so big impurity concentrations, when impurity bands are not yet formed and it is still possible to treat impurity as isolated ones. It is shown on the base of self-consistent solution of Schrödinger, Poisson and electro-neutrality equations that impurity binding energy is dependent on the degree of impurity ionization and the most noticeably for the case of edge-doped QWs.

  20. Application of Henry's Law for Binding Energies of Adsorbed Hydrogen

    Science.gov (United States)

    Gillespie, Andrew; Dohnke, Elmar; Stalla, David; Sweany, Mark; Pfeifer, Peter

    2015-03-01

    The method of isosteres is the simplest method used to calculate the differential enthalpy of adsorption. However, it is incredibly sensitive to the choice of model and respective fitting parameters. For a set of isotherms measured on a specific sample, most models converge upon a similar value at high coverage, but are inconsistent in the low pressure regime. In this talk, we investigate the application of various models for localized and mobile adsorption at low pressures in order to obtain binding energy of hydrogen to the adsorbent surface. Henry's Law analysis of the Langmuir Model of adsorption yield binding energies in excellent agreement with those obtained from the Clausius Clapeyron relation. Work supported by DOE-EERE, Award No. DE-FG36-08GO18142.

  1. Improvement in a phenomenological formula for ground state binding energies

    CERN Document Server

    Gangopadhyay, G

    2016-01-01

    The phenomenological formula for ground state binding energy derived earlier (International Journal of Modern Physics E {\\bf 20} (2011) 179) has been modified. The parameters have been obtained by fitting the latest available tabulation of experimental values. The major modifications include a new term for pairing and introduction of a new neutron magic number at $N=160$. The new formula reduced the root mean square deviation to 363 keV, a substantial improvement over the previous version of the formula.

  2. Improvement in a phenomenological formula for ground state binding energies

    OpenAIRE

    Gangopadhyay, G.

    2016-01-01

    The phenomenological formula for ground state binding energy derived earlier (International Journal of Modern Physics E {\\bf 20} (2011) 179) has been modified. The parameters have been obtained by fitting the latest available tabulation of experimental values. The major modifications include a new term for pairing and introduction of a new neutron magic number at $N=160$. The new formula reduced the root mean square deviation to 363 keV, a substantial improvement over the previous version of ...

  3. Experimental electron binding energies for thulium in different matrices

    Czech Academy of Sciences Publication Activity Database

    Inoyatov, A. K.; Kovalík, Alojz; Filosofov, D. V.; Ryšavý, Miloš; Perevoshchikov, L. L.; Yushkevich, Yu. V.; Zbořil, M.

    2015-01-01

    Roč. 202, JUL (2015), s. 46-55. ISSN 0368-2048 R&D Projects: GA MŠk LG14004; GA ČR(CZ) GAP203/12/1896 Institutional support: RVO:61389005 Keywords : Tm-169 * (169)yb * atomic environment * electron binding energy * chemical shift * natural atomic level width Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.436, year: 2014

  4. Inverting a Supernova: Neutrino Mixing, Temperatures and Binding Energy

    OpenAIRE

    Barger, V.; Marfatia, D.; Wood, B. P.

    2001-01-01

    We show that the temperatures of the emergent non-electron neutrinos and the binding energy released by a galactic Type II supernova are determinable, assuming the Large Mixing Angle (LMA) solution is correct, from observations at the Sudbury Neutrino Observatory (SNO) and at Super-Kamiokande (SK). If the neutrino mass hierarchy is inverted, either a lower or upper bound can be placed on the neutrino mixing angle $\\theta_{13}$, and the hierarchy can be deduced for adiabatic transitions. For t...

  5. Pauli exclusion operator and binding energy of nuclear matter

    OpenAIRE

    Schiller, E.; Müther, H; Czerski, P.

    1998-01-01

    Brueckner-Hartree-Fock calculations are performed for nuclear matter with an exact treatment of the Pauli exclusion operator in the Bethe-Goldstone equation. The differences in the calculated binding energy, compared to the angle-average approximation, which is commonly used, are non-negligible. These difference exhibits a specific density dependence, which shifts the calculated saturation point towards smaller densities. This effect is observed for various versions of modern models for the N...

  6. Bifurcation Analysis for Phage Lambda with Binding Energy Uncertainty

    OpenAIRE

    Ning Xu; Xue Lei; Ping Ao; Jun Zhang

    2014-01-01

    In a phage λ genetic switch model, bistable dynamical behavior can be destroyed due to the bifurcation caused by inappropriately chosen model parameters. Since the values of many parameters with biological significance often cannot be accurately acquired, it is thus of fundamental importance to analyze how and to which extent the system dynamics is influenced by model parameters, especially those parameters pertaining to binding energies. In this paper, we apply a Jacobian method to investiga...

  7. Single particle spectrum and binding energy of nuclear matter

    OpenAIRE

    Baldo, M; Fiasconaro, A.

    2000-01-01

    In non-relativistic Brueckner calculations of nuclear matter, the self-consistent single particle potential is strongly momentum dependent. To simplify the calculations, a parabolic approximation is often used in the literature. The variation in the binding energy value introduced by the parabolic approximation is quantitatively analyzed in detail. It is found that the approximation can introduce an uncertainty of 1-2 MeV near the saturation density.

  8. Pauli Exclusion Operator and Binding Energy of Nuclear Matter

    International Nuclear Information System (INIS)

    Full text: Brueckner-Hartree-Fock calculations are performed for nuclear matter with an exact treatment of the Pauli exclusion operator in the Bethe-Goldstone equation. The differences in the calculated binding energy, compared to the angle-average approximation, which is commonly used, are non-negligible. These difference exhibits a specific density dependence, which shifts the calculated saturation point towards smaller densities. This effect is observed for various versions of modern models for the NN interaction. (author)

  9. Nuclear binding energy using semi empirical mass formula

    Science.gov (United States)

    Ankita, Suthar, B.

    2016-05-01

    In the present communication, semi empirical mass formula using the liquid drop model has been presented. Nuclear binding energies are calculated using semi empirical mass formula with various constants given by different researchers. We also compare these calculated values with experimental data and comparative study for finding suitable constants is added using the error plot. The study is extended to find the more suitable constant to reduce the error.

  10. Precise determination of neutron binding energy of 64Cu

    Science.gov (United States)

    Telezhnikov, S. A.; Granja, C.; Honzatko, J.; Pospisil, S.; Tomandl, I.

    2016-05-01

    The neutron binding energy in 64Cu has been accurately measured in thermal neutron capture. A composite target of natural Cu and NaCl was used on a high flux neutron beam using a large measuring time. The γ-ray spectrum emitted in the ( n, γ) reaction was measured with a HPGe detector in large statistics (up to 106 events per channel). Intrinsic limitations of HPGe detectors, which restrict the accuracy of energy calibration, were determined. The value B n of 64Cu was determined as 7915.867(24) keV.

  11. Effects of QED and Beyond from the Atomic Binding Energy

    International Nuclear Information System (INIS)

    Atomic binding energies are calculated at utmost precision. A report on the current status of Lamb-shift predictions for hydrogenlike ions, including all quantum electrodynamical corrections to first and second order in the fine structure constant α is presented. All relevant nuclear effects are taken into account. High-precision calculations for the Lamb shift in hydrogen are presented. The hyperfine structure splitting and the g factor of a bound electron in the strong electromagnetic field of a heavy nucleus is considered. Special emphasis is also put on parity violation effects in atomic systems. For all systems possible investigations beyond precision tests of quantum electrodynamics are considered

  12. Binding energies of indirect excitons in double quantum well systems

    Science.gov (United States)

    Rossokhaty, Alex; Schmult, Stefan; Dietsche, Werner; von Klitzing, Klaus; Kukushkin, Igor

    2011-03-01

    A prerequisite towards Bose-Einstein condensation is a cold and dense system of bosons. Indirect excitons in double GaAs/AlGaAs quantum wells (DQWs) are believed to be suitable candidates. Indirect excitons are formed in asymmetric DQW structures by mass filtering, a method which does not require external electric fields. The exciton density and the electron-hole balance can be tuned optically. Binding energies are measured by a resonant microwave absorption technique. Our results show that screening of the indirect excitons becomes already relevant at densities as low as ~ 5 × 109 cm-2 and results in their destruction.

  13. Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.

    Science.gov (United States)

    Choi, Jeong-Mo; Serohijos, Adrian W R; Murphy, Sean; Lucarelli, Dennis; Lofranco, Leo L; Feldman, Andrew; Shakhnovich, Eugene I

    2015-02-17

    It has long been known that solvation plays an important role in protein-protein interactions. Here, we use a minimalistic solvation-based model for predicting protein binding energy to estimate quantitatively the contribution of the solvation factor in protein binding. The factor is described by a simple linear combination of buried surface areas according to amino-acid types. Even without structural optimization, our minimalistic model demonstrates a predictive power comparable to more complex methods, making the proposed approach the basis for high throughput applications. Application of the model to a proteomic database shows that receptor-substrate complexes involved in signaling have lower affinities than enzyme-inhibitor and antibody-antigen complexes, and they differ by chemical compositions on interfaces. Also, we found that protein complexes with components that come from the same genes generally have lower affinities than complexes formed by proteins from different genes, but in this case the difference originates from different interface areas. The model was implemented in the software PYTHON, and the source code can be found on the Shakhnovich group webpage: http://faculty.chemistry.harvard.edu/shakhnovich/software. PMID:25692584

  14. Molecular orbital momentum distributions and binding energies for nitric oxide

    International Nuclear Information System (INIS)

    Binding energy spectra of the valence electrons of the open shell molecule NO have been obtained up to 55 eV at azimuthal angles of 0 deg. and 7 deg. using binary (e,2e) spectroscopy at an impact energy of 1200 eV. The momentum distribution has been obtained for the least tightly bound (unpaired) electron. Momentum distributions have also been measured at 21.0 and 40.5 eV. The measured momentum distributions are compared with several literature wave functions of varying complexity. They are found to be in excellent agreement with those calculated using the natural spin orbital wave functions of Kouba and Ohrn (Int. J. Quant. Chem., 5 (1971) 539)

  15. Non-abelian binding energies from the lightcone bootstrap

    Science.gov (United States)

    Li, Daliang; Meltzer, David; Poland, David

    2016-02-01

    We analytically study the lightcone limit of the conformal bootstrap for 4-point functions containing scalars charged under global symmetries. We show the existence of large spin double-twist operators in various representations of the global symmetry group. We then compute their anomalous dimensions in terms of the central charge C T , current central charge C J , and the OPE coefficients of low dimension scalars. In AdS, these results correspond to the binding energy of two-particle states arising from the exchange of gravitons, gauge bosons, and light scalar fields. Using unitarity and crossing symmetry, we show that gravity is universal and attractive among different types of two-particle states, while the gauge binding energy can have either sign as determined by the representation of the two-particle state, with universal ratios fixed by the symmetry group. We apply our results to 4D {N}=1 SQCD and the 3D O( N) vector models. We also show that in a unitary CFT, if the current central charge C J stays finite when the global symmetry group becomes infinitely large, such as the N → ∞ limit of the O( N) vector model, then the theory must contain an infinite number of higher spin currents.

  16. Non-Abelian Binding Energies from the Lightcone Bootstrap

    CERN Document Server

    Li, Daliang; Poland, David

    2015-01-01

    We analytically study the lightcone limit of the conformal bootstrap for 4-point functions containing scalars charged under global symmetries. We show the existence of large spin double-twist operators in various representations of the global symmetry group. We then compute their anomalous dimensions in terms of the central charge $C_T$, current central charge $C_J$, and the OPE coefficients of low dimension scalars. In AdS, these results correspond to the binding energy of two-particle states arising from the exchange of gravitons, gauge bosons, and light scalar fields. Using unitarity and crossing symmetry, we show that gravity is universal and attractive among different types of two-particle states, while the gauge binding energy can have either sign as determined by the representation of the two-particle state, with universal ratios fixed by the symmetry group. We apply our results to 4D $\\mathcal{N}=1$ SQCD and the 3D O(N) vector models. We also show that in a unitary CFT, if the current central charge $...

  17. Decoding the nuclear genome using nuclear binding and fusion energies

    Science.gov (United States)

    Yablon, Jay R.

    2015-04-01

    In several publications the author has presented the theory that protons and neutrons and other baryons are the chromo-magnetic monopoles of Yang-Mills gauge theory and used that to deduce the up and down current quark masses from the tightly-known Q = 0 empirical electron mass and the neutron minus proton mass difference with commensurately high precision. This is then used as a springboard to closely fit a wide range of empirical nuclear binding and fusion energy data and to obtain the proton and neutron masses themselves within all experimental errors. This presentation will systematically pull all of this together and a) establishes that this way of defining current quark masses constitutes a valid measurement scheme, b) lays out the empirical support for this theory via observed nuclear binding and fusion energies as well as the proton and neutron masses themselves, c) solidifies the interface used to connect the theory to these empirical results and uncovers a mixing between the up and down current quark masses, and d) presents clearly how and why the underlying theory is very conservative, being no more and no less than a deductive mathematical synthesis of Maxwell's classical theory with both the electric and magnetic field equations merged into one, Yang-Mills gauge theory, Dirac fermion theory, the Fermi-Dirac-Pauli Exclusion Principle, and to get from classical chromodynamics to QCD, Feynman path integration.

  18. Experimental electron binding energies for thulium in different matrices

    Energy Technology Data Exchange (ETDEWEB)

    Inoyatov, A.Kh., E-mail: inoyatov@jinr.ru [Laboratory of Nuclear Problems, JINR, Dubna, Moscow Region (Russian Federation); Institute of Applied Physics, National University, Tashkent (Uzbekistan); Kovalík, A. [Laboratory of Nuclear Problems, JINR, Dubna, Moscow Region (Russian Federation); Nuclear Physics Institute of the ASCR, CZ-25068 Řež near Prague (Czech Republic); Filosofov, D.V. [Laboratory of Nuclear Problems, JINR, Dubna, Moscow Region (Russian Federation); Ryšavý, M. [Nuclear Physics Institute of the ASCR, CZ-25068 Řež near Prague (Czech Republic); Perevoshchikov, L.L.; Yushkevich, Yu.V. [Laboratory of Nuclear Problems, JINR, Dubna, Moscow Region (Russian Federation); Zbořil, M. [Institut für Kernphysik, Westfälische Wilhelms-Universität Münster, D-48149 Münster (Germany)

    2015-07-15

    Highlights: • The thulium L, M, N, O, and P subshell electron binding energies determined. • Five different matrices of the radioactive {sup 169}Yb atoms used in the investigation. • The greatest difference of 4.5 ± 0.1 eV in the average observed between the matrices. • The published N{sub 1}, N{sub 3}, and O{sub 2,3} values found to be higher by about 3 eV. • Natural widths of the thulium K, L, M, N, and O subshells also determined. - Abstract: The L{sub 1}, L{sub 2}, L{sub 3}, M{sub 1}, M{sub 2}, N{sub 1}, N{sub 3}, O{sub 1}, O{sub 2}, O{sub 3}, and P{sub 1} subshell electron binding energies (related to the Fermi level) in thulium generated by the electron capture decay of radioactive {sup 169}Yb atoms implanted at 30 keV into polycrystalline platinum and aluminum foils and deposited by vacuum evaporation on surfaces of polycrystalline platinum, carbon, and aluminum foils were determined by the internal conversion electron spectroscopy. The greatest differences in the electron binding energies (4.5 ± 0.1 eV in the average without the P{sub 1} shell and 7.0 ± 0.5 eV for the P{sub 1} shell alone) were found between the matrices of the evaporated ytterbium layer on the aluminum foil and the bulk of the high purity polycrystalline platinum. The thulium electron binding energies in the matrices of the evaporated ytterbium layers on both the platinum and carbon foils and in the aluminum bulk were observed to be the same within the experimental uncertainties. The N{sub 1}, N{sub 3}, and O{sub 2,3} electron binding energies most frequently presented in data compilations were found to be higher by about 3 eV. Natural widths of most of the K, L{sub 1}, L{sub 2}, L{sub 3}, M{sub 1}, M{sub 2}, M{sub 3}, N{sub 1}, N{sub 3}, and O{sub 1} subshells in Tm in the investigated matrices were also determined. No significant differences in the natural widths were found among the matrices. The results obtained demonstrate that the physicochemical surrounding of the

  19. An Accurate Redetermination of the $^{118}Sn$ Binding Energy

    CERN Document Server

    Borzakov, S B; Faikow-Stanczyk, H; Grigoriev, Yu V; Panteleev, T; Pospísil, S; Smotritsky, L M; Telezhnikov, S A

    2001-01-01

    The energy of well-known strong {gamma}-line from {{^198}Au}, the "gold standard", has been modified in the light of new adjustments in the fundamental constants and the value of 411.80176(12) keV was determined which is 0.29 eV lower than the latest 1999 value. An energy calibration procedure for determining the neutron binding energy, {B_n}, from complicated {(n , gamma)}-spectra has been developed. A mathematically simple minimization function consisting only of terms having as parameters the coefficients of the energy calibration curve (polynomial) is used. A priori information about the relationships among the energies of different peaks on the spectrum is taking into account by a Monte Carlo simulation. The procedure was used in obtaining of {B_n} for {{^118}Sn} and {{^64}Cu}. The {gamma}-ray spectrum from thermal neutron radiative capture by {{^117}Sn} has been measured on the IBR-2 pulsed reactor. {gamma}-rays were detected by a 72 cm^3 HPGe-detector. {B_n} for {{^64}Cu} was obtained from two {gamma}-...

  20. Self consistent single particle potential and nuclear matter binding energy

    International Nuclear Information System (INIS)

    We have obtained a self-consistent single-particle potential as a function of momentum for Fermi momenta kF= 1.4 fm. Self-consistent single particle potential is calculated from Brueckner g-matrix using Urbana v-14 interaction. Sixth order polynomial approximation is used as an input for the calculation of g-matrix. After achieving the self-consistent single particle potential we calculate the binding energy of infinite symmetric nuclear matter at different Fermi momenta, using soft-core Urbana v-14 interaction and hard-core Hamada Johnston interaction. Urbana v-14 interaction predicts overbinding of infinite nuclear matter, while HJ interaction predicts an underbound nuclear matter underbound. (author)

  1. Double binding energy differences: Mean-field or pairing effect?

    Science.gov (United States)

    Qi, Chong

    2012-10-01

    In this Letter we present a systematic analysis on the average interaction between the last protons and neutrons in atomic nuclei, which can be extracted from the double differences of nuclear binding energies. The empirical average proton-neutron interaction Vpn thus derived from experimental data can be described in a very simple form as the interplay of the nuclear mean field and the pairing interaction. It is found that the smooth behavior as well as the local fluctuations of the Vpn in even-even nuclei with N ≠ Z are dominated by the contribution from the proton-neutron monopole interactions. A strong additional contribution from the isoscalar monopole interaction and isovector proton-neutron pairing interaction is seen in the Vpn for even-even N = Z nuclei and for the adjacent odd-A nuclei with one neutron or proton being subtracted.

  2. Universal binding energy relation for cleaved and structurally relaxed surfaces

    International Nuclear Information System (INIS)

    The universal binding energy relation (UBER), derived earlier to describe the cohesion between two rigid atomic planes, does not accurately capture the cohesive properties when the cleaved surfaces are allowed to relax. We suggest a modified functional form of UBER that is analytical and at the same time accurately models the properties of surfaces relaxed during cleavage. We demonstrate the generality as well as the validity of this modified UBER through first-principles density functional theory calculations of cleavage in a number of crystal systems. Our results show that the total energies of all the relaxed surfaces lie on a single (universal) energy surface, that is given by the proposed functional form which contains an additional length-scale associated with structural relaxation. This functional form could be used in modelling the cohesive zones in crack growth simulation studies. We find that the cohesive law (stress–displacement relation) differs significantly in the case where cracked surfaces are allowed to relax, with lower peak stresses occurring at higher displacements. (paper)

  3. Quantum Monte Carlo calculation of the binding energy of the beryllium dimer

    International Nuclear Information System (INIS)

    The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be2 is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be2 from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be2, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm−1, only slightly below the 935 cm−1 value derived from experiment

  4. Effect of isovector coupling channel on the macroscopic part of the nuclear binding energy

    International Nuclear Information System (INIS)

    The effect of the isovector coupling channel on the macroscopic part of the nuclear binding energy is determined utilizing the relativistic density dependent Thomas-Fermi approach for the calculation of the macroscopic part of the nuclear binding energy, and the dependency of this effect on the numbers of neutrons and protons is studied. The isovector coupling channel leads to increased nuclear binding energy, and this effect sharpens with growing excess of the number of neutrons on the number of protons. (author)

  5. Transport Gap and exciton binding energy determination in organic semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Krause, Stefan; Schoell, Achim; Reinert, Friedrich; Umbach, Eberhard [University of Wuerzburg (Germany). Experimental Physics II; Casu, Benedetta [Inst. f. Physik. u. Theor. Chemie, Tuebingen (Germany)

    2008-07-01

    The transport gap of an organic semiconductor is defined as the energy difference between the HOMO and LUMO levels in the presence of a hole or electron, respectively, after relaxation has occurred. Its knowledge is mandatory for the optimisation of electronic devices based on these materials. UV photoelectron spectroscopy (UPS) and inverse photoelectron spectroscopy (IPES) are routinely applied to measure these molecular levels. However, the precise determination of the transport gap on the basis of the respective data is not an easy task. It involves fundamental questions about the properties of organic molecules and their condensates, about their reaction on the experimental probe, and on the evaluation of the spectroscopic data. In particular electronic relaxation processes, which occur on the time scale of the photo excitation, have to be considered adequately. We determined the transport gap for the organic semiconductors PTCDA, Alq3, DIP, CuPc, and PBI-H4. After careful data analysis and comparison to the respective values for the optical gap we obtain values for the exciton binding energies between 0.1-0.5 eV. This is considerably smaller than commonly believed and indicates a significant delocalisation of the excitonic charge over various molecular units.

  6. Quantum-Confinement Effects on Binding Energies and Optical Properties of Excitons in Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    潘晖

    2004-01-01

    Quantum-confinement effects on the binding energy and the linear optical susceptibility of excitons in quantum dots are studied. It is found that the binding energy and the linear optical susceptibility are sensitive to the barrier height and the dot size. For an infinite barrier, the binding energy of excitons decreases monotonically with the increasing dot radius, and the absorption intensity has almost the same amplitude with the increasing photon energy. For a finite barrier, the binding energy has a maximum value with the increasing dot radius, and the absorption intensity damps rapidly with the increasing photon energy. The effective mass ratio is also found to have an influence on the binding energy. The results could be confirmed by future experiments on excitons in quantum dots.

  7. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A.

    Science.gov (United States)

    Maurer, Manuela; de Beer, Stephanie B A; Oostenbrink, Chris

    2016-01-01

    The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data. PMID:27092480

  8. Total binding energy via the band structure energy of 4d group transition metals

    International Nuclear Information System (INIS)

    The binding in metals provides a basis genesis to discuss the cohesive, elastic, lattice dynamical and other allied properties of the metals. A thorough and comprehensive analysis with regard to (i) various energy terms contributing to total metallic bonding, (ii) forms of the model potential incurring the band structure part of the binding, (iii) implication of s-d hybridization and (iv) effect of electron screening, has prompted us to undertake the present study of binding in several complex metals which turn out to be superconducting at low temperatures and bear hcp, bcc and fcc configurations at room temperature i.e. yttrium (Y), zirconium (Zr), niobium (Nb), molybdenum (Mo), ruthenium (Ru), rhodium (Rh) and palladium (Pd). (author). 13 refs., 2 figs., 2 tabs

  9. Ground state normalized binding energy of impurity in asymmetric quantum wells under hydrostatic pressure

    Science.gov (United States)

    Akbas, H.; Sucu, S.; Minez, S.; Dane, C.; Akankan, O.; Erdogan, I.

    2016-06-01

    We have studied and computed variationally the impurity energy, impurity energy turning points, and ground state normalized binding energy as functions of the impurity position for shallow impurity in asymmetric quantum wells under hydrostatic pressure. We found that the normalized binding energy significantly depends on the asymmetry of the well, besides depending on the impurity position and hydrostatic pressure. Also, the dependence of the positive normalized binding energy on the pressure can be used to find out the degree of the asymmetry of the well or the impurity position in the well.

  10. Effect of the isovector coupling channel on the macroscopic part of the nuclear binding energy

    Indian Academy of Sciences (India)

    S Haddad

    2013-05-01

    The effect of isovector coupling channel on the macroscopic part of the nuclear binding energy is studied using the relativistic density-dependent Thomas–Fermi approach. The dependency of this effect on the number of neutrons and protons is also studied. The isovector coupling channel leads to increased nuclear binding energy, and this effect increases with the increasing neutron number in the nucleus.

  11. Influence of host matrices on krypton electron binding energies and KLL Auger transition energies

    Czech Academy of Sciences Publication Activity Database

    Inoyatov, A. K.; Perevoshchikov, L. L.; Kovalík, Alojz; Filosofov, D. V.; Yushkevich, Yu. V.; Ryšavý, Miloš; Lee, B. Q.; Kibédi, T.; Stuchbery, A. E.; Zhdanov, V. S.

    2014-01-01

    Roč. 197, DEC (2014), s. 64-71. ISSN 0368-2048 R&D Projects: GA ČR(CZ) GAP203/12/1896; GA MŠk LG14004 Institutional support: RVO:61389005 Keywords : Kr-83 * Rb-83 * Sr-83 * electron binding energy * KLL transitions * natural atomic level width * multiconfiguration Dirac-Fock calculations Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.436, year: 2014

  12. Formation Mechanism and Binding Energy for Regular Tetrahedral Structure of Li4

    Institute of Scientific and Technical Information of China (English)

    GOU Qing-Quan; YANG Jian-Hui; LI Ping

    2006-01-01

    The formation mechanism for the regular tetrahedral structure of Li4 cluster is proposed. The curve of the total energy versus the separation R between the two nuclei has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of-29.8279 a.u. at R=14.50 a0. When R approaches infinity the total energy of four lithium atoms has the value of-29.7121 a.u. So the binding energy of Li4 with respect to four lithium atoms is the difference of 0.1158 a.u.for the above two energy values. Therefore the binding energy per atom for Li4 is 0.029 a.u., or 0.7878 eV, which is greater than the binding energy per atom of 0.453 eV for Li2, the binding energy pcr atom of 0.494 eV for Li3 and the binding energy per atom of 0.632 eV for Li5 calculated previously by us. This means that the Li4 cluster may be formed stably in a regular tetrahedral structure of side length R=14.50 a0 with a greater binding energy.

  13. Geometry, Energy, and Some Electronic Properties of Carbon Polyprismanes: Ab Initio and Tight-Binding Study

    OpenAIRE

    Konstantin P. Katin; Shostachenko, Stanislav A.; Avkhadieva, Alina I.; Mikhail M. Maslov

    2015-01-01

    We report geometry, energy, and some electronic properties of [n,4]- and [n,5]prismanes (polyprismanes): a special type of carbon nanotubes constructed from dehydrogenated cycloalkane C4- and C5-rings, respectively. Binding energies, interatomic bonds, and the energy gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) have been calculated using density functional approach and nonorthogonal tight-binding model for the systems up to thir...

  14. Implicit ligand theory: Rigorous binding free energies and thermodynamic expectations from molecular docking

    OpenAIRE

    Minh, David D. L.

    2012-01-01

    A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor configurations only need to be sampled once, facilitating the use of binding free energy calculations in virtual screening. Demonstrative calculations on a host-guest system yield good agreement with previous free energy calculations and isothermal titration...

  15. Formation Mechanism and Binding Energy for Body-Centred Regular Octahedral Structure of Li7 Cluster

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The formation mechanism for the body-centred regular octahedral structure of Lh cluster is proposed. The curve of the total energy versus the separation R between the nucleus at tie centre and nuclei at the apexes for this structure of Lh has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of-52.169 73 a.u. at R= 5.06a0. When R approaches infinity, the totai energy of seven lithium atoms has the value of -51.996 21 a.u. So the binding energy of Lh with respect to seven lithium atoms is 0.173 52 a.u. Therefore the binding energy per atom for hit is 0.024 79 a.u. or 0.674 eV, which is greater than the binding energy per atom of 0.453 eV for Lii, the binding energy per atom of 0.494 eV for Liz and the binding energy per atom of 0.632 eV for Li& calculated previously by us. This means that the Lh cluster may be formed stably in a body-centred regular octahedral structure with a greater binding energy.

  16. Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites

    OpenAIRE

    Mustonen, Ville; Kinney, Justin; Callan, Curtis G.; Lässig, Michael

    2008-01-01

    We present a genomewide cross-species analysis of regulation for broad-acting transcription factors in yeast. Our model for binding site evolution is founded on biophysics: the binding energy between transcription factor and site is a quantitative phenotype of regulatory function, and selection is given by a fitness landscape that depends on this phenotype. The model quantifies conservation, as well as loss and gain, of functional binding sites in a coherent way. Its predictions are supported...

  17. Benchmarking ab initio binding energies of hydrogen-bonded molecular clusters based on FTIR spectroscopy

    DEFF Research Database (Denmark)

    Bork, Nicolai Christian; Du, Lin; Reiman, Heidi;

    2014-01-01

    Gibbs free binding energies in molecular complexes and clusters based on gas phase FTIR spectroscopy. The acetonitrile-HCl molecular complex is identified via its redshifted H-Cl stretching vibrational mode. We determine the Gibbs free binding energy, ΔG°295 K, to between 4.8 and 7.9 kJ mol(-1) and......Models of formation and growth of atmospheric aerosols are highly dependent on accurate cluster binding energies. These are most often calculated by ab initio electronic structure methods but remain associated with significant uncertainties. We present a computational benchmarking study of the...

  18. Biexciton binding energy in ZnSe quantum wells and quantum wires

    DEFF Research Database (Denmark)

    Wagner, Hans-Peter; Langbein, Wolfgang; Hvam, Jørn Märcher; Bacher, G.; Kümmell, T.; Forchel, Alfred

    2002-01-01

    The biexciton binding energy E-XX is investigated in ZnSe/ZnMgSe quantum wells and quantum wires as a function of the lateral confinement by transient four-wave mixing. In the quantum wells one observes for decreasing well width a significant increase in the relative binding energy, saturating for...... well widths less than 8 nm. In the quantum wires an increase of 30% is found in the smallest quantum wire structures compared to the corresponding quantum well value. A simple analytical model taking into account the quantum confinement in these low-dimensional systems is used to explain the...... experimentally observed dependence of the biexciton binding energies....

  19. Binding Energy of Molecules on Water Ice: Laboratory Measurements and Modeling

    Science.gov (United States)

    He, Jiao; Acharyya, Kinsuk; Vidali, Gianfranco

    2016-07-01

    We measured the binding energy of N2, CO, O2, CH4, and CO2 on non-porous (compact) amorphous solid water (np-ASW), of N2 and CO on porous ASW, and of NH3 on crystalline water ice. We were able to measure binding energies down to a fraction of 1% of a layer, thus making these measurements more appropriate for astrochemistry than the existing values. We found that CO2 forms clusters on the np-ASW surface even at very low coverages. The binding energies of N2, CO, O2, and CH4 decrease with coverage in the submonolayer regime. Their values at the low coverage limit are much higher than what is commonly used in gas-grain models. An empirical formula was used to describe the coverage dependence of the binding energies. We used the newly determined binding energy distributions in a simulation of gas-grain chemistry for cold cloud and hot-core models. We found that owing to the higher value of binding energy in the submonolayer regime, a fraction of all these ices remains for much longer and up to higher temperatures on the grain surface compared to the single value energies currently used in the astrochemical models.

  20. Formation Mechanism and Binding Energy for Body-Centred Regular Tetrahedral Structure of Li5

    Institute of Scientific and Technical Information of China (English)

    LI Ping; YANG Jian-Hui; GOU Qing-Quan

    2006-01-01

    The formation mechanism for the body-centred regular tetrahedral structure of Li5 cluster is proposed.The curve of the total energy versus the separation R between the nucleus at the centre and nuclei at the apexes for this structure of Li5 has been calculated by using the method of Gou's modified arrangement channel quantum mechanics(MACQM). The result shows that the curve has a minimal energy of-37.2562 a.u. at R = 14.5a0. When R approaches infinity the total energy of five lithium atoms has the value of-37.1401 a.u. So the binding energy of Li5 with respect to five lithium atoms is the difference of 0.1161 a.u. for the above two energy values. Therefore the binding energy per atom for Li5 is 0.023 22 a.u., or 0.632 eV, which is greater than the binding energy per atom of 0.453 eV for Li2 and the binding energy per atom of 0.494 eV for Li3 calculated previously by us. This means that the Li5 cluster may be formed stably in a body-centred regular tetrahedral structure with a greater binding energy.

  1. Prediction of SAMPL3 Host-Guest Affinities with the Binding Energy Distribution Analysis Method (BEDAM)

    OpenAIRE

    Gallicchio, Emilio; Ronald M Levy

    2012-01-01

    BEDAM calculations are described to predict the free energies of binding of a series of anaesthetic drugs to a recently characterized acyclic cucurbituril host. The modeling predictions, conducted as part of the SAMPL3 host-guest affinity blind challenge, are generally in good quantitative agreement with the experimental measurements. The correlation coefficient between computed and measured binding free energies is 70% with high statistical significance. Multiple conformational stereoisomers...

  2. Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model

    OpenAIRE

    Muddana, Hari S.; Gilson, Michael K.

    2012-01-01

    The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy functi...

  3. Effect of a high intensity laser beam on impurity binding energy in a nanocone

    Science.gov (United States)

    Paredes, H.; Beltrán Ríos, C. L.; Gutíerrez, W.

    2016-02-01

    This paper presents theoretical results of a study that analyzed the effect of a high- frequency laser in the ground state binding energy of a hydrogenic donnor impurity. For these results, the trigonometric sweep method and framework of the effective mass approximation is applied. The results showed that the binding energy changes depending on the laser intensity and the impurity position across of the nanocone axis. The results agree with previous results obtained in similar systems.

  4. SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations

    Directory of Open Access Journals (Sweden)

    Marharyta Petukh

    2016-04-01

    Full Text Available Predicting the effect of amino acid substitutions on protein–protein affinity (typically evaluated via the change of protein binding free energy is important for both understanding the disease-causing mechanism of missense mutations and guiding protein engineering. In addition, researchers are also interested in understanding which energy components are mostly affected by the mutation and how the mutation affects the overall structure of the corresponding protein. Here we report a webserver, the Single Amino Acid Mutation based change in Binding free Energy (SAAMBE webserver, which addresses the demand for tools for predicting the change of protein binding free energy. SAAMBE is an easy to use webserver, which only requires that a coordinate file be inputted and the user is provided with various, but easy to navigate, options. The user specifies the mutation position, wild type residue and type of mutation to be made. The server predicts the binding free energy change, the changes of the corresponding energy components and provides the energy minimized 3D structure of the wild type and mutant proteins for download. The SAAMBE protocol performance was tested by benchmarking the predictions against over 1300 experimentally determined changes of binding free energy and a Pearson correlation coefficient of 0.62 was obtained. How the predictions can be used for discriminating disease-causing from harmless mutations is discussed. The webserver can be accessed via http://compbio.clemson.edu/saambe_webserver/.

  5. Formation Mechanism and Binding Energy for Regular Octahedral Structure of Li6 Cluster

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yan-Ping; LI Ping; GOU Qing-Quan; LIU Wei-Na

    2008-01-01

    The formation mechanism for the regular octahedral structure of Li6cluster is proposed. The curve of the total energy versus the separation R between any two neighboring nuclei has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of-44.736 89 a.u. At R=5.07α0. When R approaches infinity, the total energy of six lithium atoms has the value of-44.568 17 a.u. So the binding energy of Li6 with respect to six lithium atoms is 0.1687 a.u. Therefore, the binding energy per atom for Li6 is 0.028 12 a.u., or 0.7637 eV, which is greater than the binding energy per atom of 0.453 eV for Li2 arid the binding energy per atom of 0.494 eV for Li3 calculated in our previous work. This means that the Li6 cluster may be formed in a regular octahedral structure with a greater binding energy.

  6. Influence of host matrices on krypton electron binding energies and KLL Auger transition energies

    Energy Technology Data Exchange (ETDEWEB)

    Inoyatov, A.Kh., E-mail: inoyatov@jinr.ru [Laboratory of Nuclear Problems, JINR, Dubna, Moscow Region (Russian Federation); Institute of Applied Physics, National University, Tashkent, Republic of Uzbekistan (Uzbekistan); Perevoshchikov, L.L. [Laboratory of Nuclear Problems, JINR, Dubna, Moscow Region (Russian Federation); Kovalík, A. [Laboratory of Nuclear Problems, JINR, Dubna, Moscow Region (Russian Federation); Nuclear Physics Institute of the ASCR, CZ-25068 Řež near Prague (Czech Republic); Filosofov, D.V.; Yushkevich, Yu.V. [Laboratory of Nuclear Problems, JINR, Dubna, Moscow Region (Russian Federation); Ryšavý, M. [Nuclear Physics Institute of the ASCR, CZ-25068 Řež near Prague (Czech Republic); Lee, B.Q.; Kibédi, T.; Stuchbery, A.E. [Department of Nuclear Physics, RSPE, The Australian National University, Canberra, ACT 0200 (Australia); Zhdanov, V.S. [Nuclear Physics Institute, Almaty (Kazakhstan)

    2014-12-15

    Highlights: • The K, L{sub 1–3}, M{sub 1–3} electron binding energies in Kr in the Pt bulk determined. • The K, L{sub 1–3}, M{sub 1–3} electron binding energies in Kr in an evaporated Rb layer obtained. • The krypton K, L{sub 1–3}, M{sub 1} atomic level widths determined for the both host matrices. • The Kr KL{sub 2}L{sub 3}({sup 1}D{sub 2}) Auger transition energies measured for the both host matrices. • The KL{sub 2}L{sub 3}({sup 1}D{sub 2}) energy difference between Rb and Kr in the Pt host measured. • Dirac–Fock calculations of the Kr KLL Auger transitions performed. - Abstract: The low-energy electron spectra emitted in the radioactive decay of the {sup 83}Rb and {sup 83}Sr isotopes were measured with a combined electrostatic electron spectrometer. Radioactive sources used were prepared by ion implantation of {sup 83}Sr into a high purity polycrystalline platinum foil at 30 keV and by vacuum-evaporation deposition of {sup 83}Rb on the same type of foil. From the measured conversion electron spectra, the electron binding energies (referenced to the Fermi level) for the K, L{sub 1}, L{sub 2}, L{sub 3}, M{sub 1}, M{sub 2}, and M{sub 3} shell/subshells of krypton in the platinum host were determined to be 14316.4(12), 1914.3(9), 1720.3(9), 1667.6(9), 281.5(9), 209.6(13), and 201.2(15) eV, respectively, and those for the evaporated layer were observed to be lower by 0.7(1) eV. For both host matrices, values of 2.3(2), 4.6(2), 1.7(2), 1.3(2), and 3.2(3) eV were obtained for the krypton K, L{sub 1}, L{sub 2}, L{sub 3}, and M{sub 1} natural atomic level widths, respectively. The absolute energies of 10838.5(9) and 10839.5(10) eV were measured for the KL{sub 2}L{sub 3}({sup 1}D{sub 2}) Auger transition in krypton implanted in Pt and generated in the evaporated rubidium layer, respectively. A value of 601.0(8) eV was measured for the energy difference of the KL{sub 2}L{sub 3}({sup 1}D{sub 2}) transitions in Rb and Kr in the Pt host

  7. Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles.

    Science.gov (United States)

    Sayyed-Ahmad, Abdallah; Khandelia, Himanshu; Kaznessis, Yiannis N

    2009-09-01

    We present relative binding free energy calculations for six antimicrobial peptide-micelle systems, three peptides interacting with two types of micelles. The peptides are the scorpion derived antimicrobial peptide (AMP), IsCT and two of its analogues. The micelles are dodecylphosphatidylcholine (DPC) and sodium dodecylsulphate (SDS) micelles. The interfacial electrostatic properties of DPC and SDS micelles are assumed to be similar to those of zwitterionic mammalian and anionic bacterial membrane interfaces, respectively. We test the hypothesis that the binding strength between peptides and the anionic micelle SDS can provide information on peptide antimicrobial activity, since it is widely accepted that AMPs function by binding to and disrupting the predominantly anionic lipid bilayer of the bacterial cytoplasmic membrane. We also test the hypothesis that the binding strength between peptides and the zwitterionic micelle DPC can provide information on peptide haemolytic activities, since it is accepted that they also bind to and disrupt the zwitterionic membrane of mammalian cells. Equilibrium structures of the peptides, micelles and peptide-micelle complexes are obtained from more than 300 ns of molecular dynamics simulations. A thermodynamic cycle is introduced to compute the binding free energy from electrostatic, non-electrostatic and entropic contributions. We find relative binding free energy strengths between peptides and SDS to correlate with the experimentally measured rankings for peptide antimicrobial activities, and relative free energy binding strengths between peptides and DPC to correlate with the observed rankings for peptide haemolytic toxicities. These findings point to the importance of peptide-membrane binding strength for antimicrobial activity and haemolytic activity. PMID:21113423

  8. Formation Mechanism and Binding Energy for Equilateral Triangle Structure of Li3 Cluster

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The formation mechanism for the equilateral triangle structure of Li3 cluster is proposed. The curve of the total energy versus the interatomic distance for this structure has been calculated by using the method of Gou's Modified Arrangement Channel Quantum Mechanics. The result shows that the curve has a minimal energy of-22.338 60 a.u at R = 5.82 a0. The total energy of Li3 when R approaches ∞ has the value of-22.284 09 a.u. This is also the total energy of three lithium atoms dissociated from Li3. The difference value of 0.0545 08 a.u. for the above two energy values is the dissociation energy of Li3 cluster, which is also its binding energy. Therefore the binding energy per lithium atom for Li3 is 0.018 169 a.u. = 0.494 eV, which is greater than the binding energy of 0.453 eV per atom for Li2 calculated in a previous work. This means that the Li3 cluster may be formed in the equilateral triangle structure of side length R = 5.82a0 stably with a stronger binding from the symmetrical interaction among the three lithium atoms.

  9. Theoretical prediction of the binding free energy for mutants of replication protein A.

    Science.gov (United States)

    Carra, Claudio; Saha, Janapriya; Cucinotta, Francis A

    2012-07-01

    The replication protein A (RPA) is a heterotrimeric (70, 32, and 14 kDa subunits), single stranded DNA (ssDNA) binding protein required for pivotal functions in the cell metabolism, such as chromosomal replication, prevention of hairpin formation, DNA repair and recombination, and signaling after DNA damage. Studies based on deletions and mutations have identified the high affinity ssDNA binding domains in the 70 kDa subunit of RPA, regions A and B. Individually, the domain A and B have a low affinity for ssDNA, while tandems composed of AA, AB, BB, and BA sequences bind the ssDNA with moderate to high affinity. Single and double point mutations on polar residues in the binding domains leads to a reduction in affinity of RPA for ssDNA, in particular when two hydrophilic residues are involved. In view of these results, we performed a study based on molecular dynamics simulation aimed to reproduce the experimental change in binding free energy, ΔΔG, of RPA70 mutants to further elucidate the nature of the protein-ssDNA interaction. The MM-PB(GB)SA methods implemented in Amber10 and the code FoldX were used to estimate the binding free energy. The theoretical and experimental ΔΔG values correlate better when the results are obtained by MM-PBSA calculated on individual trajectories for each mutant. In these conditions, the correlation coefficient between experimental and theoretical ΔΔG reaches a value of 0.95 despite the overestimation of the energy change by one order of magnitude. The decomposition of the MM-GBSA energy per residue allows us to correlate the change of the affinity with the residue polarity and energy contribution to the binding. The method revealed reliable predictions of the change in the affinity in function of mutations, and can be used to identify new mutants with distinct binding properties. PMID:22160652

  10. Binding Energy of Molecules on Water Ice: Laboratory Measurements and Modeling

    CERN Document Server

    He, Jiao; Vidali, Gianfranco

    2016-01-01

    We measured the binding energy of N$_2$, CO, O$_2$, CH$_4$, and CO$_2$ on non-porous (compact) amorphous solid water (np-ASW), of N$_2$ and CO on porous amorphous solid water (p-ASW), and of NH$_3$ on crystalline water ice. We were able to measure binding energies down to a fraction of 1\\% of a layer, thus making these measurements more appropriate for astrochemistry than the existing values. We found that CO$_2$ forms clusters on np-ASW surface even at very low coverages. The binding energies of N$_2$, CO, O$_2$, and CH$_4$ decrease with coverage in the submonolayer regime. Their values at the low coverage limit are much higher than what is commonly used in gas-grain models. An empirical formula was used to describe the coverage dependence of the binding energies. We used the newly determined binding energy distributions in a simulation of gas-grain chemistry for cold cloud and hot core models. We found that owing to the higher value of desorption energy in the sub-monlayer regime a fraction of all these ice...

  11. Binding energies of nucleobase complexes: Relevance to homology recognition of DNA

    Science.gov (United States)

    León, Sergio Cruz; Prentiss, Mara; Fyta, Maria

    2016-06-01

    The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and calculate their binding energies. At a second step, mismatches are incorporated into the Watson-Crick complexes in order to evaluate the variation in the binding energy with respect to the canonical Watson-Crick pairs. A linear variation of this binding energy with the degree of mismatching is observed. The binding energies for the duplets and triplets containing mismatches are further compared to the energies of the respective singlets in order to assess the degree of collectivity in these complexes. This study also suggests that mismatches do not considerably affect the energetics of canonical base pairs. Our work is highly relevant to the recognition process in DNA promoted through the RecA protein and suggests a clear distinction between recognition in singlets, and recognition in duplets or triplets. Our work assesses the importance of collectivity in the homology recognition of DNA.

  12. Atomic Mass and NuclearBinding Energy for Uup-269(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-269 (Ununpentium, atomic number Z = 115, mass number A = 269).

  13. Atomic Mass and NuclearBinding Energy for Uup-335(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-335 (Ununpentium, atomic number Z = 115, mass number A = 335).

  14. Atomic Mass and NuclearBinding Energy for Uup-332(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-332 (Ununpentium, atomic number Z = 115, mass number A = 332).

  15. Atomic Mass and NuclearBinding Energy for Uup-326(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-326 (Ununpentium, atomic number Z = 115, mass number A = 326).

  16. Atomic Mass and NuclearBinding Energy for Uup-259(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-259 (Ununpentium, atomic number Z = 115, mass number A = 259).

  17. Atomic Mass and NuclearBinding Energy for Uup-300(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-300 (Ununpentium, atomic number Z = 115, mass number A = 300).

  18. Atomic Mass and NuclearBinding Energy for Uup-317(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-317 (Ununpentium, atomic number Z = 115, mass number A = 317).

  19. Atomic Mass and NuclearBinding Energy for Uup-304(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-304 (Ununpentium, atomic number Z = 115, mass number A = 304).

  20. Atomic Mass and NuclearBinding Energy for Uup-276(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-276 (Ununpentium, atomic number Z = 115, mass number A = 276).

  1. Atomic Mass and NuclearBinding Energy for Uup-271(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-271 (Ununpentium, atomic number Z = 115, mass number A = 271).

  2. Atomic Mass and NuclearBinding Energy for Uup-321(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-321 (Ununpentium, atomic number Z = 115, mass number A = 321).

  3. Atomic Mass and NuclearBinding Energy for Uup-294(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-294 (Ununpentium, atomic number Z = 115, mass number A = 294).

  4. Atomic Mass and NuclearBinding Energy for Uup-277(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-277 (Ununpentium, atomic number Z = 115, mass number A = 277).

  5. Atomic Mass and NuclearBinding Energy for Uup-310(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-310 (Ununpentium, atomic number Z = 115, mass number A = 310).

  6. Atomic Mass and NuclearBinding Energy for Uup-306(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-306 (Ununpentium, atomic number Z = 115, mass number A = 306).

  7. Atomic Mass and NuclearBinding Energy for Uup-323(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-323 (Ununpentium, atomic number Z = 115, mass number A = 323).

  8. Atomic Mass and NuclearBinding Energy for Uup-299(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-299 (Ununpentium, atomic number Z = 115, mass number A = 299).

  9. Atomic Mass and NuclearBinding Energy for Uup-286(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-286 (Ununpentium, atomic number Z = 115, mass number A = 286).

  10. Atomic Mass and NuclearBinding Energy for Uup-282(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-282 (Ununpentium, atomic number Z = 115, mass number A = 282).

  11. Atomic Mass and NuclearBinding Energy for Uup-338(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-338 (Ununpentium, atomic number Z = 115, mass number A = 338).

  12. Atomic Mass and NuclearBinding Energy for Uup-324(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-324 (Ununpentium, atomic number Z = 115, mass number A = 324).

  13. Atomic Mass and NuclearBinding Energy for Uup-322(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-322 (Ununpentium, atomic number Z = 115, mass number A = 322).

  14. Atomic Mass and NuclearBinding Energy for Uup-305(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-305 (Ununpentium, atomic number Z = 115, mass number A = 305).

  15. Atomic Mass and NuclearBinding Energy for Uup-336(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-336 (Ununpentium, atomic number Z = 115, mass number A = 336).

  16. Atomic Mass and NuclearBinding Energy for Uup-308(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-308 (Ununpentium, atomic number Z = 115, mass number A = 308).

  17. Atomic Mass and NuclearBinding Energy for Uup-291(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-291 (Ununpentium, atomic number Z = 115, mass number A = 291).

  18. Atomic Mass and NuclearBinding Energy for Uup-320(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-320 (Ununpentium, atomic number Z = 115, mass number A = 320).

  19. Atomic Mass and NuclearBinding Energy for Uup-261(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-261 (Ununpentium, atomic number Z = 115, mass number A = 261).

  20. Atomic Mass and NuclearBinding Energy for Uup-296(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-296 (Ununpentium, atomic number Z = 115, mass number A = 296).

  1. Atomic Mass and NuclearBinding Energy for Uup-272(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-272 (Ununpentium, atomic number Z = 115, mass number A = 272).

  2. Atomic Mass and NuclearBinding Energy for Uup-258(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-258 (Ununpentium, atomic number Z = 115, mass number A = 258).

  3. Atomic Mass and NuclearBinding Energy for Uup-273(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-273 (Ununpentium, atomic number Z = 115, mass number A = 273).

  4. Atomic Mass and NuclearBinding Energy for Uup-302(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-302 (Ununpentium, atomic number Z = 115, mass number A = 302).

  5. Atomic Mass and NuclearBinding Energy for Uup-289(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-289 (Ununpentium, atomic number Z = 115, mass number A = 289).

  6. Atomic Mass and NuclearBinding Energy for Uup-334(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-334 (Ununpentium, atomic number Z = 115, mass number A = 334).

  7. Atomic Mass and NuclearBinding Energy for Uup-316(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-316 (Ununpentium, atomic number Z = 115, mass number A = 316).

  8. Atomic Mass and NuclearBinding Energy for Uup-309(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-309 (Ununpentium, atomic number Z = 115, mass number A = 309).

  9. Atomic Mass and NuclearBinding Energy for Uup-262(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-262 (Ununpentium, atomic number Z = 115, mass number A = 262).

  10. Atomic Mass and NuclearBinding Energy for Uup-319(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-319 (Ununpentium, atomic number Z = 115, mass number A = 319).

  11. Atomic Mass and NuclearBinding Energy for Uup-314(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-314 (Ununpentium, atomic number Z = 115, mass number A = 314).

  12. Atomic Mass and NuclearBinding Energy for Uup-281(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-281 (Ununpentium, atomic number Z = 115, mass number A = 281).

  13. Atomic Mass and NuclearBinding Energy for Uup-267(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-267 (Ununpentium, atomic number Z = 115, mass number A = 267).

  14. Atomic Mass and NuclearBinding Energy for Uup-329(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-329 (Ununpentium, atomic number Z = 115, mass number A = 329).

  15. Atomic Mass and NuclearBinding Energy for Uup-264(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-264 (Ununpentium, atomic number Z = 115, mass number A = 264).

  16. Atomic Mass and NuclearBinding Energy for Uup-298(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-298 (Ununpentium, atomic number Z = 115, mass number A = 298).

  17. Atomic Mass and NuclearBinding Energy for Uup-339(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-339 (Ununpentium, atomic number Z = 115, mass number A = 339).

  18. Atomic Mass and NuclearBinding Energy for Uup-278(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-278 (Ununpentium, atomic number Z = 115, mass number A = 278).

  19. Atomic Mass and NuclearBinding Energy for Uup-312(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-312 (Ununpentium, atomic number Z = 115, mass number A = 312).

  20. Atomic Mass and NuclearBinding Energy for Uup-318(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-318 (Ununpentium, atomic number Z = 115, mass number A = 318).

  1. Atomic Mass and NuclearBinding Energy for Uup-270(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-270 (Ununpentium, atomic number Z = 115, mass number A = 270).

  2. Atomic Mass and NuclearBinding Energy for Uup-263(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-263 (Ununpentium, atomic number Z = 115, mass number A = 263).

  3. Atomic Mass and NuclearBinding Energy for Uup-313(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-313 (Ununpentium, atomic number Z = 115, mass number A = 313).

  4. Atomic Mass and NuclearBinding Energy for Uup-337(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-337 (Ununpentium, atomic number Z = 115, mass number A = 337).

  5. Atomic Mass and NuclearBinding Energy for Uup-287(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-287 (Ununpentium, atomic number Z = 115, mass number A = 287).

  6. Atomic Mass and NuclearBinding Energy for Uup-279(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-279 (Ununpentium, atomic number Z = 115, mass number A = 279).

  7. Atomic Mass and NuclearBinding Energy for Uup-275(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-275 (Ununpentium, atomic number Z = 115, mass number A = 275).

  8. Atomic Mass and NuclearBinding Energy for Uup-333(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-333 (Ununpentium, atomic number Z = 115, mass number A = 333).

  9. Atomic Mass and NuclearBinding Energy for Uup-280(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-280 (Ununpentium, atomic number Z = 115, mass number A = 280).

  10. Atomic Mass and NuclearBinding Energy for Uup-266(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-266 (Ununpentium, atomic number Z = 115, mass number A = 266).

  11. Atomic Mass and NuclearBinding Energy for Uup-330(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-330 (Ununpentium, atomic number Z = 115, mass number A = 330).

  12. Atomic Mass and NuclearBinding Energy for Uup-265(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-265 (Ununpentium, atomic number Z = 115, mass number A = 265).

  13. Atomic Mass and NuclearBinding Energy for Uup-283(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-283 (Ununpentium, atomic number Z = 115, mass number A = 283).

  14. Atomic Mass and NuclearBinding Energy for Uup-297(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-297 (Ununpentium, atomic number Z = 115, mass number A = 297).

  15. Atomic Mass and NuclearBinding Energy for Uup-268(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-268 (Ununpentium, atomic number Z = 115, mass number A = 268).

  16. Atomic Mass and NuclearBinding Energy for Uup-274(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-274 (Ununpentium, atomic number Z = 115, mass number A = 274).

  17. Atomic Mass and NuclearBinding Energy for Uup-260(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-260 (Ununpentium, atomic number Z = 115, mass number A = 260).

  18. Atomic Mass and NuclearBinding Energy for Uup-307(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-307 (Ununpentium, atomic number Z = 115, mass number A = 307).

  19. Atomic Mass and NuclearBinding Energy for Uup-293(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-293 (Ununpentium, atomic number Z = 115, mass number A = 293).

  20. Atomic Mass and NuclearBinding Energy for Uup-284(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-284 (Ununpentium, atomic number Z = 115, mass number A = 284).

  1. Atomic Mass and NuclearBinding Energy for Uup-292(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-292 (Ununpentium, atomic number Z = 115, mass number A = 292).

  2. Atomic Mass and NuclearBinding Energy for Uup-328(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-328 (Ununpentium, atomic number Z = 115, mass number A = 328).

  3. Atomic Mass and NuclearBinding Energy for Uup-331(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-331 (Ununpentium, atomic number Z = 115, mass number A = 331).

  4. Atomic Mass and NuclearBinding Energy for Uup-311(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-311 (Ununpentium, atomic number Z = 115, mass number A = 311).

  5. Atomic Mass and NuclearBinding Energy for Uup-285(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-285 (Ununpentium, atomic number Z = 115, mass number A = 285).

  6. Atomic Mass and NuclearBinding Energy for Uup-315(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-315 (Ununpentium, atomic number Z = 115, mass number A = 315).

  7. Atomic Mass and NuclearBinding Energy for Uup-288(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-288 (Ununpentium, atomic number Z = 115, mass number A = 288).

  8. Atomic Mass and NuclearBinding Energy for Uup-295(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-295 (Ununpentium, atomic number Z = 115, mass number A = 295).

  9. Atomic Mass and NuclearBinding Energy for Uup-301(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-301 (Ununpentium, atomic number Z = 115, mass number A = 301).

  10. Atomic Mass and NuclearBinding Energy for Uup-303(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-303 (Ununpentium, atomic number Z = 115, mass number A = 303).

  11. Atomic Mass and NuclearBinding Energy for Uup-290(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-290 (Ununpentium, atomic number Z = 115, mass number A = 290).

  12. Atomic Mass and NuclearBinding Energy for Uup-327(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-327 (Ununpentium, atomic number Z = 115, mass number A = 327).

  13. Atomic Mass and NuclearBinding Energy for Uup-325(Ununpentium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Uup-325 (Ununpentium, atomic number Z = 115, mass number A = 325).

  14. Binding energy correction for atomic L-shell ionization by heavy charged particles

    International Nuclear Information System (INIS)

    During the process of inner shell ionization of atoms by low-velocity heavy charged particles the effective binding energy of the target electron is changed due to the presence of the incoming projectile. In the present work the binding energy corrections for the ionization of 2s and 2p sub-shells of the target atom have been calculated by employing approximate expressions for L-shell ionization based on a semi-classical approximation (SCA). The binding energy correction thus obtained has been incorporated in the classical binary encounter theory of ionization to calculate the L-shell ionization cross section of argon by the impact of low energy (50-200keV) protons. The results are compared with the available experimental data. (Auth.)

  15. Nuclear binding energies: global collective structures and local shell-model correlations

    International Nuclear Information System (INIS)

    In this contribution the global behaviour of nuclear binding energies, or alternatively two-neutron separation energies, are studied. Recent high-precision mass measurements show local deviations from an overall macroscopic behaviour, and it is shown how a consistent and simultaneously description of both can be given within the Interacting Boson Model. (orig.)

  16. Poisson-Boltzmann Calculations of Nonspecific Salt Effects on Protein-Protein Binding Free Energies

    OpenAIRE

    Bertonati, Claudia; Honig, Barry; Alexov, Emil

    2007-01-01

    The salt dependence of the binding free energy of five protein-protein hetero-dimers and two homo-dimers/tetramers was calculated from numerical solutions to the Poisson-Boltzmann equation. Overall, the agreement with experimental values is very good. In all cases except one involving the highly charged lactoglobulin homo-dimer, increasing the salt concentration is found both experimentally and theoretically to decrease the binding affinity. To clarify the source of salt effects, the salt-dep...

  17. Structural investigations into the binding mode of novel neolignans Cmp10 and Cmp19 microtubule stabilizers by in silico molecular docking, molecular dynamics, and binding free energy calculations.

    Science.gov (United States)

    Tripathi, Shubhandra; Kumar, Akhil; Kumar, B Sathish; Negi, Arvind S; Sharma, Ashok

    2016-06-01

    Microtubule stabilizers provide an important mode of treatment via mitotic cell arrest of cancer cells. Recently, we reported two novel neolignans derivatives Cmp10 and Cmp19 showing anticancer activity and working as microtubule stabilizers at micromolar concentrations. In this study, we have explored the binding site, mode of binding, and stabilization by two novel microtubule stabilizers Cmp10 and Cmp19 using in silico molecular docking, molecular dynamics (MD) simulation, and binding free energy calculations. Molecular docking studies were performed to explore the β-tubulin binding site of Cmp10 and Cmp19. Further, MD simulations were used to probe the β-tubulin stabilization mechanism by Cmp10 and Cmp19. Binding affinity was also compared for Cmp10 and Cmp19 using binding free energy calculations. Our docking results revealed that both the compounds bind at Ptxl binding site in β-tubulin. MD simulation studies showed that Cmp10 and Cmp19 binding stabilizes M-loop (Phe272-Val288) residues of β-tubulin and prevent its dynamics, leading to a better packing between α and β subunits from adjacent tubulin dimers. In addition, His229, Ser280 and Gln281, and Arg278, Thr276, and Ser232 were found to be the key amino acid residues forming H-bonds with Cmp10 and Cmp19, respectively. Consequently, binding free energy calculations indicated that Cmp10 (-113.655 kJ/mol) had better binding compared to Cmp19 (-95.216 kJ/mol). This study provides useful insight for better understanding of the binding mechanism of Cmp10 and Cmp19 and will be helpful in designing novel microtubule stabilizers. PMID:26212016

  18. Lanthanide 4f-electron binding energies and the nephelauxetic effect in wide band gap compounds

    International Nuclear Information System (INIS)

    Employing data from luminescence spectroscopy, the inter 4f-electron Coulomb repulsion energy U(6, A) in Eu 2+/3+ impurities together with the 5d-centroid energy shift ϵc(1,3+,A) in Ce3+ impurities in 40 different fluoride, chloride, bromide, iodide, oxide, sulfide, and nitride compounds has been determined. This work demonstrates that the chemical environment A affects the two energies in a similar fashion; a fashion that follows the anion nephelauxetic sequence F, O, Cl, Br, N, I, S, Se. One may then calculate U(6, A) from well established and accurate ϵc(1,3+,A) values which are then used as input to the chemical shift model proposed in Dorenbos (2012) [19]. As output it provides the chemical shift of 4f-electron binding energy and therewith the 4f-electron binding energy relative to the vacuum energy. In addition this method provides a tool to routinely establish the binding energy of electrons at the top of the valence band (work function) and the bottom of the conduction band (electron affinity) throughout the entire family of inorganic compounds. How the electronic structure of the compound and lanthanide impurities therein change with type of compound and type of lanthanide is demonstrated. -- Highlights: ► A relationship between 5d centroid shift and 4f-electron Coulomb repulsion energy is established. ► Information on the absolute 4f-electron binding energy of lanthanides in 40 compounds is provided. ► A new tool to determine absolute binding energies of electrons in valence and conduction bands is demonstrated

  19. Formation Mechanism and Binding Energy for Body-Centred Regular Icosahedral Structure of Li13 Cluster

    Institute of Scientific and Technical Information of China (English)

    LIU Wei-Na; LI Ping; GOU Qing-Quan; ZHAO Yan-Ping

    2008-01-01

    The formation mechanism for the body-centred regular icosahedral structure of Li13 cluster is proposed. The curve of the total energy versus the separation R between the nucleus at the centre and nuclei at the apexes for this structure of Li13 has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of-96.951 39 a.u. at R = 5.46a0. When R approaches to infinity, the total energy of thirteen lithium atoms has the value of-96.564 38 a.u. So the binding energy of Li13 with respect to thirteen lithium atoms is 0.387 01 a.u. Therefore the binding energy per atom for Li13 is 0.029 77 a.u. or 0.810 eV, which is greater than the binding energy per atom of 0.453 eV for Li2, 0.494 eV for Lia, 0.7878 eV for Li4, 0.632 eV for Lis, and 0.674 eV for Lit calculated by us previously. This means that the Li13 cluster may be formed stably in a body-centred regular icosahedral structure with a greater binding energy.

  20. Concavity for nuclear binding energies, thermodynamical functions and density functionals

    OpenAIRE

    Barrett, B. R.; Giraud, B. G.; Jennings, B. K.; Toberg, N. P.

    2007-01-01

    Sequences of experimental ground-state energies for both odd and even $A$ are mapped onto concave patterns cured from convexities due to pairing and/or shell effects. The same patterns, completed by a list of excitation energies, give numerical estimates of the grand potential $\\Omega(\\beta,\\mu)$ for a mixture of nuclei at low or moderate temperatures $T=\\beta^{-1}$ and at many chemical potentials $\\mu.$ The average nucleon number $(\\beta,\\mu)$ then becomes a continuous variable, allowing ext...

  1. Odd-even staggering of binding energy for nuclei in the s d shell

    Science.gov (United States)

    Fu, G. J.; Cheng, Y. Y.; Jiang, H.; Zhao, Y. M.; Arima, A.

    2016-08-01

    In this paper we study odd-even staggering phenomena of binding energy in the framework of the nuclear shell model for nuclei in the s d shell. We decompose the USDB effective interaction into the monopole interaction and multipole (residual) interactions. We extract the empirical proton-neutron interaction, the Wigner energy, and the one-neutron separation energy using calculated binding energies. The monopole interaction, which represents the spherical mean field, provides contributions to the empirical proton-neutron interaction, the symmetry energy, and the Wigner energy. It does not induce odd-even staggering of the empirical proton-neutron interaction or the one-neutron separation energy. Isovector monopole and quadrupole pairing interactions and isoscalar spin-1 pairing interactions play a key role in reproducing an additional binding energy in both even-even and odd-odd nuclei. The Wigner energy coefficients are sensitive to residual two-body interactions. The nuclear shell structure has a strong influence on the evolution of the one-neutron separation energy, but not on empirical proton-neutron interactions. The so-called three-point formula is a good probe of the shell structure.

  2. Radii and Binding Energies in Oxygen Isotopes: A Challenge for Nuclear Forces.

    Science.gov (United States)

    Lapoux, V; Somà, V; Barbieri, C; Hergert, H; Holt, J D; Stroberg, S R

    2016-07-29

    We present a systematic study of both nuclear radii and binding energies in (even) oxygen isotopes from the valley of stability to the neutron drip line. Both charge and matter radii are compared to state-of-the-art ab initio calculations along with binding energy systematics. Experimental matter radii are obtained through a complete evaluation of the available elastic proton scattering data of oxygen isotopes. We show that, in spite of a good reproduction of binding energies, ab initio calculations with conventional nuclear interactions derived within chiral effective field theory fail to provide a realistic description of charge and matter radii. A novel version of two- and three-nucleon forces leads to considerable improvement of the simultaneous description of the three observables for stable isotopes but shows deficiencies for the most neutron-rich systems. Thus, crucial challenges related to the development of nuclear interactions remain. PMID:27517768

  3. Radii and binding energies in oxygen isotopes: a puzzle for nuclear forces

    CERN Document Server

    Lapoux, V; Barbieri, C; Hergert, H; Holt, J D; Stroberg, R

    2016-01-01

    We present a systematic study of both nuclear radii and binding energies in (even) oxygen isotopes from the valley of stability to the neutron drip line. Both charge and matter radii are compared to state-of-the-art {\\it ab initio} calculations along with binding energy systematics. Experimental matter radii are obtained through a complete evaluation of the available elastic proton scattering data of oxygen isotopes. We show that, in spite of a good reproduction of binding energies, {\\it ab initio} calculations with conventional nuclear interactions derived within chiral effective field theory fail to provide a realistic description of charge and matter radii. A novel version of two- and three-nucleon forces leads to considerable improvement of the simultaneous description of the three observables for stable isotopes, but shows deficiencies for the most neutron-rich systems. Thus, crucial challenges related to the development of nuclear interactions remain.

  4. SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates.

    Directory of Open Access Journals (Sweden)

    Seungpyo Hong

    Full Text Available SH3 domains mediate signal transduction by recognizing short peptides. Understanding of the driving forces in peptide recognitions will help us to predict the binding specificity of the domain-peptide recognition and to understand the molecular interaction networks of cells. However, accurate calculation of the binding energy is a tough challenge. In this study, we propose three ideas for improving our ability to predict the binding energy between SH3 domains and peptides: (1 utilizing the structural ensembles sampled from a molecular dynamics simulation trajectory, (2 utilizing multiple peptide templates, and (3 optimizing the sequence-structure mapping. We tested these three ideas on ten previously studied SH3 domains for which SPOT analysis data were available. The results indicate that calculating binding energy using the structural ensemble was most effective, clearly increasing the prediction accuracy, while the second and third ideas tended to give better binding energy predictions. We applied our method to the five SH3 targets in DREAM4 Challenge and selected the best performing method.

  5. Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors.

    Science.gov (United States)

    Ohno, Kazuki; Mitsui, Takashi; Tanida, Yoshiaki; Matsuura, Azuma; Fujitani, Hideaki; Niimi, Tatsuya; Orita, Masaya

    2011-02-01

    Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists to predict the binding affinity accurately without detailed structural information for protein/ligand complex. We investigated the absolute binding free energies for Poly (ADP-ribose) polymerase-1 (PARP-1)/inhibitor complexes, using the MP-CAFEE method. Although each docking model was used as an input structure, it was found that the absolute binding free energies calculated by MP-CAFEE are well consistent with the experimental ones. The accuracy of this method is much higher than that using molecular mechanics Poisson-Boltzmann/surface area (MM/PBSA). Although the simulation time is quite extensive, the reliable predictor of binding free energies would be a useful tool for drug discovery projects. PMID:20480380

  6. Binding energies and electron affinities of small silicon clusters (n=2--5)

    International Nuclear Information System (INIS)

    The Gaussian-2 (G2) theoretical procedure, based on ab initio molecular orbital theory, is used to calculate the energies of Sin and Si-n (n=1--5) clusters. The G2 energies are used to derive accurate binding energies and electron affinities of these clusters. The calculated electron affinities of Si2--Si4 are in agreement to within 0.1 eV with results from recent photoelectron spectroscopic measurements

  7. Ligand binding by antibody IgE Lb4: assessment of binding site preferences using microcalorimetry, docking, and free energy simulations.

    OpenAIRE

    Sotriffer, C A; Flader, W; Cooper, A.; Rode, B M; Linthicum, D S; Liedl, K. R.; Varga, J M

    1999-01-01

    Antibody IgE Lb4 interacts favorably with a large number of different compounds. To improve the current understanding of the structural basis of this vast cross-reactivity, the binding of three dinitrophenyl (DNP) amino acids (DNP-alanine, DNP-glycine, and DNP-serine) is investigated in detail by means of docking and molecular dynamics free energy simulations. Experimental binding energies obtained by isothermal titration microcalorimetry are used to judge the results of the computational stu...

  8. Exciton size and binding energy limitations in one-dimensional organic materials

    Energy Technology Data Exchange (ETDEWEB)

    Kraner, S., E-mail: stefan.kraner@iapp.de; Koerner, C.; Leo, K. [Institut für Angewandte Photophysik, Technische Universität Dresden, Dresden (Germany); Scholz, R. [Institut für Angewandte Photophysik, Technische Universität Dresden, Dresden (Germany); Dresden Center of Computational Materials Science, Technische Universität Dresden, D-01062 Dresden (Germany); Plasser, F. [Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna (Austria)

    2015-12-28

    In current organic photovoltaic devices, the loss in energy caused by the charge transfer step necessary for exciton dissociation leads to a low open circuit voltage, being one of the main reasons for rather low power conversion efficiencies. A possible approach to avoid these losses is to tune the exciton binding energy to a value of the order of thermal energy, which would lead to free charges upon absorption of a photon, and therefore increase the power conversion efficiency towards the Shockley-Queisser limit. We determine the size of the excitons for different organic molecules and polymers by time dependent density functional theory calculations. For optically relevant transitions, the exciton size saturates around 0.7 nm for one-dimensional molecules with a size longer than about 4 nm. For the ladder-type polymer poly(benzimidazobenzophenanthroline), we obtain an exciton binding energy of about 0.3 eV, serving as a lower limit of the exciton binding energy for the organic materials investigated. Furthermore, we show that charge transfer transitions increase the exciton size and thus identify possible routes towards a further decrease of the exciton binding energy.

  9. Distribution of binding energies of a water molecule in the water liquid-vapor interface

    Energy Technology Data Exchange (ETDEWEB)

    Chempath, Shaji [Los Alamos National Laboratory; Pratt, Lawrence R [TULANE UNIV

    2008-01-01

    Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.

  10. Exciton size and binding energy limitations in one-dimensional organic materials

    International Nuclear Information System (INIS)

    In current organic photovoltaic devices, the loss in energy caused by the charge transfer step necessary for exciton dissociation leads to a low open circuit voltage, being one of the main reasons for rather low power conversion efficiencies. A possible approach to avoid these losses is to tune the exciton binding energy to a value of the order of thermal energy, which would lead to free charges upon absorption of a photon, and therefore increase the power conversion efficiency towards the Shockley-Queisser limit. We determine the size of the excitons for different organic molecules and polymers by time dependent density functional theory calculations. For optically relevant transitions, the exciton size saturates around 0.7 nm for one-dimensional molecules with a size longer than about 4 nm. For the ladder-type polymer poly(benzimidazobenzophenanthroline), we obtain an exciton binding energy of about 0.3 eV, serving as a lower limit of the exciton binding energy for the organic materials investigated. Furthermore, we show that charge transfer transitions increase the exciton size and thus identify possible routes towards a further decrease of the exciton binding energy

  11. Improved ligand binding energies derived from molecular dynamics: replicate sampling enhances the search of conformational space.

    Science.gov (United States)

    Adler, Marc; Beroza, Paul

    2013-08-26

    Does a single molecular trajectory provide an adequate sample conformational space? Our calculations indicate that for Molecular Mechanics--Poisson-Boltzmann Surface Area (MM-PBSA) measurement of protein ligand binding, a single molecular dynamics trajectory does not provide a representative sampling of phase space. For a single trajectory, the binding energy obtained by averaging over a number of molecular dynamics frames in an equilibrated system will converge after an adequate simulation time. A separate trajectory with nearly identical starting coordinates (1% randomly perturbed by 0.001 Å), however, can lead to a significantly different calculated binding energy. Thus, even though the calculated energy converges for a single molecular dynamics run, the variation across separate runs implies that a single run inadequately samples the system. The divergence in the trajectories is reflected in the individual energy components, such as the van der Waals and the electrostatics terms. These results indicate that the trajectories sample different conformations that are not in rapid exchange. Extending the length of the dynamics simulation does not resolve the energy differences observed between different trajectories. By averaging over multiple simulations, each with a nearly equivalent starting structure, we find the standard deviation in the calculated binding energy to be ∼1.3 kcal/mol. The work presented here indicates that combining MM-PBSA with multiple samples of the initial starting coordinates will produce more precise and accurate estimates of protein/ligand affinity. PMID:23845109

  12. Variations in the structures and binding energies of binary complexes with HBO

    Science.gov (United States)

    Del Bene, Janet E.; Alkorta, Ibon; Sanchez-Sanz, Goar; Elguero, José

    2012-06-01

    Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures and binding energies of binary complexes formed by HBO with a series of small molecules A. Three different types of structures have been identified, which depend on the nature of A. In one structure A:HBO, HBO acts as a weak proton donor. In the second HBO:A, HBO is a relatively strong base. The third type of complex A||HBO has HBO and A in an approximately parallel arrangement. The dipole moment of A influences both the type of complex formed and its binding energy.

  13. Binding energy of a bound polaron in a quantum well wire

    International Nuclear Information System (INIS)

    Theoretical study of the binding energies of an off-center donor hydrogenic impurity in a cylindrical quantum well wires semiconductor is presented. Calculations are performed in the framework of the effective mass approximation using the variational approach. We describe the effect of the quantum confinement by an infinitely deep potential well and we take into consideration the interaction between the charge carrier (electron and ion) and the optical phonons (confined longitudinal optical and surface optical). Our results show that the impunity binding energy depends strongly on the spatial confinement, the impurity position and the polaronic corrections. (author)

  14. Calculations of binding energies and masses of heavy quarkonia using renormalon cancellation

    CERN Document Server

    Contreras, C S; Gaete, P

    2003-01-01

    We use various methods of Borel integration to calculate the binding ground energies and masses of b-bbar and t-tbar quarkonia. The methods take into account the leading infrared renormalon structure of the hard+soft part of the binding energies E(s), and of the corresponding quark pole masses m_q, where the contributions of these singularities in M(s) = 2 m_q + E(s) cancel. Beforehand, we carry out the separation of the binding energy into its hard+soft and ultrasoft parts. The resummation formalisms are applied to expansions of m_q and E(s) in terms of quantities which do not involve renormalon ambiguity, such as MSbar quark mass, and alpha_s. The renormalization scales are different in calculations of m_q, E(s) and E(us). The MSbar mass of b quark is extracted, and the binding energies of t-tbar and the peak (resonance) energies for (t+tbar) production are obtained.

  15. Free-energy-based methods for binding profile determination in a congeneric series of CDK2 inhibitors.

    Science.gov (United States)

    Fidelak, Jérémy; Juraszek, Jarek; Branduardi, Davide; Bianciotto, Marc; Gervasio, Francesco Luigi

    2010-07-29

    Free-energy pathway methods show great promise in computing the mode of action and the free energy profile associated with the binding of small molecules with proteins, but are generally very computationally demanding. Here we apply a novel approach based on metadynamics and path collective variables. We show that this combination is able to find an optimal reaction coordinate and the free energy profile of binding with explicit solvent and full flexibility, while minimizing human intervention and computational costs. We apply it to predict the binding affinity of a congeneric series of 5 CDK2 inhibitors. The predicted binding free energy profiles are in accordance with experiment. PMID:20593892

  16. Microsolvation effects on the electron binding energies of halide anions

    Science.gov (United States)

    Dolgounitcheva, O.; Zakrzewski, V. G.; Streit, L.; Ortiz, J. V.

    2014-02-01

    Ab initio electron propagator calculations in the partial third order (P3) and P3+ approximations were performed to obtain vertical electron detachment energies (VEDEs) of fluoride and chloride clusters with one through three molecules of water. Larger clusters of F- and Cl- with six water molecules were also treated with and without the polarisable continuum model (PCM). For the smaller clusters, good agreement between calculated VEDEs and peak positions in photoelectron spectra is achieved. Large shifts in VEDEs are observed for both hexameric fluoride-water and chloride-water complexes when the PCM is applied. Significant changes in coordination geometries about the chloride anion also occur in this model. In all fluoride complexes, Dyson orbitals for the lowest VEDEs are delocalised over oxygen atoms. On the contrary, for the case of chloride-water clusters, the Dyson orbitals corresponding to the lowest VEDEs are localised on the anion.

  17. Estimating binding free energy of a putative growth factors EGF-VEGF complex - a computational bioanalytical study.

    Science.gov (United States)

    Lin, Meng-Han; Chang, C Allen; Fischer, Wolfgang B

    2016-08-01

    Epidermal growth factor (EGF) and homodimeric vascular endothelial growth factor (VEGF) bind to cell surface receptors. They are responsible for cell growth and angiogenesis, respectively. Docking of the individual proteins as monomeric units using ZDOCK 2.3.2 reveals a partial blocking of the receptor binding site of VEGF by EGF. The receptor binding site of EGF is not affected by VEGF. The calculated binding energy is found to be intermediate between the binding energies calculated for Alzheimer's Aß42 and the barnase/barstar complex. PMID:26338536

  18. Elucidating the Energetics of Entropically Driven Protein–Ligand Association: Calculations of Absolute Binding Free Energy and Entropy

    Science.gov (United States)

    Deng, Nan-jie; Zhang, Peng; Cieplak, Piotr; Lai, Luhua

    2014-01-01

    The binding of proteins and ligands is generally associated with the loss of translational, rotational, and conformational entropy. In many cases, however, the net entropy change due to binding is positive. To develop a deeper understanding of the energetics of entropically driven protein–ligand binding, we calculated the absolute binding free energies and binding entropies for two HIV-1 protease inhibitors Nelfinavir and Amprenavir using the double-decoupling method with molecular dynamics simulations in explicit solvent. For both ligands, the calculated absolute binding free energies are in general agreement with experiments. The statistical error in the computed ΔG(bind) due to convergence problem is estimated to be ≥2 kcal/mol. The decomposition of free energies indicates that, although the binding of Nelfinavir is driven by nonpolar interaction, Amprenavir binding benefits from both nonpolar and electrostatic interactions. The calculated absolute binding entropies show that (1) Nelfinavir binding is driven by large entropy change and (2) the entropy of Amprenavir binding is much less favorable compared with that of Nelfinavir. Both results are consistent with experiments. To obtain qualitative insights into the entropic effects, we decomposed the absolute binding entropy into different contributions based on the temperature dependence of free energies along different legs of the thermodynamic pathway. The results suggest that the favorable entropic contribution to binding is dominated by the ligand desolvation entropy. The entropy gain due to solvent release from binding site appears to be more than offset by the reduction of rotational and vibrational entropies upon binding. PMID:21899337

  19. Elucidating the energetics of entropically driven protein-ligand association: calculations of absolute binding free energy and entropy.

    Science.gov (United States)

    Deng, Nan-jie; Zhang, Peng; Cieplak, Piotr; Lai, Luhua

    2011-10-20

    The binding of proteins and ligands is generally associated with the loss of translational, rotational, and conformational entropy. In many cases, however, the net entropy change due to binding is positive. To develop a deeper understanding of the energetics of entropically driven protein-ligand binding, we calculated the absolute binding free energies and binding entropies for two HIV-1 protease inhibitors Nelfinavir and Amprenavir using the double-decoupling method with molecular dynamics simulations in explicit solvent. For both ligands, the calculated absolute binding free energies are in general agreement with experiments. The statistical error in the computed ΔG(bind) due to convergence problem is estimated to be ≥2 kcal/mol. The decomposition of free energies indicates that, although the binding of Nelfinavir is driven by nonpolar interaction, Amprenavir binding benefits from both nonpolar and electrostatic interactions. The calculated absolute binding entropies show that (1) Nelfinavir binding is driven by large entropy change and (2) the entropy of Amprenavir binding is much less favorable compared with that of Nelfinavir. Both results are consistent with experiments. To obtain qualitative insights into the entropic effects, we decomposed the absolute binding entropy into different contributions based on the temperature dependence of free energies along different legs of the thermodynamic pathway. The results suggest that the favorable entropic contribution to binding is dominated by the ligand desolvation entropy. The entropy gain due to solvent release from binding site appears to be more than offset by the reduction of rotational and vibrational entropies upon binding. PMID:21899337

  20. Alignment of RNA molecules: Binding energy and statistical properties of random sequences

    Energy Technology Data Exchange (ETDEWEB)

    Valba, O. V., E-mail: valbaolga@gmail.com [Moscow Institute of Physics and Technology (State University) (Russian Federation); Nechaev, S. K., E-mail: sergei.nechaev@gmail.com [Universite Paris Sud, LPTMS (France); Tamm, M. V., E-mail: thumm.m@gmail.com [Moscow State University (Russian Federation)

    2012-02-15

    A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energy between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.

  1. Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain.

    Science.gov (United States)

    Anisimov, Victor M; Cavasotto, Claudio N

    2011-07-30

    The accurate and efficient calculation of binding free energies is essential in computational biophysics. We present a linear-scaling quantum mechanical (QM)-based end-point method termed MM/QM-COSMO to calculate binding free energies in biomolecular systems, with an improved description of entropic changes. Molecular dynamics trajectories are re-evaluated using a semiempirical Hamiltonian and a continuum solvent model; translational and rotational entropies are calculated using configurational integrals, and internal entropy is calculated using the harmonic oscillator approximation. As an application, we studied the binding of a series of phosphotyrosine tetrapeptides to the human Lck SH2 domain, a key component in intracellular signal transduction, modulation of which can have therapeutic relevance in the treatment of cancer, osteoporosis, and autoimmune diseases. Calculations with molecular mechanics Poisson-Boltzmann, and generalized Born surface area methods showed large discrepancies with experimental data stemming from the enthalpic component, in agreement with an earlier report. The empirical force field-based solvent interaction energy scoring function yielded improved results, with average unsigned error of 3.6 kcal/mol, and a better ligand ranking. The MM/QM-COSMO method exhibited the best agreement both for absolute (average unsigned error = 0.7 kcal/mol) and relative binding free energy calculations. These results show the feasibility and promise of a full QM-based end-point method with an adequate balance of accuracy and computational efficiency. PMID:21484840

  2. PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity.

    Science.gov (United States)

    Liu, Xiao; Liu, Jinfeng; Zhu, Tong; Zhang, Lujia; He, Xiao; Zhang, John Z H

    2016-05-23

    Improving the accuracy of scoring functions for estimating protein-ligand binding affinity is of significant interest as well as practical utility in drug discovery. In this work, PBSA_E, a new free energy estimator based on the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) descriptors, has been developed. This free energy estimator was optimized using high-quality experimental data from a training set consisting of 145 protein-ligand complexes. The method was validated on two separate test sets containing 121 and 130 complexes. Comparison of the binding affinities predicted using the present method with those obtained using three popular scoring functions, i.e., GlideXP, GlideSP, and SYBYL_F, demonstrated that the PBSA_E method is more accurate. This new energy estimator requires a MM/PBSA calculation of the protein-ligand binding energy for a single complex configuration, which is typically obtained by optimizing the crystal structure. The present study shows that PBSA_E has the potential to become a robust tool for more reliable estimation of protein-ligand binding affinity in structure-based drug design. PMID:27088302

  3. Photon Binding Energy during Self-trapping and filaments' Self-Organisation

    Science.gov (United States)

    Dantu, Subbarao; Uma, R.; Goyal, Sanjeev

    2000-10-01

    Self-trapping profiles of laser beams in one space dimension and in cylindrical geometry are obtained for saturating-type nonlinearities computationally. The relavant nonlinear Shrodinger equations are solved adjusting for the nonlinear wavenumber shifts till self-trapping is achieved.Note that in one space dimension case the self-trapping condition is the same as for soliton formation. The modelling of the self-trapped beams is done using an approximate gaussian ansatz. Self-consistency then demands that the refractive index profile be approximated by a suitable parabolic profile in space corresponding to two nearby turning points being present simultaneously. The estimation of the location of the turning points is accomplished by using the scheme of approximation on the refractive index in momentum space as suggested by Subbarao et.al.(Phys.Plasmas vol.5, pp.3440-3450 (1998)). This scheme automatically also suggests the method to estimate the per photon binding energy in the self-trapped beam that indicates the strength of self-trapping.The photon binding energy vs. the laser beam intensity is the required photon binding energy curve.Being so similar to the nuclear binding energy curve in shape, it also goes on to suggest how to accomplish more stable self-trapped structures by the fusion or fission of self-trapped filaments thereby giving rise to a new form of self-organisation.

  4. Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin.

    Science.gov (United States)

    Koonammackal, Mathew Varghese; Nellipparambil, Unnikrishnan Viswambharan Nair; Sudarsanakumar, Chellappanpillai

    2011-11-01

    Curcumin is a natural phytochemical that exhibits a wide range of pharmacological properties, including antitumor and anticancer activities. The similarity in the shape of curcumin to DNA minor groove binding drugs is the motivation for exploring its binding affinity in the minor grooves of DNA sequences. Interactions of curcumin with DNA have not been extensively examined, while its pharmacological activities have been studied and documented in depth. Curcumin was docked with two DNA duplexes, d(GTATATAC)(2) and d(CGCGATATCGCG)(2), and molecular dynamics simulations of the complexes were performed in explicit solvent to determine the stability of the binding. In all systems, the curcumin is positioned in the minor groove in the A·T region, and was stably bound throughout the simulation, causing only minor modifications to the structural parameters of DNA. Water molecules were found to contribute to the stability of the binding of the ligand. Free energy analyses of the complexes were performed with MM-PBSA, and the binding affinities that were calculated are comparable to the values reported for other similar nucleic acid-ligand systems, indicating that curcumin is a suitable natural molecule for the development of minor groove binding drugs. PMID:21287216

  5. Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors.

    Science.gov (United States)

    Wright, David W; Hall, Benjamin A; Kenway, Owain A; Jha, Shantenu; Coveney, Peter V

    2014-03-11

    The use of molecular simulation to estimate the strength of macromolecular binding free energies is becoming increasingly widespread, with goals ranging from lead optimization and enrichment in drug discovery to personalizing or stratifying treatment regimes. In order to realize the potential of such approaches to predict new results, not merely to explain previous experimental findings, it is necessary that the methods used are reliable and accurate, and that their limitations are thoroughly understood. However, the computational cost of atomistic simulation techniques such as molecular dynamics (MD) has meant that until recently little work has focused on validating and verifying the available free energy methodologies, with the consequence that many of the results published in the literature are not reproducible. Here, we present a detailed analysis of two of the most popular approximate methods for calculating binding free energies from molecular simulations, molecular mechanics Poisson-Boltzmann surface area (MMPBSA) and molecular mechanics generalized Born surface area (MMGBSA), applied to the nine FDA-approved HIV-1 protease inhibitors. Our results show that the values obtained from replica simulations of the same protease-drug complex, differing only in initially assigned atom velocities, can vary by as much as 10 kcal mol(-1), which is greater than the difference between the best and worst binding inhibitors under investigation. Despite this, analysis of ensembles of simulations producing 50 trajectories of 4 ns duration leads to well converged free energy estimates. For seven inhibitors, we find that with correctly converged normal mode estimates of the configurational entropy, we can correctly distinguish inhibitors in agreement with experimental data for both the MMPBSA and MMGBSA methods and thus have the ability to rank the efficacy of binding of this selection of drugs to the protease (no account is made for free energy penalties associated with

  6. SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations

    OpenAIRE

    Marharyta Petukh; Luogeng Dai; Emil Alexov

    2016-01-01

    Predicting the effect of amino acid substitutions on protein–protein affinity (typically evaluated via the change of protein binding free energy) is important for both understanding the disease-causing mechanism of missense mutations and guiding protein engineering. In addition, researchers are also interested in understanding which energy components are mostly affected by the mutation and how the mutation affects the overall structure of the corresponding protein. Here we report a webserver,...

  7. Determination of the Exciton Binding Energy Using Photothermal and Photoluminescence Spectroscopy

    Science.gov (United States)

    Strzałkowski, K.; Zakrzewski, J.; Maliński, M.

    2013-04-01

    In this paper, experimental photoluminescence (PL) and piezoelectric photothermal (PPT) spectra of selected II-VI binary crystals are presented and analyzed. The quantitative analysis of the photothermal spectra was performed using a modified and extended Jackson-Amer model. The values of the bandgap energies of investigated semiconductors were computed from the PT amplitude and phase spectra. From the temperature dependence of the exciton emission so-called "excitonic energy gaps" have been determined. It follows from the theory that the exciton binding energy is the difference of these two values of energy gaps derived from PPT and PL spectroscopy.

  8. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy

    Science.gov (United States)

    Duan, Li L.; Feng, Guo Q.; Zhang, Qing G.

    2016-01-01

    Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding. PMID:27507430

  9. Structure parameters and external electric field effects on exciton binding energies of CdTe/ZnTe quantum dots

    International Nuclear Information System (INIS)

    We study the effects of the structure parameters of self-assembled CdTe/ZnTe quantum dots (QDs) under an electric field on the exciton binding energies due to Coulomb interaction between electrons and holes with a finite-element method based on the linear elasticity theory of solids and the eight-band k ·p Hamiltonian. The exciton binding energy is shown to decrease with increasing base width of the QD, regardless of its height. We point out that the monotonic decrease in the exciton binding energy is due to the confinement of the electron and the hole wavefunctions inside the QD. The exciton binding energy is also found to decrease as the wetting layer thickness increases, which can be attributed to the dipole-like wavefunction of the hole. The fact that the electron and the hole energies decrease parabolically and the exciton binding energy decreases with increasing electric field due to the Stark effect is demonstrated.

  10. Reveal of small alkanes and isomers using calculated core and valence binding energy spectra and total momentum cross sections

    OpenAIRE

    Yang, Zejin; Wang, Feng

    2013-01-01

    The present study revealed quantum mechanically that the C1s binding energy spectra of the small alkanes (upto six carbons) provide a clear picture of isomeric chemical shift in linear alkanes and branched isomers, whereas the valence binding energy spectra contain more sensitive information regarding the length of the carbon chains. Total momentum cross sections of the alkanes exhibit the information of the chain length as well as constitutional isomers of the small alkanes. The C1s binding ...

  11. Development of computational methods for the prediction of protein structure, protein binding, and mutational effects using free energy calculations.

    OpenAIRE

    Becker, Caroline

    2014-01-01

    A molecular understanding of protein-protein or protein-ligand binding is of crucial importance for the design of proteins or ligands with defined binding characteristics. The comprehensive analysis of biomolecular binding and the coupled rational in silico design of protein-ligand interfaces requires both, accurate and computationally fast methods for the prediction of free energies. Accurate free energy methods usually involve atomistic molecular dynamics simulations that are computationall...

  12. Free Energy Simulations of a GTPase: GTP and GDP Binding to Archaeal Initiation Factor 2

    OpenAIRE

    Satpati, Priyadarshi; Clavaguéra, Carine; Ohanessian, Gilles; Simonson, Thomas

    2011-01-01

    Archaeal initiation factor 2 (aIF2) is a protein involved in the initiation of protein biosynthesis. In its GTP-bound, “ON” conformation, aIF2 binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, “OFF” conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP and its dependence on the ON or OFF conformational state of aIF2, molecular dynamics free energy simulations (MDFE) are a tool of choice. However, the validity of the computed free ene...

  13. Nuclear binding energies: Global collective structure and local shell-model correlations

    International Nuclear Information System (INIS)

    Nuclear binding energies and two-neutron separation energies are analysed starting from the liquid-drop model and the nuclear shell model in order to describe the global trends of the above observables. We subsequently concentrate on the Interacting Boson Model (IBM) and discuss a new method in order to provide a consistent description of both, ground-state and excited-state properties. We address the artefacts that appear when crossing mid-shell using the IBM formulation and perform detailed numerical calculations for nuclei situated in the 50-82 shell. We also concentrate on local deviations from the above global trends in binding energy and two-neutron separation energies that appear in the neutron-deficient Pb region. We address possible effects on the binding energy, caused by mixing of low-lying 0+ intruder states into the ground state, using configuration mixing in the IBM framework. We also study ground-state properties using a macroscopic-microscopic model. Detailed comparisons with recent experimental data in the Pb region are amply discussed

  14. Free energy calculations to estimate ligand-binding affinities in structure-based drug design.

    Science.gov (United States)

    Reddy, M Rami; Reddy, C Ravikumar; Rathore, R S; Erion, Mark D; Aparoy, P; Reddy, R Nageswara; Reddanna, P

    2014-01-01

    Post-genomic era has led to the discovery of several new targets posing challenges for structure-based drug design efforts to identify lead compounds. Multiple computational methodologies exist to predict the high ranking hit/lead compounds. Among them, free energy methods provide the most accurate estimate of predicted binding affinity. Pathway-based Free Energy Perturbation (FEP), Thermodynamic Integration (TI) and Slow Growth (SG) as well as less rigorous end-point methods such as Linear interaction energy (LIE), Molecular Mechanics-Poisson Boltzmann./Generalized Born Surface Area (MM-PBSA/GBSA) and λ-dynamics have been applied to a variety of biologically relevant problems. The recent advances in free energy methods and their applications including the prediction of protein-ligand binding affinity for some of the important drug targets have been elaborated. Results using a recently developed Quantum Mechanics (QM)/Molecular Mechanics (MM) based Free Energy Perturbation (FEP) method, which has the potential to provide a very accurate estimation of binding affinities to date has been discussed. A case study for the optimization of inhibitors for the fructose 1,6- bisphosphatase inhibitors has been described. PMID:23947646

  15. Imaging G protein-coupled receptors while quantifying their ligand-binding free-energy landscape.

    Science.gov (United States)

    Alsteens, David; Pfreundschuh, Moritz; Zhang, Cheng; Spoerri, Patrizia M; Coughlin, Shaun R; Kobilka, Brian K; Müller, Daniel J

    2015-09-01

    Imaging native membrane receptors and testing how they interact with ligands is of fundamental interest in the life sciences but has proven remarkably difficult to accomplish. Here, we introduce an approach that uses force-distance curve-based atomic force microscopy to simultaneously image single native G protein-coupled receptors in membranes and quantify their dynamic binding strength to native and synthetic ligands. We measured kinetic and thermodynamic parameters for individual protease-activated receptor-1 (PAR1) molecules in the absence and presence of antagonists, and these measurements enabled us to describe PAR1's ligand-binding free-energy landscape with high accuracy. Our nanoscopic method opens an avenue to directly image and characterize ligand binding of native membrane receptors. PMID:26167642

  16. (n,γ) Reactions in heavy nuclei: Manifestations of nuclear structure at excitation energies up to the neutron binding energy

    International Nuclear Information System (INIS)

    At present, information about the excitation of 40 nuclei from the mass region 114≤A≤200 and about their subsequent decays into given lowly lying levels of those nuclei has been obtained for excitation energies in the region extending up to the neutron binding energy. A comparison of the experimentally observed intensities of such two-photon cascades with the results of calculations based on the statistical theory of gamma decay reveals that, in order to predict the parameters of such processes to a precision comparable to that achievable in modern experiments, it is necessary to take into account the effect of the structure of excited nuclear states up to neutron binding energy

  17. Analytical formulas for carrier density and Fermi energy in semiconductors with a tight-binding band

    International Nuclear Information System (INIS)

    Analytical formulas for evaluating the relation of carrier density and Fermi energy for semiconductors with a tight-binding band have been proposed. The series expansions for a carrier density with fast convergency have been obtained by means of a Bessel function. A simple and analytical formula for Fermi energy has been derived with the help of the Gauss integration method. The results of the proposed formulas are in good agreement with accurate numerical solutions. The formulas have been successfully used in the calculation of carrier density and Fermi energy in a miniband superlattice system. Their accuracy is in the order of 10−5. (paper)

  18. Assessment of Density Functional Methods for Exciton Binding Energies and Related Optoelectronic Properties

    CERN Document Server

    Lee, Jui-Che; Lin, Shiang-Tai

    2015-01-01

    The exciton binding energy, the energy required to dissociate an excited electron-hole pair into free charge carriers, is one of the key factors to the optoelectronic performance of organic materials. However, it remains unclear whether modern quantum-mechanical calculations, mostly based on Kohn-Sham density functional theory (KS-DFT) and time-dependent density functional theory (TDDFT), are reliably accurate for exciton binding energies. In this study, the exciton binding energies and related optoelectronic properties (e.g., the ionization potentials, electron affinities, fundamental gaps, and optical gaps) of 121 small- to medium-sized molecules are calculated using KS-DFT and TDDFT with various density functionals. Our KS-DFT and TDDFT results are compared with those calculated using highly accurate CCSD and EOM-CCSD methods, respectively. The omegaB97, omegaB97X, and omegaB97X-D functionals are shown to generally outperform (with a mean absolute error of 0.36 eV) other functionals for the properties inve...

  19. Calculation of positron binding energies using the generalized any particle propagator theory

    International Nuclear Information System (INIS)

    We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ∼0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach

  20. Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2.

    Science.gov (United States)

    Satpati, Priyadarshi; Clavaguéra, Carine; Ohanessian, Gilles; Simonson, Thomas

    2011-05-26

    Archaeal initiation factor 2 (aIF2) is a protein involved in the initiation of protein biosynthesis. In its GTP-bound, "ON" conformation, aIF2 binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, "OFF" conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP and its dependence on the ON or OFF conformational state of aIF2, molecular dynamics free energy simulations (MDFE) are a tool of choice. However, the validity of the computed free energies depends on the simulation model, including the force field and the boundary conditions, and on the extent of conformational sampling in the simulations. aIF2 and other GTPases present specific difficulties; in particular, the nucleotide ligand coordinates a divalent Mg(2+) ion, which can polarize the electronic distribution of its environment. Thus, a force field with an explicit treatment of electronic polarizability could be necessary, rather than a simpler, fixed charge force field. Here, we begin by comparing a fixed charge force field to quantum chemical calculations and experiment for Mg(2+):phosphate binding in solution, with the force field giving large errors. Next, we consider GTP and GDP bound to aIF2 and we compare two fixed charge force fields to the recent, polarizable, AMOEBA force field, extended here in a simple, approximate manner to include GTP. We focus on a quantity that approximates the free energy to change GTP into GDP. Despite the errors seen for Mg(2+):phosphate binding in solution, we observe a substantial cancellation of errors when we compare the free energy change in the protein to that in solution, or when we compare the protein ON and OFF states. Finally, we have used the fixed charge force field to perform MDFE simulations and alchemically transform GTP into GDP in the protein and in solution. With a total of about 200 ns of molecular dynamics, we obtain good convergence and a reasonable statistical uncertainty, comparable to the force

  1. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

    Science.gov (United States)

    Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

    2016-06-30

    In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27117350

  2. Binding energy of excitons formed from spatially separated electrons and holes in insulating quantum dots

    International Nuclear Information System (INIS)

    It is found that the binding energy of the ground state of an exciton formed from an electron and a hole spatially separated from each other (the hole is moving within a quantum dot, and the electron is localized above the spherical (quantum dot)–(insulating matrix) interface) in a nanosystem containing insulating Al2O3 quantum dots is substantially increased (by nearly two orders of magnitude) compared to the exciton binding energy in an Al2O3 single crystal. It is established that, in the band gap of an Al2O3 nanoparticle, a band of exciton states (formed from spatially separated electrons and holes) appears. It is shown that there exists the possibility of experimentally detecting the ground and excited exciton states in the band gap of Al2O3 nanoparticles at room temperature from the absorption spectrum of the nanosystem

  3. On the release of binding energy and accretion power in core collapse-like environments

    CERN Document Server

    Socrates, Aristotle

    2008-01-01

    All accretion models of gamma-ray bursts share a common assumption: accretion power and gravitational binding energy is released and then dissipated locally, with the mass of its origin. This is equivalent to the Shakura-Sunyaev 1973 (SS73) prescription for the dissipation of accretion power and subsequent conversion into radiate output. Since their seminal paper, broadband observations of quasars and black hole X-ray binaries insist that the SS73 prescription cannot wholly describe their behavior. In particular, optically thick black hole accretion flows are almost universally accompanied by coronae whose relative power by far exceeds anything seen in studies of stellar chromospheric and coronal activity. In this note, we briefly discuss the possible repercussions of freeing accretion models of GRBs from the SS73 prescription. Our main conclusion is that the efficiency of converting gravitational binding energy into a GRB power can be increased by an order of magnitude or more.

  4. Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles

    OpenAIRE

    Sayyed-Ahmad, Abdallah; Khandelia, Himanshu; Kaznessis, Yiannis N.

    2009-01-01

    We present relative binding free energy calculations for six antimicrobial peptide–micelle systems, three peptides interacting with two types of micelles. The peptides are the scorpion derived antimicrobial peptide (AMP), IsCT and two of its analogues. The micelles are dodecylphosphatidylcholine (DPC) and sodium dodecylsulphate (SDS) micelles. The interfacial electrostatic properties of DPC and SDS micelles are assumed to be similar to those of zwitterionic mammalian and anionic bacterial mem...

  5. Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

    OpenAIRE

    Wright, David W.; Hall, Benjamin A.; Kenway, Owain A.; Jha, Shantenu; Coveney*, Peter V

    2014-01-01

    The use of molecular simulation to estimate the strength of macromolecular binding free energies is becoming increasingly widespread, with goals ranging from lead optimization and enrichment in drug discovery to personalizing or stratifying treatment regimes. In order to realize the potential of such approaches to predict new results, not merely to explain previous experimental findings, it is necessary that the methods used are reliable and accurate, and that their limitations are thoroughly...

  6. Binding energy of finite nuclei in Jastrow-Factor-Cluster method with applications in helium

    International Nuclear Information System (INIS)

    A general expression for the binding energy of finite nuclei in the Jastrow-Factor-Cluster method is developed upto the three-body cluster term with centre of mass correction. It is applied in mass A = 3 and 4 with the standard Chakkalakal function and the average Pauli condition. Compared to the previous work of Afnan (1969) better saturation properties are obtained for two- and three-body truncation. Convergence is also better. (orig.)

  7. Relationships between ligand binding sites, protein architecture and correlated paths of energy and conformational fluctuations

    International Nuclear Information System (INIS)

    The statistical thermodynamics basis of energy and residue position fluctuations is explained for native proteins. The protein and its surroundings are treated as a canonical system with emphasis on the effects of energy exchange between the two. Fluctuations of the energy are related to fluctuations of residue positions, which in turn are related to the connectivity matrix of the protein, thus establishing a connection between energy fluctuation pathways and protein architecture. The model gives the locations of hotspots for ligand binding and identifies the pathways of energy conduction within the protein. Results are discussed in terms of two sets of models, the BPTI and 12 proteins that contain the PDZ domain. A possible use of the model for determining functionally similar domains in a diverse set of proteins is pointed out

  8. Exciton Binding energies and effective masses in Organo-lead Tri-Halide Perovskites

    Science.gov (United States)

    Portugall, Oliver; Miyata, Atsuhiko; Mitioglu, Anatol; Plochocka, Paulina; Wang, Jacob Tse-Wei; Stranks, Samuel; Snaith, Henry; Nicholas, Robin; Lncmi Toulouse Team; Oxford University Team

    2015-03-01

    Solid-state perovskite-based solar cells have made a dramatic impact on emerging PV research with efficiencies of over 17% already achieved. However, to date the basic electronic properties of the perovskites such as the electron and hole effective masses and the exciton binding energy are not well known. We have measured both for methyl ammonium lead tri-iodide using magneto absorption in very high magnetic fields up to 150T showing that the exciton binding energy at low temperatures is only 16 meV, a value three times smaller than previously thought and sufficiently small to completely transform the way in which the devices must operate. Landau level spectroscopy shows that the reduced effective mass of 0.104 me is also smaller than previously thought. In addition by using a fast pulse 150T magnet we measure the band structure change due to the structural phase transition that occurs in this system at around 160K. We also observe Landau levels in the high temperature phase as used for device production, which has a very similar effective mass and the analysis suggests an exciton binding energy which is even smaller than in the low temperature phase.

  9. Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.

    Science.gov (United States)

    Sulea, Traian; Vivcharuk, Victor; Corbeil, Christopher R; Deprez, Christophe; Purisima, Enrico O

    2016-07-25

    Affinity modulation of antibodies and antibody fragments of therapeutic value is often required in order to improve their clinical efficacies. Virtual affinity maturation has the potential to quickly focus on the critical hotspot residues without the combinatorial explosion problem of conventional display and library approaches. However, this requires a binding affinity scoring function that is capable of ranking single-point mutations of a starting antibody. We focus here on assessing the solvated interaction energy (SIE) function that was originally developed for and is widely applied to scoring of protein-ligand binding affinities. To this end, we assembled a structure-function data set called Single-Point Mutant Antibody Binding (SiPMAB) comprising several antibody-antigen systems suitable for this assessment, i.e., based on high-resolution crystal structures for the parent antibodies and coupled with high-quality binding affinity measurements for sets of single-point antibody mutants in each system. Using this data set, we tested the SIE function with several mutation protocols based on the popular methods SCWRL, Rosetta, and FoldX. We found that the SIE function coupled with a protocol limited to sampling only the mutated side chain can reasonably predict relative binding affinities with a Spearman rank-order correlation coefficient of about 0.6, outperforming more aggressive sampling protocols. Importantly, this performance is maintained for each of the seven system-specific component subsets as well as for other relevant subsets including non-alanine and charge-altering mutations. The transferability and enrichment in affinity-improving mutants can be further enhanced using consensus ranking over multiple methods, including the SIE, Talaris, and FOLDEF energy functions. The knowledge gained from this study can lead to successful prospective applications of virtual affinity maturation. PMID:27367467

  10. A nonorthogonal tight-binding total energy model for molecular simulations

    International Nuclear Information System (INIS)

    A nonorthogonal tight-binding (TB) total energy model for molecular simulations has been developed in spirit of extended-Hueckel theory. The semiempirical potential parameters for H, C, O elements are fitted from density functional theory (DFT) calculations. The test calculations on small inorganic molecules, hydrocarbons, fullerenes, and large organic molecules show its reliability and transferability. In particular, the atomization energies and the gaps between highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO gaps) from TB model compare well with DFT results for a variety of molecules. Thus, our TB model can be used in the large scale simulation of molecules and carbon-based materials

  11. Cellulose chain binding free energy drives the processive move of cellulases on the cellulose surface.

    Science.gov (United States)

    Wang, Yefei; Zhang, Shujun; Song, Xiangfei; Yao, Lishan

    2016-09-01

    Processivity is essential for cellulases in their catalysis of cellulose hydrolysis. But what drives the processive move is not well understood. In this work, we use Trichoderma reesei Cel7B as a model system and show that its processivity is directly correlated to the binding free energy difference of a cellulose chain occupying the binding sites -7 to +2 and that occupying sites -7 to -1. Several mutants that have stronger interactions with glycosyl units in sites +1 and +2 than the wild type enzyme show higher processivity. The results suggest that after the release of the product cellobiose located in sites +1 and +2, the enzyme pulls the cellulose chain to fill the vacant sites, which propels its processive move on the cellulose surface. Biotechnol. Bioeng. 2016;113: 1873-1880. © 2016 Wiley Periodicals, Inc. PMID:26928155

  12. Precision measurements of high-energy conversion electron lines and determination of neutron binding energies

    International Nuclear Information System (INIS)

    The paper first discusses the energy accuracy of the BILL conversion electron spectrometer at the Grenoble high flux reactor. With an improved temperature stabilisation of the magnets, an energy accuracy of ΔE/E -5 can be reached. After this, highly exact measurements of high-energy conversion electron lines of the 200Hg, 114Cd, 165Dy, 168Er, 239U nuclei and the 13C, 28Al 3H and 92Zr photoelectron lines were carried out. Energy calibration of the spectrometer was carried out in the 1.5 MeV to 6.5 MeV range with intensive high-energy transitions of the 200Hg nucleus. Systematic calibration errors could be investigated by means of combinations between the calibration lines. A calibration for absolute energies was obtained by comparing low-energy gamma transitions of 200Hg with the 411.8 keV gold standard. (orig.)

  13. The Successive OH Binding Energies of Sc(OH)n+ for n=1-3

    Science.gov (United States)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Arnold, James O. (Technical Monitor)

    1996-01-01

    The geometries of Sc(OH)n+, for n = 1-3, have been optimized using density functional theory, in conjunction with the B3LYP hybrid functional. The zero-point energies are computed at the same level of theory. The successive OH bond energies have been computed at the CCSD(T) level for ScOH+ and Sc(OH)2+. The computed result for ScOD+ is in excellent agreement with the recent experiment of Armentrout and co-workers. There is a dramatic drop for the third OH, because Sc+ has only two valence electrons and therefore the bonding changes when the third OH is added. The difference between the B3LYP and CCSD(T) OH binding energies for the first two OH groups is discussed.

  14. Constraining the gravitational binding energy of PSR J0737-3039B using terrestrial nuclear data

    International Nuclear Information System (INIS)

    We show that the gravitational binding energy of a neutron star of a given mass is correlated with the slope of the nuclear symmetry energy at 1-2 times nuclear saturation density for equations of state without significant softening (i.e., those that predict maximum masses Mmax>1.44M· in line with the largest accurately measured neutron star mass). Applying recent laboratory constraints on the slope of the symmetry energy to this correlation we extract a constraint on the baryon mass of the lower mass member of the double pulsar binary system, PSR J0737-3039B. We compare with independent constraints derived from modeling the progenitor star of J0737-3039B up to and through its collapse under the assumption that it formed in an electron capture supernova. The two sets of constraints are consistent only if L < or approx. 70 MeV.

  15. Resonance energy transfer study on the proximity relationship between the GTP binding site and the rifampicin binding site of Escherichia coli RNA polymerase

    International Nuclear Information System (INIS)

    Terbium(III) upon complexation with guanosine 5'-triphosphate showed remarkable enhancement of fluorescence emission at 488 and 545 nm when excited at 295 nm. Analysis of the binding data yielded a value for the mean Kd between Tb(III) and GTP of 0.2 μM, with three binding sites for TB(III) on GTP. 31P and 1H NMR measurements revealed that Tb(III) mainly binds the phosphate moiety of GTP. Fluorescence titration of the emission signals of the TbGTP complex with varying concentrations of Escherichia coli RNA polymerase resulted in a Kd values of 4 μM between the TbGTP and the enzyme. It was observed that TbGTP can be incorporated in the place of GTP during E. coli RNA polymerase catalyzed abortive synthesis of dinucleotide tetraphosphate at T7A2 promoter. Both the substrate TbGTP and the inhibitor of the initiation of transcription rifampicin bind to the β-subunit of E. coli RNA polymerase. This allows the measurement of the fluorescence excited-state energy transfer from the donor TbGTP-RNA polymerase to the acceptor rifampicin. Both emission bands of Tb(III) overlap with the rifampicin absorption, and the distances at 50% efficiency of energy transfer were calculated to be 28 and 24 angstrom for the 488- and 545-nm emission bands, respectively. The distance between the substrate binding site and the rifampicin binding site on the β-subunit of E. coli RNA polymerase was measured to be around 30 angstrom. This suggest that the nature of inhibition of transcription by rifampicin is essentially noncompetitive with the substrate

  16. Addendum: Triton and hypertriton binding energies calculated from SU_6 quark-model baryon-baryon interactions

    CERN Document Server

    Fujiwara, Y; Kohno, M; Miyagawa, K

    2007-01-01

    Previously we calculated the binding energies of the triton and hypertriton, using an SU_6 quark-model interaction derived from a resonating-group method of two baryon clusters. In contrast to the previous calculations employing the energy-dependent interaction kernel, we present new results using a renormalized interaction, which is now energy independent and reserves all the two-baryon data. The new binding energies are slightly smaller than the previous values. In particular the triton binding energy turns out to be 8.14 MeV with a charge-dependence correction of the two-nucleon force, 190 keV, being included. This indicates that about 350 keV is left for the energy which is to be accounted for by three-body forces.

  17. Anisotropic Lithium Insertion Behavior in Silicon Nanowires: Binding Energy, Diffusion Barrier, and Strain Effect

    KAUST Repository

    Zhang, Qianfan

    2011-05-19

    Silicon nanowires (SiNWs) have recently been shown to be promising as high capacity lithium battery anodes. SiNWs can be grown with their long axis along several different crystallographic directions. Due to distinct atomic configuration and electronic structure of SiNWs with different axial orientations, their lithium insertion behavior could be different. This paper focuses on the characteristics of single Li defects, including binding energy, diffusion barriers, and dependence on uniaxial strain in [110], [100], [111], and [112] SiNWs. Our systematic ab initio study suggests that the Si-Li interaction is weaker when the Si-Li bond direction is aligned close to the SiNW long axis. This results in the [110] and [111] SiNWs having the highest and lowest Li binding energy, respectively, and it makes the diffusion barrier along the SiNW axis lower than other pathways. Under external strain, it was found that [110] and [001] SiNWs are the most and least sensitive, respectively. For diffusion along the axial direction, the barrier increases (decreases) under tension (compression). This feature results in a considerable difference in the magnitude of the energy barrier along different diffusion pathways. © 2011 American Chemical Society.

  18. The binding energy of soliton molecules in dispersion-managed optical fibers

    International Nuclear Information System (INIS)

    Solitons in dispersion managed optical fibers can form stable bound states known as soliton molecules. In this work, a mathematical model based on the variational approximation has been proposed, which describes the propagation of soliton molecules in optical fibers. Analytic results are compared with numerical simulation of the nonlinear Schrodinger equation, and qualitative agreement between them is demonstrated. The advantage of the proposed model consists in the possibility to estimate the binding energy of solitons in the molecule and interpretation of the decay of a molecule into separate solitons. The results can be useful in the design of communication systems where optical solitons are employed as carriers of information. (authors)

  19. Accurate core-electron binding energy shifts from density functional theory

    International Nuclear Information System (INIS)

    Current review covers description of density functional methods of calculation of accurate core-electron binding energy (CEBE) of second and third row atoms; applications of calculated CEBEs and CEBE shifts (ΔCEBEs) in elucidation of topics such as: hydrogen-bonding, peptide bond, polymers, DNA bases, Hammett substituent (σ) constants, inductive and resonance effects, quantitative structure activity relationship (QSAR), and solid state effect (WD). This review limits itself to works of mainly Chong and his coworkers for the period post-2002. It is not a fully comprehensive account of the current state of the art.

  20. Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study

    OpenAIRE

    Honarparvar, Bahareh; Pawar, Sachin A; Alves, Cláudio Nahum; Lameira, Jerônimo; Maguire, Glenn EM; José Rogério A. Silva; Govender, Thavendran; Kruger, Hendrik G.

    2015-01-01

    Background Novel pentacycloundecane (PCU)-lactone-CO-EAIS peptide inhibitors were designed, synthesized, and evaluated against wild-type C-South African (C-SA) HIV-1 protease. Three compounds are reported herein, two of which displayed IC50 values of less than 1.00 μM. A comparative MM-PB(GB)SA binding free energy of solvation values of PCU-lactam and lactone models and their enantiomers as well as the PCU-lactam-NH-EAIS and lactone-CO-EAIS peptide inhibitors and their corresponding diastereo...

  1. Accurate core-electron binding energy shifts from density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Takahata, Yuji, E-mail: taka@iqm.unicamp.b [Amazonas State University, School of Engineering, Av. Darcy Vargas, 1200, Parque 10 - CEP 69065-020, Manaus, Amazonas (Brazil); Department of Chemistry, University of Campinas-UNICAMP, Campinas 13084-862, Sao Paulo (Brazil); Marques, Alberto Dos Santos [Amazonas State University, School of Engineering, Av. Darcy Vargas, 1200, Parque 10 - CEP 69065-020, Manaus, Amazonas (Brazil)

    2010-05-15

    Current review covers description of density functional methods of calculation of accurate core-electron binding energy (CEBE) of second and third row atoms; applications of calculated CEBEs and CEBE shifts (DELTACEBEs) in elucidation of topics such as: hydrogen-bonding, peptide bond, polymers, DNA bases, Hammett substituent (sigma) constants, inductive and resonance effects, quantitative structure activity relationship (QSAR), and solid state effect (WD). This review limits itself to works of mainly Chong and his coworkers for the period post-2002. It is not a fully comprehensive account of the current state of the art.

  2. Folding model analysis of Λ binding energies and three-body ΛNN force

    International Nuclear Information System (INIS)

    Working within the framework of the folding model, we analyze the Λ binding energy data of light hypernuclei with effective two-body ΛN plus three-body ΛNN interaction. The two-body density for the core nucleus required for evaluating the three-body force contribution is obtained in terms of the centre of mass pair correlation. It is found that except for Λ5He the data are fairly well explained. The three-body force seems to account for the density dependence of the effective two-body ΛN interaction proposed earlier. (author). 13 refs, 2 tabs

  3. Evolution of Structure in Nuclei: Meditation by Sub-Shell Modifications and Relation to Binding Energies

    Science.gov (United States)

    Casten, R. F.; Cakirli, R. B.

    2009-03-01

    Understanding the development of configuration mixing, coherence, collectivity, and deformation in nuclei is one of the crucial challenges in nuclear structure physics, and one which has become all the more important with the advent of next generation facilities for the study of exotic nuclei. We will discuss recent work on phase/shape transitional behavior in nuclei, and the role of changes in sub-shell structure in mediating such transitional regions. We will also discuss a newly found, much deeper, link between nuclear structure and nuclear binding energies.

  4. Evolution of Structure in Nuclei: Meditation by Sub-Shell Modifications and Relation to Binding Energies

    International Nuclear Information System (INIS)

    Understanding the development of configuration mixing, coherence, collectivity, and deformation in nuclei is one of the crucial challenges in nuclear structure physics, and one which has become all the more important with the advent of next generation facilities for the study of exotic nuclei. We will discuss recent work on phase/shape transitional behavior in nuclei, and the role of changes in sub-shell structure in mediating such transitional regions. We will also discuss a newly found, much deeper, link between nuclear structure and nuclear binding energies. (author)

  5. The formation mechanism and the binding energy of the body-centred regular tetrahedral structure of He+5

    Institute of Scientific and Technical Information of China (English)

    李萍; 熊勇; 芶清泉; 张建平

    2002-01-01

    We propose the formation mechanism of the body-centred regular tetrahedral structure of the He+5 cluster. The total energy curve for this structure has been calculated by using a modified arrangement channel quantum mechanics method. The result shows that a minimal energy of -13.9106 a.u. occurs at a separation of 1.14a0 between the nucleus at the centre and nuclei at the apexes. Therefore we obtain the binding energy of 0.5202 a.u. for this structure. This means that the He+5 cluster may be stable with a high binding energy in a body-centred regular tetrahedral structure.

  6. Using nonfluorescent Förster resonance energy transfer acceptors in protein binding studies.

    Science.gov (United States)

    Ruan, Qiaoqiao; Skinner, Joseph P; Tetin, Sergey Y

    2009-10-15

    The purpose of this article is to highlight the versatility of nonfluorescent Förster resonance energy transfer (FRET) acceptors in determination of protein equilibrium dissociation constants and kinetic rates. Using a nonfluorescent acceptor eliminates the necessity to spectrally isolate the donor fluorescence when performing binding titrations covering a broad range of reagent concentrations. Moreover, random distribution of the donor and acceptor chromophores on the surface of proteins increases the probability of FRET occurring on their interaction. Three high-affinity antibodies are presented in this study as characteristic protein systems. Monoclonal antibody (mAb) 106.3 binds brain natriuretic peptide (BNP)5-13(C10A) and full-length BNP1-32 with the dissociation constants 0.26+/-0.01 and 0.05+/-0.02 nM, respectively, which was confirmed by kinetic measurements. For anti-hCG (human chorionic gonadotropin) mAb 8F11, studied at two incorporation ratios (IRs=1.9 and 3.8) of the nonfluorescent FRET acceptor, K(D) values of 0.04+/-0.02 and 0.059(-0.004)(+0.006) nM, respectively, were obtained. Likewise, the binding of goat anti-hamster immunoglobulin G (IgG) antibody was not affected by conjugation and yielded K(D) values of 1.26+/-0.04, 1.25+/-0.05, and 1.14+/-0.04 nM at IRs of 1.7, 4.7, and 8.1, respectively. We conclude that this FRET-based method offers high sensitivity, practical simplicity, and versatility in protein binding studies. PMID:19563765

  7. Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

    Science.gov (United States)

    Duan, Lili; Liu, Xiao; Zhang, John Z H

    2016-05-01

    Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect. PMID:27058988

  8. On the Binding Energy and the Charge Symmetry Breaking in A<=16 Lambda-hypernuclei

    CERN Document Server

    Botta, E; Feliciello, A

    2016-01-01

    Recent achievements in hypernuclear spectroscopy, in particular the determination of the $\\Lambda$-binding energy B$_{\\Lambda}$ by high precision magnetic spectrometry, contributed to stimulate considerably the search for Charge Symmetry Breaking effects in $\\Lambda$-hypernuclei isomultiplets. We have reorganized the results from the FINUDA experiment and we have produced a list of B$_{\\Lambda}$ values for hypernuclei with A$\\leq$16 considering only the data from magnetic spectrometers with an absolute calibration of the energy scale (FINUDA at DA$\\Phi$NE and electroproduction experiments). By comparing them with the corresponding B$_{\\Lambda}$ from the emulsion experiments, we observe that there is a systematic small difference that is taken into account. A synopsis of all the results on B$_{\\Lambda}$ so far published is finally suggested. Several interesting conclusions are drawn, among which the equality within the errors of B$_{\\Lambda}$ for the A=7, 12, 16 isomultiplets, based only on recent spectrometri...

  9. Odd-even staggerings on nuclear binding energy described by the covariant density functional theory

    CERN Document Server

    Wang, Long Jun; Dong, Jian Min; Long, Wen Hui

    2013-01-01

    The odd-even staggerings (OES) on nuclear binding energies are studied systematically within the covariant density functional (CDF) theories, specifically the relativistic Hartree-Fock-Bogoliubov (RHFB) and the relativistic Hartree-Bogoliubov (RHB) theories. Taking the finite-range Gogny force D1S as an effective pairing interaction, both CDF models can provide appropriate descriptions on the OESs of nuclear binding energies for C, O, Ca, Ni, Zr, Sn, Ce, Gd and Pb isotopes as well as for N=50 and 82 isotones. However, due to the inconsistence between the non-relativistic pairing interaction and the relativistic effective Lagrangians, there exist some systematical discrepancies from the data, i.e., the underestimated OESs in light C and O isotopes and the overestimated ones in heavy region, respectively. Such discrepancies can be eliminated partially by introducing a $Z$- or $N$-dependent strength factor into the pairing force Gogny D1S. In addition, successful descriptions of the occupation numbers of Sn isot...

  10. Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy.

    Science.gov (United States)

    Manohar, Suresh; Mantz, Amber R; Bancroft, Kevin E; Hui, Chung-Yuen; Jagota, Anand; Vezenov, Dmitri V

    2008-12-01

    We measured the force required to peel single-stranded DNA molecules from single-crystal graphite using chemical force microscopy. Force traces during retraction of a tip chemically modified with oligonucleotides displayed characteristic plateaus with abrupt force jumps, which we interpreted as a steady state peeling process punctuated by complete detachment of one or more molecules. We were able to differentiate between bases in pyrimidine homopolymers; peeling forces were 85.3 - 4.7 pN for polythymine and 60.8 +/- 5.5 pN for polycytosine, substantially independent of salt concentration and the rate of detachment. We developed a model for peeling a freely jointed chain from the graphite surface and estimated the average binding energy per monomer to be 11.5 +/- 0.6 k(B)T and 8.3 +/- 0.7 k(B)T in the cases of thymine and cytosine nucleotides, respectively. The equilibrium free-energy profile simulated using molecular dynamics had a potential well of 18.9 k(B)T for thymidine, showing that nonelectrostatic interactions dominate the binding. The discrepancy between the experiment and theory indicates that not all bases are adsorbed on the surface or that there is a population of conformations in which they adsorb. Force spectroscopy using oligonucleotides covalently linked to AFM tips provides a flexible and unambiguous means to quantify the strength of interactions between DNA and a number of substrates, potentially including nanomaterials such as carbon nanotubes. PMID:19368004

  11. Positive XPS binding energy shift of supported CuN-clusters governed by initial state effects

    International Nuclear Information System (INIS)

    Highlights: • Size dependent initial and final state effects of mass-selected deposited clusters. • Initial state effect dominates positive XPS shift in supported Cu-clusters. • Size dependent Coulomb correlation shift in the Auger final state of Cu cluster. • Size-dependent Auger parameter analysis. • Positive XPS shift differs from negative surface core level shift in crystalline copper. - Abstract: An initial state effect is established as origin for the positive 2p core electron binding energy shift found for CuN-clusters supported by a thin silica layer of a p-doped Si(1 0 0) wafer. Using the concept of the Auger parameter and taking into account the usually neglected Coulomb correlation shift in the Auger final state (M4,5M4,5) it is shown that the initial state shift is comparable to the measured XPS shift while the final state relaxation shift contributes only marginally to the binding energy shift. The cluster results differ from the negative surface core-level shift of crystalline copper which has been explained in terms of a final state relaxation effect

  12. Binding energy of excitons formed from spatially separated electrons and holes in insulating quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Pokutnyi, S. I., E-mail: pokutnyi-sergey@inbox.ru [National Academy of Sciences of Ukraine, Chuiko Institute of Surface Chemistry (Ukraine); Kulchin, Yu. N.; Dzyuba, V. P. [Russian Academy of Sciences, Institute of Automation and Control Processes, Far East Branch (Russian Federation)

    2015-10-15

    It is found that the binding energy of the ground state of an exciton formed from an electron and a hole spatially separated from each other (the hole is moving within a quantum dot, and the electron is localized above the spherical (quantum dot)–(insulating matrix) interface) in a nanosystem containing insulating Al{sub 2}O{sub 3} quantum dots is substantially increased (by nearly two orders of magnitude) compared to the exciton binding energy in an Al{sub 2}O{sub 3} single crystal. It is established that, in the band gap of an Al{sub 2}O{sub 3} nanoparticle, a band of exciton states (formed from spatially separated electrons and holes) appears. It is shown that there exists the possibility of experimentally detecting the ground and excited exciton states in the band gap of Al{sub 2}O{sub 3} nanoparticles at room temperature from the absorption spectrum of the nanosystem.

  13. Chaperone driven polymer translocation through Nanopore: spatial distribution and binding energy

    CERN Document Server

    Abdolvahab, Rouhollah Haji

    2016-01-01

    Chaperones are binding proteins which work as a driving force to bias the biopolymer translocation by binding to it near the pore and preventing its backsliding. Chaperones may have different spatial distribution. Recently we show the importance of their spatial distribution in translocation and how it effects on sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. As a result of the exponential distribution of chaperones, energy dependency of the translocation time will changed and one see a minimum in translocation time versus effective energy curve. The same trend can be seen in scaling exponent of time versus polymer length, $\\beta$ ($T\\sim\\beta$). Interestingly in some special cases e.g. chaperones of size $\\lambda=6$ and with exponential distribution rate of $\\alpha=5$, the minimum reaches even to amount of less than $1$ ($\\beta<1$). We explain the possibility of this rare result and base on a theoretical discussion we show that by taking into acc...

  14. An accurate redetermination of the sup 1 sup 1 sup 8 Sn binding energy

    CERN Document Server

    Borzakov, S B; Faikow-Stanczyk, H; Grigoriev, Y V; Panteleev, T; Pospísil, S; Smotritsky, L M; Telezhnikov, S A

    2002-01-01

    The energy of well-known strong gamma line from sup 1 sup 9 sup 8 Au, the 'gold standard', has been modified in the light of new adjustments in the fundamental constants and the value of 411.80176(12) keV was determined, which is 0.29 eV lower than the latest 1999 value. An energy calibration procedure for determining the neutron binding energy, B sub n , from complicated (n, gamma) spectra has been developed. A mathematically simple minimization function consisting only of terms having as parameters the coefficients of the energy calibration curve (polynomial) is used. A priori information about the relationships among the energies of different peaks on the spectrum is taken into account by a Monte-Carlo simulation. The procedure was used in obtaining B sub n for sup 1 sup 1 sup 8 Sn. The gamma-ray spectrum from thermal neutron radiative capture by sup 1 sup 1 sup 7 Sn has been measured on the IBR-2 pulsed reactor. gamma-rays were detected by a 72 cm sup 3 HPGe detector. For a better determination of B sub n...

  15. Effect of magnetic field on the impurity binding energy of the excited states in spherical quantum dot

    Indian Academy of Sciences (India)

    E Sadeghi; Gh Rezaie

    2010-10-01

    The effect of external magnetic field on the excited state energies in a spherical quantum dot was studied. The impurity energy and binding energy were calculated using the variational method within the effective mass approximation and finite barrier potential. The results showed that by increasing the magnetic field, the energy would be increased. The results obtained by this method were compared with the previous investigations.

  16. Correlating hydrogen oxidation and evolution activity on platinum at different pH with measured hydrogen binding energy

    Energy Technology Data Exchange (ETDEWEB)

    Sheng, WC; Zhuang, ZB; Gao, MR; Zheng, J; Chen, JGG; Yan, YS

    2015-01-08

    The hydrogen oxidation/evolution reactions are two of the most fundamental reactions in distributed renewable electrochemical energy conversion and storage systems. The identification of the reaction descriptor is therefore of critical importance for the rational catalyst design and development. Here we report the correlation between hydrogen oxidation/evolution activity and experimentally measured hydrogen binding energy for polycrystalline platinum examined in several buffer solutions in a wide range of electrolyte pH from 0 to 13. The hydrogen oxidation/evolution activity obtained using the rotating disk electrode method is found to decrease with the pH, while the hydrogen binding energy, obtained from cyclic voltammograms, linearly increases with the pH. Correlating the hydrogen oxidation/evolution activity to the hydrogen binding energy renders a monotonic decreasing hydrogen oxidation/evolution activity with the hydrogen binding energy, strongly supporting the hypothesis that hydrogen binding energy is the sole reaction descriptor for the hydrogen oxidation/evolution activity on monometallic platinum.

  17. Correlating hydrogen oxidation and evolution activity on platinum at different pH with measured hydrogen binding energy

    Science.gov (United States)

    Sheng, Wenchao; Zhuang, Zhongbin; Gao, Minrui; Zheng, Jie; Chen, Jingguang G.; Yan, Yushan

    2015-01-01

    The hydrogen oxidation/evolution reactions are two of the most fundamental reactions in distributed renewable electrochemical energy conversion and storage systems. The identification of the reaction descriptor is therefore of critical importance for the rational catalyst design and development. Here we report the correlation between hydrogen oxidation/evolution activity and experimentally measured hydrogen binding energy for polycrystalline platinum examined in several buffer solutions in a wide range of electrolyte pH from 0 to 13. The hydrogen oxidation/evolution activity obtained using the rotating disk electrode method is found to decrease with the pH, while the hydrogen binding energy, obtained from cyclic voltammograms, linearly increases with the pH. Correlating the hydrogen oxidation/evolution activity to the hydrogen binding energy renders a monotonic decreasing hydrogen oxidation/evolution activity with the hydrogen binding energy, strongly supporting the hypothesis that hydrogen binding energy is the sole reaction descriptor for the hydrogen oxidation/evolution activity on monometallic platinum.

  18. Quantum mechanical treatment of binding energy between DNA nucleobases and carbon nanotube: A DFT analysis

    Science.gov (United States)

    Chehel Amirani, Morteza; Tang, Tian; Cuervo, Javier

    2013-12-01

    The interactions between DNA and carbon nanotubes (CNTs) have been widely studied in recent years. The binding process of DNA with CNT as well as the electronic properties of DNA/CNT hybrids constitutes an interesting yet complicated problem. The binding energy (BE) of the hybridization is one of the most extensively studied parameters for the problem. In this work, density functional theory (DFT) was used to perform geometry optimization of neutral nucleobases including adenine, cytosine, guanine and thymine absorbed on a zigzag (7,0) single-walled CNT and to evaluate the basis set superposition error corrected BE of the optimized configuration. All DFT calculations were performed using the M05-2X functional. The 6-31G(d) basis set was used for the optimization step and single point energy calculations were done using the 6-31G(d,p) basis set. For each nucleobase, we examined the influence of the initial configuration (IC) on the BE value. In particular, we considered 24 different ICs for each nucleobase, and each IC was subjected to an independent optimization and BE calculation. Our results showed that different ICs result in very different BE values and can even change the order of the BE corresponding to different nucleobases. The difference in the BE for a particular nucleobase caused by changes in its IC can be comparable to the difference in the BE between different nucleobases at the same initial position relative to the CNT. This provides an explanation for the discrepancies that exist in the literature on the nucleobase/CNT BE, and suggests that the potential energy surface between the nucleobases and the CNT can have many local minima and care should be exercised in the calculation and interpretation of the BE.

  19. The impacts of electronic state hybridization on the binding energy of single phosphorus donor electrons in extremely downscaled silicon nanostructures

    Science.gov (United States)

    The Anh, Le; Moraru, Daniel; Manoharan, Muruganathan; Tabe, Michiharu; Mizuta, Hiroshi

    2014-08-01

    We present the density functional theory calculations of the binding energy of the Phosphorus (P) donor electrons in extremely downscaled single P-doped Silicon (Si) nanorods. In past studies, the binding energy of donor electrons was evaluated for the Si nanostructures as the difference between the ionization energy for the single P-doped Si nanostructures and the electron affinity for the un-doped Si nanostructures. This definition does not take into account the strong interaction of donor electron states and Si electron states explicitly at the conductive states and results in a monotonous increase in the binding energy by reducing the nanostructure's dimensions. In this paper, we introduce a new approach to evaluate the binding energy of donor electrons by combining the projected density of states (PDOS) analysis and three-dimensional analysis of associated electron wavefunctions. This enables us to clarify a gradual change of the spatial distribution of the 3D electron wavefunctions (3DWFs) from the donor electron ground state, which is fully localized around the P donor site to the first conductive state, which spreads over the outer Si nanorods contributing to current conduction. We found that the energy of the first conductive state is capped near the top of the atomistic effective potential at the donor site with respect to the surrounding Si atoms in nanorods smaller than about 27 a0. This results in the binding energy of approximately 1.5 eV, which is virtually independent on the nanorod's dimensions. This fact signifies a good tolerance of the binding energy, which governs the operating temperature of the single dopant-based transistors in practice. We also conducted the computationally heavy transmission calculations of the single P-doped Si nanorods connected to the source and drain electrodes. The calculated transmission spectra are discussed in comparison with the atomistic effective potential distributions and the PDOS-3DWFs method.

  20. Accurate calculation of binding energies for molecular clusters - Assessment of different models

    Science.gov (United States)

    Friedrich, Joachim; Fiedler, Benjamin

    2016-06-01

    In this work we test different strategies to compute high-level benchmark energies for medium-sized molecular clusters. We use the incremental scheme to obtain CCSD(T)/CBS energies for our test set and carefully validate the accuracy for binding energies by statistical measures. The local errors of the incremental scheme are benchmark values are ΔE = - 278.01 kJ/mol for (H2O)10, ΔE = - 221.64 kJ/mol for (HF)10, ΔE = - 45.63 kJ/mol for (CH4)10, ΔE = - 19.52 kJ/mol for (H2)20 and ΔE = - 7.38 kJ/mol for (H2)10 . Furthermore we test state-of-the-art wave-function-based and DFT methods. Our benchmark data will be very useful for critical validations of new methods. We find focal-point-methods for estimating CCSD(T)/CBS energies to be highly accurate and efficient. For foQ-i3CCSD(T)-MP2/TZ we get a mean error of 0.34 kJ/mol and a standard deviation of 0.39 kJ/mol.

  1. Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

    OpenAIRE

    Tanida, Yoshiaki; Ito, Masakatsu; Fujitani, Hideaki

    2007-01-01

    The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J. Chem. Phys. ${\\bf 123}$, 084108 (2005)]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a ...

  2. Towards understanding the unbound state of drug compounds: Implications for the intramolecular reorganization energy upon binding.

    Science.gov (United States)

    Foloppe, Nicolas; Chen, I-Jen

    2016-05-15

    There has been an explosion of structural information for pharmaceutical compounds bound to biological targets, but the conformations and dynamics of compounds free in solution are poorly characterized, if at all. Yet, knowledge of the unbound state is essential to understand the fundamentals of molecular recognition, including the much debated conformational intramolecular reorganization energy of a compound upon binding (ΔEReorg). Also, dependable observation of the unbound compounds is important for ligand-based drug discovery, e.g. with pharmacophore modelling. Here, these questions are addressed with long (⩾0.5μs) state-of-the-art molecular dynamics (MD) simulations of 26 compounds (including 7 approved drugs) unbound in explicit solvent. These compounds were selected to be chemically diverse, with a range of flexibility, and good quality bioactive X-ray structures. The MD-simulated free compounds are compared to their bioactive structure and conformers generated with ad hoc sampling in vacuo or with implicit generalized Born (GB) aqueous solvation models. The GB conformational models clearly depart from those obtained in explicit solvent, and suffer from conformational collapse almost as severe as in vacuo. Thus, the global energy minima in vacuo or with GB are not suitable representations of the unbound state, which can instead be extensively sampled by MD simulations. Many, but not all, MD-simulated compounds displayed some structural similarity to their bioactive structure, supporting the notion of conformational pre-organization for binding. The ligand-protein complexes were also simulated in explicit solvent, to estimate ΔEReorg as an enthalpic difference ΔHReorg between the intramolecular energies in the bound and unbound states. This fresh approach yielded ΔHReorg values⩽6kcal/mol for 18 out of 26 compounds. For three particularly polar compounds 15⩽ΔHReorg⩽20kcal/mol, supporting the notion that ΔHReorg can be substantial. Those large

  3. Reveal of small alkanes and isomers using calculated core and valence binding energy spectra and total momentum cross sections

    CERN Document Server

    Yang, Zejin

    2013-01-01

    The present study revealed quantum mechanically that the C1s binding energy spectra of the small alkanes (upto six carbons) provide a clear picture of isomeric chemical shift in linear alkanes and branched isomers, whereas the valence binding energy spectra contain more sensitive information regarding the length of the carbon chains. Total momentum cross sections of the alkanes exhibit the information of the chain length as well as constitutional isomers of the small alkanes. The C1s binding energies of small alkanes (including isomers) are position specific and the terminal carbons have the lowest energies. The length of an alkane chain does not apparently affect the C1s energies so that the terminal carbons (289.11 eV) of pentane are almost the same as those of hexane. The valence binding energy spectra of the alkanes are characterized by inner valence and outer valence regions which are separated by an energy gap at approximately 17 eV. The intensities of the total momentum cross sections of the alkanes ar...

  4. Electronic structure and binding energy relaxation of ScZr atomic alloying

    Science.gov (United States)

    Bo, Maolin; Guo, Yongling; Yang, Xuexian; He, Junjie; Liu, Yonghui; Peng, Cheng; Huang, Yongli; Sun, Chang Q.

    2016-07-01

    We examined the combined effect of atomic under- and hetero-coordination on the bond relaxation and electronic binding energy of Sc, Zr, and ScZr alloying using a combination of the bond-order-length-strength (BOLS) correlation and density functional theory (DFT) calculations. Observations strongly emphasize the relevance of core-level shifts as reliable X-ray photoelectron spectroscopy experimental descriptors of core-shell catalysis reactivity, along with under-coordinated atoms in bimetallic transition metal systems. The BOLS-DFT method provides enhanced catalysis reactivity and detects surface and alloy configurations, opening up the possibility to investigate more complex systems with irregularly under- and hetero-coordinated atoms.

  5. Orbital momentum distributions and binding energies for the complete valence shell of molecular iodine

    International Nuclear Information System (INIS)

    The complete valence shell binding energy spectrum (8-43eV) of I2 has been measured by using electron momentum spectroscopy at 1000eV. The complete inner valence region, corresponding to ionization from the 10 σu and 10 σg orbitals, has been measured for the first time and shows extensive splitting of the ionization strength due to electron correlation effects in the ion. Many-body calculations using the Green's function method have been carried out and are compared with the data. Momentum distributions, measured in both the outer and inner valence regions, are compared with those given by SCF orbital wave functions calculated with a number of different basis sets. Computed orbital position and momentum density maps for oriented I2 molecules are discussed in comparison with the measured and calculated spherically averaged momentum distributions

  6. Relativistic motion of the Λ in hypernuclei and phenomenological analysis of its binding energy

    International Nuclear Information System (INIS)

    A phenomenological analysis of the ground state binding energy BΛ of a Λ-particle in hypernuclei, which is based on the Dirac equation with scalar potential and fourth component of vector potential of rectangular shapes and of the same radius, is presented. Analytic expressions are obtained for the corresponding small and large component radial wave functions and the eigenvalue equation for BΛ is also given. The latter leads to approximate ''semiempirical mass-formulae'': BΛ - BΛ(A), for ''sufficiently large'' values of the mass number of the core nucleus A. In addition, estimates are performed for BΛ and also for the (average) effective mass of the Λ-particle and for the ''depth'' of the ''Schroedinger-equivalent potential'' by fitting the values of BΛ, (resulting either from the numerical solution of the eigenvalue equation or from approximate analytic expressions) to experimental data. (author). 35 refs, 9 tabs

  7. OMP decarboxylase: phosphodianion binding energy is used to stabilize a vinyl carbanion intermediate.

    Science.gov (United States)

    Goryanova, Bogdana; Amyes, Tina L; Gerlt, John A; Richard, John P

    2011-05-01

    Orotidine 5'-monophosphate decarboxylase (OMPDC) catalyzes the exchange for deuterium from solvent D(2)O of the C-6 proton of 1-(β-d-erythrofuranosyl)-5-fluorouracil (FEU), a phosphodianion truncated product analog. The deuterium exchange reaction of FEU is accelerated 1.8 × 10(4)-fold by 1 M phosphite dianion (HPO(3)(2-)). This corresponds to a 5.8 kcal/mol stabilization of the vinyl carbanion-like transition state, which is similar to the 7.8 kcal/mol stabilization of the transition state for OMPDC-catalyzed decarboxylation of a truncated substrate analog by bound HPO(3)(2-). These results show that the intrinsic binding energy of phosphite dianion is used in the stabilization of the vinyl carbanion-like transition state common to the decarboxylation and deuterium exchange reactions. PMID:21486036

  8. Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

    KAUST Repository

    Beke-Somfai, Tamás

    2010-01-26

    Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP. © 2009 American Chemical Society.

  9. Spin assignments of nuclear levels above the neutron binding energy in $^{88}$Sr

    CERN Multimedia

    Neutron resonances reveal nuclear levels in the highly excited region of the nucleus around the neutron binding energy. Nuclear level density models are therefore usually calibrated to the number of observed levels in neutron-induced reactions. The gamma-ray cascade from the decay of the highly excited compound nucleus state to the ground state show dierences dependent on the initial spin. This results in a dierence in the multiplicity distribution which can be exploited. We propose to use the 4${\\pi}$ total absorption calorimeter (TAC) at the n TOF facility to determine the spins of resonances formed by neutrons incident on a metallic $^{87}$Sr sample by measuring the gamma multiplicity distributions for the resolved resonances. In addition we would like to use the available enriched $^{87}$Sr target for cross section measurements with the C$\\scriptscriptstyle{6}$D$\\scriptscriptstyle{6}$ detector setup.

  10. Comparison of experimental and theoretical binding and transition energies in the actinide region

    International Nuclear Information System (INIS)

    The present status of experimental and theoretical binding and transition energy determinations is reviewed. Experimental data and the most recent theoretical predictions are compared for the energies of Kα1 X-rays, M series X-rays, K-LL Auger electrons, K, L3, M and N levels, and the 4f spin-orbit splitting. In addition, the Kα1 and L3 data are fitted by Moseley-type diagrams, and data on the shallow levels and the valence bands of actinide oxides are discussed. Comparison shows that the single-particle Dirac-Fock theory and the inclusion of quantum-electrodynamic contributions predicts energies of the innermost levels generally within the accuracy of data, that is in the order of magnitude of 1 eV. However, in the N, O... shells large deviations do occur presumably due to strong many-electron interactions. The inclusion of many-electron effects in the relativistic theory remains a challenge, as do experimental investigations affording an accuracy of better than 1 eV for the various electronic levels. (Auth.)

  11. Experimental determination of the deuterium binding energy with vacancies in tungsten

    Science.gov (United States)

    Zibrov, M.; Ryabtsev, S.; Gasparyan, Yu.; Pisarev, A.

    2016-08-01

    Deuterium (D) interaction with vacancies in tungsten (W) was studied using thermal desorption spectroscopy (TDS). In order to obtain a TDS spectrum with a prominent peak corresponding to D release from vacancies, a special procedure comprising damaging of a recrystallized W sample by low fluences of 10 keV/D ions, its annealing, and subsequent low-energy ion implantation, was utilized. This experimental sequence was performed several times in series; the only difference was the TDS heating rate that varied in the range of 0.15-4 K/s. The sum of the D binding energy (Eb) with vacancies and the activation energy for D diffusion (ED) in W was then directly determined from the slope of the Arrhenius-like plot ln(β / Tm2) versus 1/Tm, where β - heating rate and Tm - position of the respective peak in the TDS spectrum. The determined value of Eb + ED was 1.56 ± 0.06 eV.

  12. Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.

    Science.gov (United States)

    Kmunícek, J; Luengo, S; Gago, F; Ortiz, A R; Wade, R C; Damborský, J

    2001-07-31

    Comparative binding energy (COMBINE) analysis was conducted for 18 substrates of the haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 (DhlA): 1-chlorobutane, 1-chlorohexane, dichloromethane, 1,2-dichloroethane, 1,2-dichloropropane, 2-chloroethanol, epichlorohydrine, 2-chloroacetonitrile, 2-chloroacetamide, and their brominated analogues. The purpose of the COMBINE analysis was to identify the amino acid residues determining the substrate specificity of the haloalkane dehalogenase. This knowledge is essential for the tailoring of this enzyme for biotechnological applications. Complexes of the enzyme with these substrates were modeled and then refined by molecular mechanics energy minimization. The intermolecular enzyme-substrate energy was decomposed into residue-wise van der Waals and electrostatic contributions and complemented by surface area dependent and electrostatic desolvation terms. Partial least-squares projection to latent structures analysis was then used to establish relationships between the energy contributions and the experimental apparent dissociation constants. A model containing van der Waals and electrostatic intermolecular interaction energy contributions calculated using the AMBER force field explained 91% (73% cross-validated) of the quantitative variance in the apparent dissociation constants. A model based on van der Waals intermolecular contributions from AMBER and electrostatic interactions derived from the Poisson-Boltzmann equation explained 93% (74% cross-validated) of the quantitative variance. COMBINE models predicted correctly the change in apparent dissociation constants upon single-point mutation of DhlA for six enzyme-substrate complexes. The amino acid residues contributing most significantly to the substrate specificity of DhlA were identified; they include Asp124, Trp125, Phe164, Phe172, Trp175, Phe222, Pro223, and Leu263. These residues are suitable targets for modification by site-directed mutagenesis. PMID

  13. First-principles calculation on binding energy of an interstitial hydrogen atom around a screw dislocation in BCC iron

    International Nuclear Information System (INIS)

    The binding energy of an interstitial hydrogen atom at various lattice sites around the a0/2[111] screw dislocation core in BCC iron has been determined using the first-principles calculation. The calculation was based on the core structure of a screw dislocation with symmetric displacement field, which was obtained using the large-scale supercell containing 231 atoms and 1 x 1 x 4 k-point samplings. The binding or trapping energy of a hydrogen atom at both the t-site (tetrahedral site) and o-site (octahedral site) near a core is found to be approximately 0.2 eV. (author)

  14. Effects of Crossed Electric and Magnetic Fields on Shallow Donor Impurity Binding Energy in a Parabolic Quantum Well

    Institute of Scientific and Technical Information of China (English)

    E. Kasapoglu; H. Sari; I. S(o)kmen

    2004-01-01

    @@ We have calculated variationally the ground state binding energy of a hydrogenic donor impurity in a parabolic quantum well in the presence of crossed electric and magnetic fields. These homogeneous crossed fields are such that the magnetic field is parallel to the heterostructure layers and the electric field is applied perpendicular to the magnetic field. The dependence of the donor impurity binding energy to the well width and the strength of the electric and magnetic fields are discussed. We hope that the obtained results will provide important improvements in device applications, especially for a suitable choice of both fields in the narrow well widths.

  15. Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations

    DEFF Research Database (Denmark)

    Poongavanam, Vasanthanathan; Olsen, Lars; Jørgensen, Flemming Steen;

    2010-01-01

    , and methods based on statistical mechanics. In the present investigation, we started from an LIE model to predict the binding free energy of structurally diverse compounds of cytochrome P450 1A2 ligands, one of the important human metabolizing isoforms of the cytochrome P450 family. The data set...... includes both substrates and inhibitors. It appears that the electrostatic contribution to the binding free energy becomes negligible in this particular protein and a simple empirical model was derived, based on a training set of eight compounds. The root mean square error for the training set was 3.7 k...

  16. Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods.

    Directory of Open Access Journals (Sweden)

    Shuhua Shi

    Full Text Available The p53-MDMX interaction has attracted extensive attention of anti-cancer drug development in recent years. This current work adopted molecular dynamics (MD simulations and cross-correlation analysis to investigate conformation changes of MDMX caused by inhibitor bindings. The obtained information indicates that the binding cleft of MDMX undergoes a large conformational change and the dynamic behavior of residues obviously change by the presence of different structural inhibitors. Two different methods of binding free energy predictions were employed to carry out a comparable insight into binding mechanisms of four inhibitors PMI, pDI, WK23 and WW8 to MDMX. The data show that the main factor controlling the inhibitor bindings to MDMX arises from van der Waals interactions. The binding free energies were further divided into contribution of each residue and the derived information gives a conclusion that the hydrophobic interactions, such as CH-CH, CH-π and π-π interactions, are responsible for the inhibitor associations with MDMX.

  17. Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods.

    Science.gov (United States)

    Shi, Shuhua; Zhang, Shaolong; Zhang, Qinggang

    2015-01-01

    The p53-MDMX interaction has attracted extensive attention of anti-cancer drug development in recent years. This current work adopted molecular dynamics (MD) simulations and cross-correlation analysis to investigate conformation changes of MDMX caused by inhibitor bindings. The obtained information indicates that the binding cleft of MDMX undergoes a large conformational change and the dynamic behavior of residues obviously change by the presence of different structural inhibitors. Two different methods of binding free energy predictions were employed to carry out a comparable insight into binding mechanisms of four inhibitors PMI, pDI, WK23 and WW8 to MDMX. The data show that the main factor controlling the inhibitor bindings to MDMX arises from van der Waals interactions. The binding free energies were further divided into contribution of each residue and the derived information gives a conclusion that the hydrophobic interactions, such as CH-CH, CH-π and π-π interactions, are responsible for the inhibitor associations with MDMX. PMID:26513747

  18. Optimizing the Binding Energy of Hydrogen on Nanostructured Carbon Materials through Structure Control and Chemical Doping

    Energy Technology Data Exchange (ETDEWEB)

    Jie Liu

    2011-02-01

    The DOE Hydrogen Sorption Center of Excellence (HSCoE) was formed in 2005 to develop materials for hydrogen storage systems to be used in light-duty vehicles. The HSCoE and two related centers of excellence were created as follow-on activities to the DOE Office of Energy Efficiency and Renewable Energy’s (EERE’s) Hydrogen Storage Grand Challenge Solicitation issued in FY 2003. The Hydrogen Sorption Center of Excellence (HSCoE) focuses on developing high-capacity sorbents with the goal to operate at temperatures and pressures approaching ambient and be efficiently and quickly charged in the tank with minimal energy requirements and penalties to the hydrogen fuel infrastructure. The work was directed at overcoming barriers to achieving DOE system goals and identifying pathways to meet the hydrogen storage system targets. To ensure that the development activities were performed as efficiently as possible, the HSCoE formed complementary, focused development clusters based on the following four sorption-based hydrogen storage mechanisms: 1. Physisorption on high specific surface area and nominally single element materials 2. Enhanced H2 binding in Substituted/heterogeneous materials 3. Strong and/or multiple H2 binding from coordinated but electronically unsatruated metal centers 4. Weak Chemisorption/Spillover. As a member of the team, our group at Duke studied the synthesis of various carbon-based materials, including carbon nanotubes and microporous carbon materials with controlled porosity. We worked closely with other team members to study the effect of pore size on the binding energy of hydrogen to the carbon –based materials. Our initial project focus was on the synthesis and purification of small diameter, single-walled carbon nanotubes (SWNTs) with well-controlled diameters for the study of their hydrogen storage properties as a function of diameters. We developed a chemical vapor deposition method that synthesized gram quantities of carbon nanotubes with

  19. Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.

    Science.gov (United States)

    Wu, Kuan-Wei; Chen, Po-Chin; Wang, Jun; Sun, Ying-Chieh

    2012-10-01

    In the present study, we carried out thermodynamic integration molecular dynamics simulation for a pair of analogous inhibitors binding with Erk kinase to investigate how computation performs in reproducing the relative binding free energy. The computation with BCC-AM1 charges for ligands gave -1.1 kcal/mol, deviated from experimental value of -2.3 kcal/mol by 1.2 kcal/mol, in good agreement with experimental result. The error of computed value was estimated to be 0.5 kcal/mol. To obtain convergence, switching vdw interaction on and off required approximately 10 times more CPU time than switching charges. Residue-based contributions and hydrogen bonding were analyzed and discussed. Furthermore, subsequent simulation using RESP charge for ligand gave ΔΔG of -1.6 kcal/mol. The computed results are better than the result of -5.6 kcal/mol estimated using PBSA method in a previous study. Based on these results, we further carried out computations to predict ΔΔG for five new analogs, focusing on placing polar and nonpolar functional groups at the meta site of benzene ring shown in the Fig. 1, to see if these ligands have better binding affinity than the above ligands. The computations resulted that a ligand with polar -OH group has better binding affinity than the previous examined ligand by ~2.0 kcal/mol and two other ligands have better affinity by ~1.0 kcal/mol. The predicted better inhibitors of this kind should be of interest to experimentalist for future experimental enzyme and/or cell assays. PMID:22986633

  20. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.

    Directory of Open Access Journals (Sweden)

    Marharyta Petukh

    2015-07-01

    Full Text Available A new methodology termed Single Amino Acid Mutation based change in Binding free Energy (SAAMBE was developed to predict the changes of the binding free energy caused by mutations. The method utilizes 3D structures of the corresponding protein-protein complexes and takes advantage of both approaches: sequence- and structure-based methods. The method has two components: a MM/PBSA-based component, and an additional set of statistical terms delivered from statistical investigation of physico-chemical properties of protein complexes. While the approach is rigid body approach and does not explicitly consider plausible conformational changes caused by the binding, the effect of conformational changes, including changes away from binding interface, on electrostatics are mimicked with amino acid specific dielectric constants. This provides significant improvement of SAAMBE predictions as indicated by better match against experimentally determined binding free energy changes over 1300 mutations in 43 proteins. The final benchmarking resulted in a very good agreement with experimental data (correlation coefficient 0.624 while the algorithm being fast enough to allow for large-scale calculations (the average time is less than a minute per mutation.

  1. Transitions, cross sections and neutron binding energy in 186Re by Prompt Gamma Activation Analysis

    Science.gov (United States)

    Lerch, A. G.; Hurst, A. M.; Firestone, R. B.; Revay, Zs.; Szentmiklosi, L.; McHale, S. R.; McClory, J. W.; Detwiler, B.; Carroll, J. J.

    2014-03-01

    The nuclide 186Re possesses an isomer with 200,000 year half-life while its ground state has a half-life of 3.718 days. It is also odd-odd and well-deformed nucleus, so should exhibit a variety of other interesting nuclear-structure phenomena. However, the available nuclear data is rather sparse; for example, the energy of the isomer is only known to within + 7 keV and, with the exception of the J?=1- ground state, every proposed level is tentative in the ENSDF. Previously, Prompt Gamma Activation Analysis (PGAA) was utilized to study natRe with 186,188Re being produced via thermal neutron capture. Recently, an enriched 185Re target was irradiated by thermal neutrons at the Budapest Research Reactor to build on those results. Prompt (primary and secondary) and delayed gamma-ray transitions were measured with a large-volume, Compton-suppressed HPGe detector. Absolute cross sections for each gamma transition were deduced and corrected for self attenuation within the sample. Fifty-two primary gamma-ray transitions were newly identified and used to determine a revised value of the neutron binding energy. DICEBOX was used to simulate the decay scheme and the total radiative thermal neutron capture cross section was found to be 97+/-3 b Supported by DTRA (Detwiler) through HDTRA1-08-1-0014.

  2. Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

    Directory of Open Access Journals (Sweden)

    Caselle Michele

    2007-09-01

    Full Text Available Abstract Background Specific binding of proteins to DNA is one of the most common ways gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a simple recognition code, therefore the prediction of DNA target sequences is not straightforward. DNA-protein interactions can be studied using computational methods which can complement the current experimental methods and offer some advantages. In the present work we use physical effective potentials to evaluate the DNA-protein binding affinities for the λ repressor-DNA complex for which structural and thermodynamic experimental data are available. Results The binding free energy of two molecules can be expressed as the sum of an intermolecular energy (evaluated using a molecular mechanics forcefield, a solvation free energy term and an entropic term. Different solvation models are used including distance dependent dielectric constants, solvent accessible surface tension models and the Generalized Born model. The effect of conformational sampling by Molecular Dynamics simulations on the computed binding energy is assessed; results show that this effect is in general negative and the reproducibility of the experimental values decreases with the increase of simulation time considered. The free energy of binding for non-specific complexes, estimated using the best energetic model, agrees with earlier theoretical suggestions. As a results of these analyses, we propose a protocol for the prediction of DNA-binding target sequences. The possibility of searching regulatory elements within the bacteriophage λ genome using this protocol is explored. Our analysis shows good prediction capabilities, even in absence of any thermodynamic data and information on the naturally recognized sequence. Conclusion This study supports the conclusion that physics-based methods can offer a completely complementary

  3. First principle calculations of core-level binding energy and Auger kinetic energy shifts in metallic solids

    Energy Technology Data Exchange (ETDEWEB)

    Olovsson, Weine, E-mail: weine.olovsson@gmail.co [Department of Materials Science and Engineering, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto 606-8501 (Japan); Marten, Tobias [Department of Physics, Chemistry and Biology (IFM), Linkoeping University, SE-581 83 Linkoeping (Sweden); Holmstroem, Erik [Instituto de Fisica, Universidad Austral de Chile, Valdivia (Chile); Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Johansson, Boerje [Department of Physics and Materials Science, Uppsala University, P.O. Box 530, SE-751 21 Uppsala (Sweden); Applied Materials Physics, Department of Materials and Engineering, Royal Institute of Technology (KTH), SE-100 44 Stockholm (Sweden); Abrikosov, Igor A. [Department of Physics, Chemistry and Biology (IFM), Linkoeping University, SE-581 83 Linkoeping (Sweden)

    2010-05-15

    We present a brief overview of recent theoretical studies of the core-level binding energy shift (CLS) in solid metallic materials. The focus is on first principles calculations using the complete screening picture, which incorporates the initial (ground state) and final (core-ionized) state contributions of the electron photoemission process in X-ray photoelectron spectroscopy (XPS), all within density functional theory (DFT). Considering substitutionally disordered binary alloys, we demonstrate that on the one hand CLS depend on average conditions, such as volume and overall composition, while on the other hand they are sensitive to the specific local atomic environment. The possibility of employing layer resolved shifts as a tool for characterizing interface quality in fully embedded thin films is also discussed, with examples for CuNi systems. An extension of the complete screening picture to core-core-core Auger transitions is given, and new results for the influence of local environment effects on Auger kinetic energy shifts in fcc AgPd are presented.

  4. Insights into affinity and specificity in the complexes of α-lytic protease and its inhibitor proteins: binding free energy from molecular dynamics simulation†

    OpenAIRE

    Deng, Nan-Jie; Cieplak, Piotr

    2009-01-01

    We report the binding free energy calculation and its decomposition for the complexes of α-lytic protease and its protein inhibitors using molecular dynamics simulation. Standard mechanism serine protease inhibitors eglin C and OMTKY3 are known to have strong binding affinity for many serine proteases. Their binding loops have significant similarities, including a common P1 Leu as the main anchor in the binding interface. However, recent experiments demonstrate that the two inhibitors have va...

  5. The Shifts of Band Gap and Binding Energies of Titania/Hydroxyapatite Material

    Directory of Open Access Journals (Sweden)

    Nguyen Thi Truc Linh

    2014-01-01

    Full Text Available The titania/hydroxyapatite (TiO2/HAp product was prepared by precipitating hydroxyapatite in the presence of TiO(OH2 gel in the hydrothermal system. The characteristics of the material were determined by using the measurements such as X-ray photoemission spectroscopy (XPS, X-ray diffraction (XRD, diffuse reflectance spectra (DRS, transmission electron microscopy (TEM, scanning electron microscopy (SEM, and energy dispersive X-ray (EDX. The XPS analysis showed that the binding energy values of Ca (2p1/2, 2p3/2, P (2p1/2, 2p3/2, and O 1s levels related to hydroxyapatite phase whereas those of Ti (2p3/2, 2p1/2 levels corresponded with the characterization of titanium (IV in TiO2. The XRD result revealed that TiO2/HAp sample had hydroxyapatite phase, but anatase or rutile phases were not found out. TEM image of TiO2/HAp product showed that the surface of the plate-shaped HAp particles had a lot of smaller particles which were considered as the compound of Ti. The experimental band gap of TiO2/HAp material calculated by the DRS measurement was 3.6 eV, while that of HAp pure was 5.3 eV and that of TiO2 pure was around 3.2 eV. The shift of the band gap energy of TiO2 in the range of 3.2–3.6 eV may be related to the shifts of Ti signals of XPS spectrum.

  6. Study of the Binding Energies between Unnatural Amino Acids and Engineered Orthogonal Tyrosyl-tRNA Synthetases

    Science.gov (United States)

    Ren, Wei; Truong, Tan M.; Ai, Hui-Wang

    2015-07-01

    We utilized several computational approaches to evaluate the binding energies of tyrosine (Tyr) and several unnatural Tyr analogs, to several orthogonal aaRSes derived from Methanocaldococcus jannaschii and Escherichia coli tyrosyl-tRNA synthetases. The present study reveals the following: (1) AutoDock Vina and ROSETTA were able to distinguish binding energy differences for individual pairs of favorable and unfavorable aaRS-amino acid complexes, but were unable to cluster together all experimentally verified favorable complexes from unfavorable aaRS-Tyr complexes; (2) MD-MM/PBSA provided the best prediction accuracy in terms of clustering favorable and unfavorable enzyme-substrate complexes, but also required the highest computational cost; and (3) MM/PBSA based on single energy-minimized structures has a significantly lower computational cost compared to MD-MM/PBSA, but still produced sufficiently accurate predictions to cluster aaRS-amino acid interactions. Although amino acid-aaRS binding is just the first step in a complex series of processes to acylate a tRNA with its corresponding amino acid, the difference in binding energy, as shown by MD-MM/PBSA, is important for a mutant orthogonal aaRS to distinguish between a favorable unnatural amino acid (unAA) substrate from unfavorable natural amino acid substrates. Our computational study should assist further designing and engineering of orthogonal aaRSes for the genetic encoding of novel unAAs.

  7. Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

    Energy Technology Data Exchange (ETDEWEB)

    Tanida, Yoshiaki [Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi, Kanagawa (Japan)], E-mail: tanida@labs.fujitsu.com; Ito, Masakatsu; Fujitani, Hideaki [Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi, Kanagawa (Japan)

    2007-08-16

    The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C.D. Snow, M.R. Shirts, E.J. Sorin, V.S. Pande, J. Chem. Phys. 123 (2005) 084108]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a parallel computing system is also developed. To further reduce the computational cost, the adequate non-uniform intervals of coupling constant {lambda}, connecting two equilibrium states, namely bound and unbound, are determined. The absolute binding energies {delta}G thus obtained have effective linear relation between the computed and experimental values. If the results of two other different methods are compared, thermodynamic integration (TI) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda et al. [H. Gouda, I.D. Kuntz, D.A. Case, P.A. Kollman, Biopolymers 68 (2003) 16], the predictive accuracy of the relative values {delta}{delta}G is almost comparable to that of TI: the correlation coefficients (R) obtained are 0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energies meanwhile, a constant energy shift of {approx}-7 kcal/mol against the experimental values is evident. To solve this problem, several presumable reasons are investigated.

  8. Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

    Science.gov (United States)

    Tanida, Yoshiaki; Ito, Masakatsu; Fujitani, Hideaki

    2007-08-01

    The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C.D. Snow, M.R. Shirts, E.J. Sorin, V.S. Pande, J. Chem. Phys. 123 (2005) 084108]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a parallel computing system is also developed. To further reduce the computational cost, the adequate non-uniform intervals of coupling constant λ, connecting two equilibrium states, namely bound and unbound, are determined. The absolute binding energies Δ G thus obtained have effective linear relation between the computed and experimental values. If the results of two other different methods are compared, thermodynamic integration (TI) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda et al. [H. Gouda, I.D. Kuntz, D.A. Case, P.A. Kollman, Biopolymers 68 (2003) 16], the predictive accuracy of the relative values ΔΔ G is almost comparable to that of TI: the correlation coefficients ( R) obtained are 0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energies meanwhile, a constant energy shift of ˜-7 kcal/mol against the experimental values is evident. To solve this problem, several presumable reasons are investigated.

  9. Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

    International Nuclear Information System (INIS)

    The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C.D. Snow, M.R. Shirts, E.J. Sorin, V.S. Pande, J. Chem. Phys. 123 (2005) 084108]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a parallel computing system is also developed. To further reduce the computational cost, the adequate non-uniform intervals of coupling constant λ, connecting two equilibrium states, namely bound and unbound, are determined. The absolute binding energies ΔG thus obtained have effective linear relation between the computed and experimental values. If the results of two other different methods are compared, thermodynamic integration (TI) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda et al. [H. Gouda, I.D. Kuntz, D.A. Case, P.A. Kollman, Biopolymers 68 (2003) 16], the predictive accuracy of the relative values ΔΔG is almost comparable to that of TI: the correlation coefficients (R) obtained are 0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energies meanwhile, a constant energy shift of ∼-7 kcal/mol against the experimental values is evident. To solve this problem, several presumable reasons are investigated

  10. A shell-model investigation of the binding energies of some exotic isotopes of sodium and magnesium

    International Nuclear Information System (INIS)

    Standard shell-model calculations of the binding energies of the neutron-rich isotopes of sodium and magnesium are in strong disagreement with the experimental values near N=20. It is shown that the discrepancy can be explained by allowing neutron excitations from the dsub(3/2) shell into the fsub(7/2) shell. (author)

  11. Noncovalent Interactions of Tiopronin-Protected Gold Nanoparticles with DNA: Two Methods to Quantify Free Energy of Binding

    OpenAIRE

    Prado-Gotor, R.; Grueso, E

    2014-01-01

    The binding of gold nanoparticles capped with N-(2-mercaptopropionyl)glycine (Au@tiopronin) with double-stranded DNA has been investigated and quantified in terms of free energies by using two different approaches. The first approach follows the DNA conformational changes induced by gold nanoparticles using the CD technique. The second methodology consists in the use of pyrene-1-carboxaldehyde as a fluorescent probe. This second procedure implies the determination of the “true” free energy of...

  12. Coordination-resolved local bond relaxation, electron binding-energy shift, and Debye temperature of Ir solid skins

    International Nuclear Information System (INIS)

    Highlights: • Cohesive energy of the representative bond determines the core-level shift. • XPS derives the energy level of an isolated atom and its bulk shift. • XPS derives the local bond length, bond energy, binding energy density. • Thermal XPS resolves the Debye temperature and atomic cohesive energy. - Abstract: Numerical reproduction of the measured 4f7/2 energy shift of Ir(1 0 0), (1 1 1), and (2 1 0) solid skins turns out the following: (i) the 4f7/2 level of an isolated Ir atom shifts from 56.367 eV to 60.332 eV by 3.965 eV upon bulk formation; (ii) the local energy density increases by up to 130% and the atomic cohesive energy decreases by 70% in the skin region compared with the bulk values. Numerical match to observation of the temperature dependent energy shift derives the Debye temperature that varies from 285.2 K (Surface) to 315.2 K (Bulk). We clarified that the shorter and stronger bonds between under-coordinated atoms cause local densification and quantum entrapment of electron binding energy, which perturbs the Hamiltonian and the core shifts in the skin region

  13. Measurement of the binding energy of ultracold $^{87}$Rb$^{133}$Cs molecules using an offset-free optical frequency comb

    CERN Document Server

    Molony, Peter K; Gregory, Philip D; Kliese, Russell; Puppe, Thomas; Sueur, C Ruth Le; Aldegunde, Jesus; Hutson, Jeremy M; Cornish, Simon L

    2016-01-01

    We report the binding energy of $^{87}$Rb$^{133}$Cs molecules in their rovibrational ground state measured using an offset-free optical frequency comb based on difference frequency generation technology. We create molecules in the absolute ground state using stimulated Raman adiabatic passage (STIRAP) with a transfer efficiency of 88\\%. By measuring the absolute frequencies of our STIRAP lasers, we find the energy-level difference from an initial weakly-bound Feshbach state to the rovibrational ground state with a resolution of 5 kHz over an energy-level difference of more than 114 THz; this lets us discern the hyperfine splitting of the ground state. Combined with theoretical models of the Feshbach state binding energies and ground-state hyperfine structure, we determine a zero-field binding energy of $h\\times114\\,268\\,135\\,237(5)(50)$ kHz. To our knowledge, this is the most accurate determination to date of the dissociation energy of a molecule.

  14. Why baryons are Yang-Mills magnetic monopoles, validated by nuclear binding energies and proton and neutron masses

    Science.gov (United States)

    Yablon, Jay R.

    2013-10-01

    Evidence is summarized from four recent papers that baryons including protons and neutrons are magnetic monopoles of non-commuting Yang-Mills gauge theories: 1) Protons and neutrons are ``resonant cavities'' with binding energies determined strictly by the masses of the quarks they contain. This is proven true at parts-per million accuracy for each of the 2H, 3H,3He, 4He binding energies and the neutron minus proton mass difference. 2) Respectively, each free proton and neutron contains 7.64 MeV and 9.81 MeV of mass/energy used to confine its quarks. When these nucleons bind, some, never all, of this energy is released and the mass deficit goes into binding. The balance continues to confine quarks. 56Fe releases 99.8429% of this energy for binding, more than any other nuclide. 3) Once we consider the Fermi vev one also finds an entirely theoretical explanation of proton and neutron masses, which also connects within experimental errors to the CKM quark mixing angles. 4) A related GUT explains fermion generation replication based on generator loss during symmetry breaking, and answers Rabi's question ``who ordered this?'' 5) Nuclear physics is governed by combining Maxwell's two classical equations into one equation using non-commuting gauge fields in view of Dirac theory and Fermi-Dirac-Pauli Exclusion. 6) Atoms themselves are core magnetic charges (nucleons) paired with orbital electric charges (electrons and elusive neutrinos), with the periodic table itself revealing an electric/magnetic symmetry of Maxwell's equations often pondered but heretofore unrecognized for a century and a half.

  15. High level theoretical study of binding and of the potential energy surface in benzene–hydride system

    International Nuclear Information System (INIS)

    Graphical abstract: In-plane minimum geometries for benzene–H− non-covalent adducts: linear adduct (left) with the hydride ion hydrogen bonded to one aromatic hydrogen; bifurcated adduct (right), with the hydride ion hydrogen bonded to two adjacent aromatic hydrogens. Highlights: ► Theoretical study on covalent and non-covalent binding in benzene–hydride. ► Two non-covalent stable adducts were characterized in the in-plane geometry. ► Significant sections of the potential energy surface were determined. ► Formation of a very stable C6H7- anion upon covalent binding to carbon. - Abstract: High level ab initio calculations were performed on the interaction of the hydride anion with benzene, a system of potential interest for modelling the interactions occurring in hydrogen rich planetary atmospheres. We investigated both non-covalent and covalent binding, exploring the complete basis set limit using highly correlated MP2 and CCSD(T) levels of theory. Two non-covalent minima on the potential energy surface have been characterized, and found to correspond to moderately strong hydrogen bonding interactions. To gain further insight on the nature of binding, the total interaction energy was decomposed into its physically meaningful components and selected sections of the potential energy surface were calculated. Moreover, we found that H− can easily covalently bind to one of the carbon atoms of benzene to form a stable C6H7− anion, a global minimum on the potential energy surface, characterized by a puckered geometry, with a carbon atom bending out of the benzene plane. A slightly less stable planar C6H7− structure was also identified, corresponding to the transition state for the flipping motion of the puckered species.

  16. Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations.

    Science.gov (United States)

    Lu, Haiting; Huang, Xiaoqin; AbdulHameed, Mohamed Diwan M; Zhan, Chang-Guo

    2014-04-01

    Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been performed to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson-Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2A6-inhibitor binding affinity are two crucial internuclear distances, that is, the distance between the heme iron atom of CYP2A6 and the coordinating atom of the inhibitor, and the hydrogen-bonding distance between the N297 side chain of CYP2A6 and the pyridine nitrogen of the inhibitor. The combined MD simulations and QM/MM-PBSA calculations have led to dynamic CYP2A6-inhibitor binding structures that are consistent with the observed dynamic behaviors and structural features of CYP2A6-inhibitor binding, and led to the binding free energies that are in good agreement with the experimentally-derived binding free energies. The agreement between the calculated binding free energies and the experimentally-derived binding free energies suggests that the combined MD and QM/MM-PBSA approach may be used as a valuable tool to accurately predict the CYP2A6-inhibitor binding affinities in future computational design of new, potent and selective CYP2A6 inhibitors. PMID:24631364

  17. Electron momentum distributions and binding energies for the valence orbitals of hydrogen bromide and hydrogen iodide

    International Nuclear Information System (INIS)

    Electron binding energy spectra and momentum distributions have been obtained for the valence orbitals of HBr and HI using noncoplanar symmetric electron coincidence spectroscopy at 1200 e V. The weakly bonding inner valence ns orbitals, which have not been observed previously, have their spectroscopic (pole) strength severely split among a number of ion states. For HBr the strength of the 'main' inner valence (ns) transition is 0.42 +- 0.03 whereas for HI it is 0.37 +- 0.04, in close agreement with the value observed for the valence s orbitals of the corresponding isoelectronic inert-gas atoms. The spectroscopic strength for the two outermost orbitals is found to be close to unity, in agreement with many-body Green's function calculations. The measured momentum distributions are compared with several spherically averaged MO momentum distributions, as well as (for HBr) with a Green's function calculation of the generalized overlap amplitude (GOA). The GOA momentum distributions are in excellent agreement with the HBr data, both in shape and relative magnitude. Not all of the MO momentum distributions are in reasonable agreement with the data. Comparison is also made with the calculated momentum distributions for Kr, Br, Xe and I. (orig.)

  18. Electron momentum distributions and binding energies for the valence orbitals of hydrogen bromide and hydrogen iodide

    International Nuclear Information System (INIS)

    The electron binding energy spectra and momentum distributions have been obtained for the valence orbitals of HBr and HI using noncoplanar symmetric electron coincidence spectroscopy at 1200eV. The weakly bonding inner valence ns orbitals, which have not been previously observed, have their spectroscopic (pole) strength severely split among a number of ion states. For HBr the strength of the main inner valence (ns) transition is 0.42 0.03 whereas for HI it is 0.37 0.04, in close agreement with that observed for the valence s orbitals of the corresponding isoelectronic inert gas atoms. The spectroscopic strength for the two outermost orbitals is found to be close to unity, in agreement with many body Green's function calculations. The measured momentum distributions are compared with several spherically averaged MO momentum distributions, as well as (for HBr) with a Green's function calculation of the generalized overlap amplitude (GOA). The GOA momentum distributions are in excellent agreement with the HBr data, both in shape and relative magnitude. Not all of the MO momentum distributions are in reasonable agreement with the data. Comparison is also made with the calculated momentum distributions for Kr, Br, Xe and I

  19. Exciton Binding Energy in Organic-Inorganic Tri-Halide Perovskites.

    Science.gov (United States)

    Askar, Abdelrahman M; Shankar, Karthik

    2016-06-01

    The recent dramatic increase in the power conversion efficiencies of organic-inorganic tri-halide perovskite solar cells has triggered intense research worldwide and created a paradigm shift in the photovoltaics field. It is crucial to develop a solid understanding of the photophysical processes underlying solar cell operation in order to both further improve the photovoltaic performance of perovskite solar cells as well as to exploit the broader optoelectronic applications of the tri-halide perovskites. In this short review, we summarize the main research findings about the binding energy of excitons in tri-halide perovskite materials and find that a value in the range of 2-22 meV at room temperature would be a safe estimate. Spontaneous free carrier generation is the dominant process taking place directly after photoexcitation in organic-inorganic tri-halide perovskites at room temperature, which eliminates the exciton diffusion bottleneck present in organic solar cells and constitutes a major contributing factor to the high photovoltaic performance of this material. PMID:27427650

  20. A fluorescence resonance energy transfer method for measuring the binding of inhibitors to stromelysin.

    Science.gov (United States)

    Epps, D E; Mitchell, M A; Petzold, G L; VanDrie, J H; Poorman, R A

    1999-11-15

    A sensitive fluorescence resonance energy transfer method was developed for the direct measurement of the dissociation constants of stromelysin inhibitors. The method is applied to the thiadiazole class of stromelysin inhibitors and it takes advantage of the fact that, upon binding to the active site of enzyme, the thiadiazole ring, with its absorbance centered at 320 nm, is able to quench the fluorescence of the tryptophan residues surrounding the catalytic site. The changes in fluorescence are proportional to the occupancy of the active site: Analysis of the fluorescence versus inhibitor concentration data yields dissociation constants that are in agreement with the corresponding competitive inhibitory constants measured by a catalytic rate assay. The affinity of nonthiadiazole inhibitors of stromelysin-such as hydroxamic acids and others-can be determined from the concentration-dependent displacement of a thiadiazole of known affinity. Using this displacement method, we determined the affinities of a number of structurally diverse inhibitors toward stromelysin. Since the three tryptophan residues located in the vicinity of the active site of stromelysin are conserved in gelatinase and collagenase, the method should also be applicable to inhibitors of other matrix metalloproteinases. PMID:10552897

  1. Isotopic dependence of the nuclear charge radii and binding energies in the relativistic Hartree-Fock formalism

    Energy Technology Data Exchange (ETDEWEB)

    Niembro, R., E-mail: niembror@unican.es; Marcos, S.; Lopez-Quelle, M. [Universidad de Cantabria (Spain); Savushkin, L. N. [St. Petersburg University for Telecommunications (Russian Federation)

    2012-03-15

    Relativistic nonlinear models based on the Hartree and Hartree-Fock approximations, including the {sigma}, {omega}, {pi}, and {rho} mesons, are worked out to explore the behavior of the nuclear charge radii and the binding energies of several isotopic chains. We find a correlation between the magnitude of the anomalous kink effect (KE) in the Pb isotopic family and the compressibility modulus (K) of nuclear matter. The KE appears to be sensitive, in particular, to the mechanisms which control the K value. The influence of the symmetry energy on the Ca isotopic chain is also studied. The behavior of the charge radii of single-particle states for some special cases and its repercussion on the nuclear charge radius is analyzed. The effect of pairing correlations on the models improves considerably the quality of the results in both binding energy and KE.

  2. Subsite binding energies of an exo-polygalacturonase using isothermal titration calorimetry

    Science.gov (United States)

    Thermodynamic parameters for binding of a series of galacturonic acid oligomers to an exo-polygalacturonase, RPG16 from Rhizopus oryzae, were determined by isothermal titration calorimetry. Binding of oligomers varying in chain length from two to five galacturonic acid residues is an exothermic proc...

  3. Determination of the cationic amphiphilic drug-DNA binding mode and DNA-assisted fluorescence resonance energy transfer amplification

    Science.gov (United States)

    Yaseen, Zahid; Banday, Abdul Rouf; Hussain, Mohammed Aamir; Tabish, Mohammad; Kabir-ud-Din

    2014-03-01

    Understanding the mechanism of drug-DNA binding is crucial for predicting the potential genotoxicity of drugs. Agarose gel electrophoresis, absorption, steady state fluorescence, and circular dichroism have been used in exploring the interaction of cationic amphiphilic drugs (CADs) such as amitriptyline hydrochloride (AMT), imipramine hydrochloride (IMP), and promethazine hydrochloride (PMT) with calf thymus or pUC19 DNA. Agarose gel electrophoresis assay, along with absorption and steady state fluorescence studies, reveal interaction between the CADs and DNA. A comparative study of the drugs with respect to the effect of urea, iodide induced quenching, and ethidium bromide (EB) exclusion assay reflects binding of CADs to the DNA primarily in an intercalative fashion. Circular dichroism data also support the intercalative mode of binding. Besides quenching, there is fluorescence exchange energy transfer (FRET) in between CADs and EB using DNA as a template.

  4. Influence of position dependent effective mass on donor binding energy in square and V-shaped quantum wells in the presence of a magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Panahi, H., E-mail: t-panahi@guilan.ac.ir [Department of Physics, University of Guilan, 41335-1914 Rasht (Iran, Islamic Republic of); Golshahi, S. [Department of Physics, Rasht Branch, Islamic Azad University, Rasht (Iran, Islamic Republic of); Doostdar, M. [Department of Physics, University of Guilan, 41335-1914 Rasht (Iran, Islamic Republic of)

    2013-06-01

    In this paper we have calculated variationally the ground state binding energy of a hydrogenic donor impurity in square quantum well and V-shaped quantum well as a function of the well width in the presence of magnetic fields with both constant and position dependent effective mass. The wave function of electrons confined to donor impurity within the quantum well is considered as the two dimensional and three dimensional trial wave functions. It has been found that by increasing the well width, the binding energy decreases smoothly to bulk values while its steepness is sharper in square quantum well in comparison with V-shaped quantum well. Increasing the magnetic field leads to the enhancement of binding energy. At higher magnetic fields, by increasing the well width, binding energy tends to a constant value. The effect of position dependent effective mass on the enhancement of binding energy is more evident in comparison with constant effective mass one.

  5. Influence of position dependent effective mass on donor binding energy in square and V-shaped quantum wells in the presence of a magnetic field

    International Nuclear Information System (INIS)

    In this paper we have calculated variationally the ground state binding energy of a hydrogenic donor impurity in square quantum well and V-shaped quantum well as a function of the well width in the presence of magnetic fields with both constant and position dependent effective mass. The wave function of electrons confined to donor impurity within the quantum well is considered as the two dimensional and three dimensional trial wave functions. It has been found that by increasing the well width, the binding energy decreases smoothly to bulk values while its steepness is sharper in square quantum well in comparison with V-shaped quantum well. Increasing the magnetic field leads to the enhancement of binding energy. At higher magnetic fields, by increasing the well width, binding energy tends to a constant value. The effect of position dependent effective mass on the enhancement of binding energy is more evident in comparison with constant effective mass one

  6. Steric and allosteric effects of fatty acids on the binding of warfarin to human serum albumin revealed by molecular dynamics and free energy calculations.

    Science.gov (United States)

    Fujiwara, Shin-Ichi; Amisaki, Takashi

    2011-01-01

    Human serum albumin (HSA) binds with drugs and fatty acids (FAs). This study was initiated to elucidate the relationship between the warfarin binding affinity of HSA and the positions of bound FA molecules. Molecular dynamics simulations of 11 HSA-warfarin-myristate complexes were performed. HSA-warfarin binding free energy was then calculated for each of the complexes by the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method. The results indicated that the magnitude of the binding free energy was smaller in HSA-warfarin complexes that had 4 or more myristate molecules than in complexes with no myristate molecules. The unfavorable effect on the HSA-warfarin binding affinity was caused sterically by the binding of a myristate molecule to the FA binding site closest to the warfarin binding site. On the other hand, the magnitude of HSA-warfarin binding free energy was largest when 3 myristate molecules were bound to the high-affinity sites. The strongest HSA-warfarin binding was attributable to favorable entropic contribution related to larger atomic fluctuations of the amino acid residues at the warfarin binding site. In the binding of 2 myristate molecules to the sites with the highest and second-highest affinities, allosteric modulation that enhanced electrostatic interactions between warfarin and some of the amino acid residues around the warfarin binding site was observed. This study clarified the structural and energetic properties of steric/allosteric effects of FAs on the HSA-warfarin binding affinity and illustrated the approach to analyze protein-ligand interactions in situations such that multiple ligands bind to the other sites of the protein. PMID:21720037

  7. Binding and Adsorption Energies of Heavy Metal Ions with Hapli-Udic Argosol and Ferri-Udic Argosol Particles

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Gibbs free binding energy and adsorption energy between cations and charged soil particles were used to evaluate the interactions between ions and soil particles. The distribution of Gibbs free adsorption energies could not be determined experimentally before the development of Wien effect measurements in dilute soil suspensions. In the current study, energy relationships between heavy metal ions and particles of Hapli-Udic Argosol (Alfisol) and Ferri-Udic Argosol were inferred from Wien effect measurements in dilute suspensions of homoionic soil particles (< 2 μm) of the two soils, which were saturated with ions of five heavy metals, in deionized water. The mean Gibbs free binding energies of the heavy metal ions with Hapli-Udic Argosol and Ferri-Udic Argosol particles diminished in the order of Pb2+>Cd2+>Cu2+> Zn2+ >Cr3+, where the range of binding energies for Hapli-Udic Argosol (7.25-9.32 kJ mol-1) was similar to that for Ferri-Udic Argosol (7.43-9.35 kJ mol-1). The electrical field-dependent mean Gibbs free adsorption energies of these heavy metal ions for Hapli-Udic Argosol and for Ferri-Udic Argosol descended in the order: Cu2+≥ Cd2+≥ Pb2+ > Zn2+>Cr3+,and Cd2+ >Cu2+>Pb2+>Zn2+>Cr3+, respectively. The mean Gibbs free adsorption energies of Cu2+, Zn2+, Cd2+,Pb2+, and Cr3+ at a field strength of 200 kV cm-1, for example, were in the range of 0.8-3.2 kJ mol-1 for the two soils.

  8. Shedding Light on the EOS-Gravity Degeneracy and Constraining the Nuclear Symmetry Energy from the Gravitational Binding Energy of Neutron Stars

    OpenAIRE

    He Xiao-Tao; Fattoyev F. J.; Li Bao-An; Newton W. G.

    2016-01-01

    A thorough understanding of properties of neutron stars requires both a reliable knowledge of the equation of state (EOS) of super-dense nuclear matter and the strong-field gravity theories simultaneously. To provide information that may help break this EOS-gravity degeneracy, we investigate effects of nuclear symmetry energy on the gravitational binding energy of neutron stars within GR and the scalar-tensor subset of alternative gravity models. We focus on effects of the slope $L$ of nuclea...

  9. Influence of geometrical factor on binding energy of Cooper pairs in YBa2Cu3O7-δ compound

    Science.gov (United States)

    Ibrahim, Saeed O.; Mustafa, Bassam M.

    2016-03-01

    In this research the influence of geometrical factors on binding energy between Cooper pairs are investigated for the high temperature superconducting (YBa2Cu3O7-δ) compound. This is done by using a model considering that the formation of Cooper pairs happens during tunneling mechanism of holes between the two CuO2 layers in the YBCO crystal which are considered as forming adjacent ridged potential wells. According to this model binding energy is: Eb i n=4/√{2 }m3/2 π2ħ3p ×∫U-0(U -0-E) exp [-2/(d -Rc) ħ √{2 m (U -E ) } ] √{E } d E 0 is a work function, ħ is the Plank's constant, m is the electron mass, and U is the height of the potential barrier, E is the energy, Rc is the electron cloud radius in tunneling direction and d is the distance between the two CuO2 planes. In the above model two effects of geometrical factors were ignored, considering that ridges in the two CuO2 layers as having rectangular shape, but in reality the ridges in the potential well are of triangular shape. Also the model considers the distance between layers as constant but really the distant d is variable due to the triangular geometry. In this work we consider both effects that affect the density of state in the potential well and the tunneling probability. Then binding energy between the Cooper pairs, is calculated.

  10. Molecular Dynamics Simulation of Tryptophan Hydroxylase-1: Binding Modes and Free Energy Analysis to Phenylalanine Derivative Inhibitors

    Directory of Open Access Journals (Sweden)

    Liang Ouyang

    2013-05-01

    Full Text Available Serotonin is a neurotransmitter that modulates many central and peripheral functions. Tryptophan hydroxylase-1 (TPH1 is a key enzyme of serotonin synthesis. In the current study, the interaction mechanism of phenylalanine derivative TPH1 inhibitors was investigated using molecular dynamics (MD simulations, free energy calculations, free energy decomposition analysis and computational alanine scanning. The predicted binding free energies of these complexes are consistent with the experimental data. The analysis of the individual energy terms indicates that although the van der Waals and electrostatics interaction contributions are important in distinguishing the binding affinities of these inhibitors, the electrostatic contribution plays a more crucial role in that. Moreover, it is observed that different configurations of the naphthalene substituent could form different binding patterns with protein, yet lead to similar inhibitory potency. The combination of different molecular modeling techniques is an efficient way to interpret the interaction mechanism of inhibitors and our work could provide valuable information for the TPH1 inhibitor design in the future.

  11. Binding energy referencing for XPS in alkali metal-based battery materials research (I): Basic model investigations

    International Nuclear Information System (INIS)

    Highlights: • We point to a not seriously solved conflict in energy scale referencing of Li metal samples in XPS. • Model experiments at Li-, Na-metal and Li-doped HOPG samples were used to classify the effects. • Binding energy shifts up to 3 eV are observed when the alkaline metal is present in metallic state. • A phenomenological explanation based on an electrostatic interaction is suggested. • Consequences for energy scale correction depending on the kind of surface species are followed. - Abstract: For the investigation of chemical changes in Li- and Na-ion battery electrode systems, X-ray photoelectron spectroscopy (XPS) is a well-accepted method. Charge compensation and referencing of the binding energy (BE) scale is necessary to account for the involved mostly non-conducting species. Motivated by a conflict in energy scale referencing of Li-metal samples discussed earlier by several authors, further clarifying experimental results on several Li containing reference materials are presented and extended by similar experiments for Na. When correlating the peak positions of characteristic chemical species in all the different prepared model sample states, there seems to be a systematic deviation in characteristic binding energies of several eV if lithium is present in its metallic state. Similar results were found for sodium. The observations are furthermore confirmed by the implementation of inert artificial energy reference material, such as implanted argon or deposited gold. The behavior is associated with the high reactivity of metallic lithium and a phenomenological explanation is proposed for the understanding of the observations. Consequences for data interpretation in Li-ion battery research will be discussed for various applications in part (II)

  12. Binding energy referencing for XPS in alkali metal-based battery materials research (I): Basic model investigations

    Energy Technology Data Exchange (ETDEWEB)

    Oswald, S., E-mail: s.oswald@ifw-dresden.de

    2015-10-01

    Highlights: • We point to a not seriously solved conflict in energy scale referencing of Li metal samples in XPS. • Model experiments at Li-, Na-metal and Li-doped HOPG samples were used to classify the effects. • Binding energy shifts up to 3 eV are observed when the alkaline metal is present in metallic state. • A phenomenological explanation based on an electrostatic interaction is suggested. • Consequences for energy scale correction depending on the kind of surface species are followed. - Abstract: For the investigation of chemical changes in Li- and Na-ion battery electrode systems, X-ray photoelectron spectroscopy (XPS) is a well-accepted method. Charge compensation and referencing of the binding energy (BE) scale is necessary to account for the involved mostly non-conducting species. Motivated by a conflict in energy scale referencing of Li-metal samples discussed earlier by several authors, further clarifying experimental results on several Li containing reference materials are presented and extended by similar experiments for Na. When correlating the peak positions of characteristic chemical species in all the different prepared model sample states, there seems to be a systematic deviation in characteristic binding energies of several eV if lithium is present in its metallic state. Similar results were found for sodium. The observations are furthermore confirmed by the implementation of inert artificial energy reference material, such as implanted argon or deposited gold. The behavior is associated with the high reactivity of metallic lithium and a phenomenological explanation is proposed for the understanding of the observations. Consequences for data interpretation in Li-ion battery research will be discussed for various applications in part (II)

  13. Magnetic field-dependent of binding energy in GaN/InGaN/GaN spherical QDQW nanoparticles

    Science.gov (United States)

    El Ghazi, Haddou; Jorio, Anouar; Zorkani, Izeddine

    2013-10-01

    Simultaneous study of magnetic field and impurity's position effects on the ground-state shallow-donor binding energy in GaN│InGaN│GaN (core│well│shell) spherical quantum dot-quantum well (SQDQW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated within the framework of the effective-mass approximation and an infinite deep potential describing the quantum confinement effect. A Ritz variational approach is used taking into account of the electron-impurity correlation and the magnetic field effect in the trial wave-function. It appears that the binding energy depends strongly on the external magnetic field, the impurity's position and the structure radius. It has been found that: (i) the magnetic field effect is more marked in large layer than in thin layer and (ii) it is more pronounced in the spherical layer center than in its extremities.

  14. Application of the step-wise regression procedure to the semi-empirical formulae of the nuclear binding energy

    International Nuclear Information System (INIS)

    Most of the binding energy semi-empirical terms without the deformation corrections used by P.A. Seeger are arranged in a multiple linear regression form. The stepwise regression procedure with 95% confidence levels for acceptance and rejection of variables is applied for seeking a model for calculating binding energies of even-even (E-E) nuclei through a significance testing of each basic term. Partial F-values are taken as estimates for the significance of each term. The residual standard deviation and the overall F-value are used for selecting the best linear regression model. (E-E) nuclei are taken into sets lying between two successive proton and neutron magic numbers. The present work is in favour of the magic number 126 followed by 164 for the neutrons and indecisive in supporting the recently predicted proton magic number 114 rather than the previous one, 126. (author)

  15. The effects of electron binding energy corrections on Monte Carlo models in the diagnostic x-ray energy range

    International Nuclear Information System (INIS)

    Full text: The effects of incorporating electron binding energy corrections for incoherent scatter (BEC) into Monte Carlo models of X-ray transport in the diagnostic energy range have been examined. The inclusion of BEC can significantly increase computing overhead both in terms of data storage and execution time. In a modern PC application, data storage is unlikely to be a significant problem. However, execution time is a major consideration when assessing the relative usefulness of Monte Carlo systems. If the effectiveness of including BEC is barely more than equivocal, as is the case in some of the studies reported here, then a decision to include them requires consideration of the photon energy being modelled and the data being sought. This work seeks to clarify the real significance of inclusion of BEC by examining their effects without the confounding influence of coherent scattering effects. A Monte Carlo computer code has been developed to study a variety of X-ray transport phenomena. Models of radiation dose deposition in a semi-infinite medium, a similar model in tissue using a realistic source spectrum and diverging beam geometry, a simulation of pencil beam bone densitometry measurements, models of barrier penetration by X-rays and models of the angular distribution of scattered radiation have been undertaken. Results of previous studies have been confirmed. Models of radiation dose deposition for 10 keV, 30 keV and 100 keV photons have shown that inclusion of BEC has only a small effect upon values of total depth dose. Differences are of the same order of magnitude as the standard deviation of the results. A larger effect was noted for the values of dose due to scattered photons. This effect reached a maximum of 7% at 30 keV. Similar results were obtained from a model using a realistic source spectrum and diverging beam geometry. In the simulation of bone densitometry measurements the effects are significant (i.e. of the order of 10%). The angular

  16. Total energy calculation of perovskite, BaTiO3, by self-consistent tight binding method

    Indian Academy of Sciences (India)

    B T Cong; P N A Huy; P K Schelling; J W Halley

    2003-01-01

    We present results of numerical computation on some characteristics of BaTiO3 such as total energy, lattice constant, density of states, band structure etc using self-consistent tight binding method. Besides strong Ti–O bond between 3 on titanium and 2 orbital on oxygen states, we also include weak hybridization between the Ba 6 and O 2 states. The results are compared with those of other more sophisticated methods.

  17. A New Model for Calculating the Binding Energy of Lithium Nucleus under the Generalized Yukawa Potential and Hellmann Potential

    OpenAIRE

    Ghazvini, M; Salehi, N; Rajabi, A. A.

    2014-01-01

    In this paper, the Schr\\"odinger equation for 6-body system is studied. We solved this equation for lithium nucleus by using supersymmetry method with the specific potentials. These potentials are Yukawa potential, the generalized Yukawa potential and Hellmann potential. The results of our model for all calculations show that the ground state binding energy of Lithium nucleus with these potentials are very close to the ones obtained in experiments.

  18. The effect of Fermi momentum cutoff on the binding energy of closed-shell nuclei in the LOCV framework

    International Nuclear Information System (INIS)

    The ground-state binding energies of the light symmetric closed-shell nuclei, i.e., 4He, 12C, 16O and 40Ca, and the heavy asymmetric ones, i.e., 48Ca, 90Zr and 120Sn, are calculated in the harmonic oscillator (HOS) basis, by imposing the relative Fermi momentum cutoff of two point-like interacting nucleons on the density-dependent average effective interactions (DDAEI). The DDAEI are generated through the lowest order constrained variational (LOCV) method calculations for the asymmetric nuclear matter with the operator and the channel-dependent-type bare nucleon-nucleon potentials, such as the Argonne Av18jmax=2 and the Reid soft core, Reid68, interactions. In the framework of the harmonic oscillator shell model, the cutoff is imposed by defining the maximum value of the relative quantum numbers (RQNmax) in two ways: (1) the RQNmax of the last shell and (2) the RQNmax of each shell, in the ground state of the nucleus. It is shown that present results on the binding energies and the root-mean-square radius are closer to the corresponding experimental data than our previous works with the same DDAEI potentials, but without the cutoff constraint. However, for the light symmetric nuclei, the second scheme gives less binding energy and larger root-mean-square radius compared to the first one, while the situation is reversed for the heavier nuclei.

  19. Configuration space method for calculating binding energies of exciton complexes in quasi-1D/2D semiconductors

    Science.gov (United States)

    Bondarev, Igor

    A configuration space method, pioneered by Landau and Herring in studies of molecular binding and magnetism, is developed to obtain universal asymptotic relations for lowest energy exciton complexes (trion, biexciton) in confined semiconductor nanostructures such as nanowires and nanotubes, as well as coupled quantum wells. Trions are shown to be more stable (have greater binding energy) than biexcitons in strongly confined quasi-1D structures with small reduced electron-hole masses. Biexcitons are more stable in less confined quasi-1D structures with large reduced electron-hole masses. The theory predicts a crossover behavior, whereby trions become less stable than biexcitons as the transverse size of the quasi-1D nanostructure increases, which might be observed on semiconducting carbon nanotubes of increasing diameters. This method is also efficient in calculating binding energies for trion-type electron-hole complexes formed by indirect excitons in double coupled quantum wells, quasi-2D nanostructures that show new interesting electroabsorption/refraction phenomena. Supported by DOE-DE-SC0007117.

  20. Toward an Accurate and Inexpensive Estimation of CCSD(T)/CBS Binding Energies of Large Water Clusters.

    Science.gov (United States)

    Sahu, Nityananda; Singh, Gurmeet; Nandi, Apurba; Gadre, Shridhar R

    2016-07-21

    Owing to the steep scaling behavior, highly accurate CCSD(T) calculations, the contemporary gold standard of quantum chemistry, are prohibitively difficult for moderate- and large-sized water clusters even with the high-end hardware. The molecular tailoring approach (MTA), a fragmentation-based technique is found to be useful for enabling such high-level ab initio calculations. The present work reports the CCSD(T) level binding energies of many low-lying isomers of large (H2O)n (n = 16, 17, and 25) clusters employing aug-cc-pVDZ and aug-cc-pVTZ basis sets within the MTA framework. Accurate estimation of the CCSD(T) level binding energies [within 0.3 kcal/mol of the respective full calculation (FC) results] is achieved after effecting the grafting procedure, a protocol for minimizing the errors in the MTA-derived energies arising due to the approximate nature of MTA. The CCSD(T) level grafting procedure presented here hinges upon the well-known fact that the MP2 method, which scales as O(N(5)), can be a suitable starting point for approximating to the highly accurate CCSD(T) [that scale as O(N(7))] energies. On account of the requirement of only an MP2-level FC on the entire cluster, the current methodology ultimately leads to a cost-effective solution for the CCSD(T) level accurate binding energies of large-sized water clusters even at the complete basis set limit utilizing off-the-shelf hardware. PMID:27351269

  1. Combined effects of hydrostatic pressure and electric field on the donor binding energy and polarizability in laterally coupled double InAs/GaAs quantum-well wires

    International Nuclear Information System (INIS)

    This work is concerned with the theoretical study of the combined effects of applied electric field and hydrostatic pressure on the binding energy and impurity polarizability of a donor impurity in laterally coupled double InAs/GaAs quantum-well wires. calculations have been made in the effective mass and parabolic band approximations and using a variational method. The results are reported for different configurations of wire and barriers widths, impurity position, and electric field and hydrostatic pressure strengths. Our results show that for symmetrical structures the binding energy is an even function of the impurity position along the growth direction of the structure. Also, we found that for hydrostatic pressure strength up to 38 kbar, the binding energy increases linearly with hydrostatic pressure, while for larger values of hydrostatic pressure the binding energy has a nonlinear behavior. Finally, we found that the hydrostatic pressure can increase the coupling between the two parallel quantum well wires.

  2. Insights into affinity and specificity in the complexes of alpha-lytic protease and its inhibitor proteins: binding free energy from molecular dynamics simulation.

    Science.gov (United States)

    Deng, Nan-Jie; Cieplak, Piotr

    2009-07-01

    We report the binding free energy calculation and its decomposition for the complexes of alpha-lytic protease and its protein inhibitors using molecular dynamics simulation. Standard mechanism serine protease inhibitors eglin C and OMTKY3 are known to have strong binding affinity for many serine proteases. Their binding loops have significant similarities, including a common P1 Leu as the main anchor in the binding interface. However, recent experiments demonstrate that the two inhibitors have vastly different affinity towards alpha-lytic protease (ALP), a bacterial serine protease. OMTKY3 inhibits the enzyme much more weakly (by approximately 10(6) times) than eglin C. Moreover, a variant of OMTKY3 with five mutations, OMTKY3M, has been shown to inhibit 10(4) times more strongly than the wild-type inhibitor. The underlying mechanisms for the unusually large difference in binding affinities and the effect of mutation are not well understood. Here we use molecular dynamics simulation with molecular mechanics-Poisson Boltzmann/surface area method (MM-PB/SA) to investigate quantitatively the binding specificity. The calculated absolute binding free energies correctly differentiate the thermodynamic stabilities of these protein complexes, but the magnitudes of the binding affinities are systematically overestimated. Analysis of the binding free energy components provides insights into the molecular mechanism of binding specificity. The large DeltaDeltaG(bind) between eglin C and wild type OMTKY3 towards ALP is mainly attributable to the stronger nonpolar interactions in the ALP-eglin C complex, arising from a higher degree of structural complementarity. Here the electrostatic interaction contributes to a lesser extent. The enhanced inhibition in the penta-mutant OMTKY3M over its wild type is entirely due to an overall improvement in the solvent-mediated electrostatic interactions in the ALP-OMTKY3M complex. The results suggest that for these protein-complexes and

  3. Roles of binding energy and diffusion length of singlet and triplet excitons in organic heterojunction solar cells

    International Nuclear Information System (INIS)

    The influence of binding energy and diffusion length on the dissociation of excitons in organic solids is studied. The binding energy and excitonic Bohr radius of singlet and triplet excitons are calculated and compared using the dissociation energy of 0.3 eV, which is provided by the lowest unoccupied molecular orbital offset in heterojunction organic solar cells. A relation between the diffusion coefficient and diffusion length of singlet and triplet excitons is derived using the Foerster and Dexter transfer processes and are plotted as a function of the donor-acceptor separation. The diffusion length reduces nearly to a zero if the distance between donor and acceptor is increased to more than 1.5 nm. It is found that the donor-acceptor separation needs to be ≤ 1.5 nm for easy dissociation on singlet excitons leading to better conversion efficiency in heterojunction organic solar cells. (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  4. Roles of binding energy and diffusion length of singlet and triplet excitons in organic heterojunction solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Narayan, Monishka Rita [Centre for Renewable Energy and Low Emission Technology, Charles Darwin University, Darwin, NT 0909 (Australia); Singh, Jai [School of Engineering and IT, Charles Darwin University, Darwin, NT 0909 (Australia)

    2012-12-15

    The influence of binding energy and diffusion length on the dissociation of excitons in organic solids is studied. The binding energy and excitonic Bohr radius of singlet and triplet excitons are calculated and compared using the dissociation energy of 0.3 eV, which is provided by the lowest unoccupied molecular orbital offset in heterojunction organic solar cells. A relation between the diffusion coefficient and diffusion length of singlet and triplet excitons is derived using the Foerster and Dexter transfer processes and are plotted as a function of the donor-acceptor separation. The diffusion length reduces nearly to a zero if the distance between donor and acceptor is increased to more than 1.5 nm. It is found that the donor-acceptor separation needs to be {<=} 1.5 nm for easy dissociation on singlet excitons leading to better conversion efficiency in heterojunction organic solar cells. (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  5. What can be learned from binding energy differences about nuclear structure: the example of delta V_{pn}

    OpenAIRE

    Bender, Michael; Heenen, Paul-Henri

    2011-01-01

    We perform an analysis of a binding energy difference called delta V_{pn}(N,Z) =- 1/4(E(Z,N)-E(Z,N-2)-E(Z-2,N)+ E(Z-2,N-2) in the framework of a realistic nuclear model. Using the angular-momentum and particle-number projected generator coordinate method and the Skyrme interaction SLy4, we analyze the contribution brought to delta V_{pn} by static deformation and dynamic fluctuations around the mean-field ground state. Our method gives a good overall description of delta V_{pn} throughout the...

  6. Application of object-oriented programming in a time-dependent density-functional theory calculation of exciton binding energies

    CERN Document Server

    Yang, Zeng-hui

    2013-01-01

    This paper discusses the benefits of object-oriented programming to scientific computing, using our recent calculations of exciton binding energies with time-dependent density-functional theory (arXiv: 1302.6972) as a case study. We find that an object-oriented approach greatly facilitates the development, the debugging, and the future extension of the code by promoting code reusing. We show that parallelism is added easily in our code in a object-oriented fashion with ScaLAPACK, Boost::MPI and OpenMP.

  7. Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation.

    Directory of Open Access Journals (Sweden)

    Luigi Capoferri

    Full Text Available Prediction of human Cytochrome P450 (CYP binding affinities of small ligands, i.e., substrates and inhibitors, represents an important task for predicting drug-drug interactions. A quantitative assessment of the ligand binding affinity towards different CYPs can provide an estimate of inhibitory activity or an indication of isoforms prone to interact with the substrate of inhibitors. However, the accuracy of global quantitative models for CYP substrate binding or inhibition based on traditional molecular descriptors can be limited, because of the lack of information on the structure and flexibility of the catalytic site of CYPs. Here we describe the application of a method that combines protein-ligand docking, Molecular Dynamics (MD simulations and Linear Interaction Energy (LIE theory, to allow for quantitative CYP affinity prediction. Using this combined approach, a LIE model for human CYP 1A2 was developed and evaluated, based on a structurally diverse dataset for which the estimated experimental uncertainty was 3.3 kJ mol-1. For the computed CYP 1A2 binding affinities, the model showed a root mean square error (RMSE of 4.1 kJ mol-1 and a standard error in prediction (SDEP in cross-validation of 4.3 kJ mol-1. A novel approach that includes information on both structural ligand description and protein-ligand interaction was developed for estimating the reliability of predictions, and was able to identify compounds from an external test set with a SDEP for the predicted affinities of 4.6 kJ mol-1 (corresponding to 0.8 pKi units.

  8. Insights into affinity and specificity in the complexes of α-lytic protease and its inhibitor proteins: binding free energy from molecular dynamics simulation†

    Science.gov (United States)

    Cieplak, Piotr

    2014-01-01

    We report the binding free energy calculation and its decomposition for the complexes of α-lytic protease and its protein inhibitors using molecular dynamics simulation. Standard mechanism serine protease inhibitors eglin C and OMTKY3 are known to have strong binding affinity for many serine proteases. Their binding loops have significant similarities, including a common P1 Leu as the main anchor in the binding interface. However, recent experiments demonstrate that the two inhibitors have vastly different affinity towards α-lytic protease (ALP), a bacterial serine protease. OMTKY3 inhibits the enzyme much more weakly (by ~106 times) than eglin C. Moreover, a variant of OMTKY3 with five mutations, OMTKY3M, has been shown to inhibit 104 times more strongly than the wild-type inhibitor. The underlying mechanisms for the unusually large difference in binding affinities and the effect of mutation are not well understood. Here we use molecular dynamics simulation with molecular mechanics–Poisson Boltzmann/surface area method (MM-PB/SA) to investigate quantitatively the binding specificity. The calculated absolute binding free energies correctly differentiate the thermodynamic stabilities of these protein complexes, but the magnitudes of the binding affinities are systematically overestimated. Analysis of the binding free energy components provides insights into the molecular mechanism of binding specificity. The large ΔΔGbind between eglin C and wild type OMTKY3 towards ALP is mainly attributable to the stronger nonpolar interactions in the ALP-eglin C complex, arising from a higher degree of structural complementarity. Here the electrostatic interaction contributes to a lesser extent. The enhanced inhibition in the penta-mutant OMTKY3M over its wild type is entirely due to an overall improvement in the solvent-mediated electrostatic interactions in the ALP-OMTKY3M complex. The results suggest that for these protein-complexes and similar enzyme-inhibitor systems

  9. Measurement of the minimum binding energy of the 2p sigma molecular orbital formed in heavy ion collisions

    International Nuclear Information System (INIS)

    In order to study the minimum 2p sigma binding energy and its collision broadening, a copper ion beam was extracted from the Cs-sputter source and accelerated by the EN-tandem at Western Michigan University. Copper beams of ten different energies between 3 and 56 MeV were directed onto a pure thin (approx. 50μg) and a pure thick (approx. 5 mg) copper target. The x-rays emitted under 900 were reduced in intensity with an 11 mil thick pure aluminum absorber and observed with an 80mm2 Si(Li) detector. We were able to obtain quite intense 2p sigma MO-spectra with Cu-beams as slow as 3, 4, 5 and 7 MeV for thick as well as the thin targets

  10. QED radiative corrections and many-body effects in atoms: vacuum polarization and binding energy shifts in alkali metals

    Science.gov (United States)

    Ginges, J. S. M.; Berengut, J. C.

    2016-05-01

    We calculate vacuum polarization corrections to the binding energies in neutral alkali atoms Na through to the superheavy element E119. We employ the relativistic Hartree–Fock method to demonstrate the importance of relaxation of the electronic core and the correlation potential method to study the effects of second and higher orders of perturbation theory. These many-body effects are sizeable for all orbitals, though particularly important for orbitals with angular momentum quantum number l\\gt 0. The orders of magnitude enhancement for d waves produces shifts that, for Rb and the heavier elements, are larger than those for p waves and only an order of magnitude smaller than the s-wave shifts. The many-body enhancement mechanisms that operate for vacuum polarization apply also to the larger self-energy corrections.

  11. Electric field and position effects on the binding energy of a shallow donor in quantum dot-quantum well

    International Nuclear Information System (INIS)

    The binding energy is estimated for a shallow donor confined to move in GaAs-Ga1-xAlxAs Quantum Dot-Quantum Well (QDQW) in the presence of a uniform electric field. In this work the variational method, within the effective mass approximation is used in the case of an infinitely deep well. We present our results as functions of the size of the QDQW and for several values of the electric field strength. The binding energy depends on the inner and the outer radius of the QDQW, decreasing when the electric field increases and depending strongly on the donor position. The stark effect is more important when the impurity is located at the center of the (QDQW) and becomes less important when the donor moves toward the extremities of the spherical layer. We have demonstrated the existence of a critical value of radius ratio which can be used to distinguish the tree dimension confinement from the spherical surface confinement. Our results are explained on the basis of qualitative arguments and asymptotic analyses. (author)

  12. Positive XPS binding energy shift of supported Cu{sub N}-clusters governed by initial state effects

    Energy Technology Data Exchange (ETDEWEB)

    Peters, S.; Peredkov, S. [Technische Universität Berlin, IOAP, Strasse des 17. Juni 135, 10623 Berlin (Germany); Al-Hada, M. [Department of Physics, College of Education and Linguistics, University of Amran (Yemen); Neeb, M., E-mail: matthias.neeb@helmholtz-berlin.de [Helmholtz-Zentrum Berlin, Wilhelm-Conrad-Röntgen-Campus Adlershof, Elektronenspeicherring BESSY II, Albert-Einstein-Straße 15, 12489 Berlin (Germany); Eberhardt, W. [Technische Universität Berlin, IOAP, Strasse des 17. Juni 135, 10623 Berlin (Germany); DESY, Center for Free Electron Laser Science (CFEL), Notkestr. 85, 22607 Hamburg (Germany)

    2014-01-01

    Highlights: • Size dependent initial and final state effects of mass-selected deposited clusters. • Initial state effect dominates positive XPS shift in supported Cu-clusters. • Size dependent Coulomb correlation shift in the Auger final state of Cu cluster. • Size-dependent Auger parameter analysis. • Positive XPS shift differs from negative surface core level shift in crystalline copper. - Abstract: An initial state effect is established as origin for the positive 2p core electron binding energy shift found for Cu{sub N}-clusters supported by a thin silica layer of a p-doped Si(1 0 0) wafer. Using the concept of the Auger parameter and taking into account the usually neglected Coulomb correlation shift in the Auger final state (M{sub 4,5}M{sub 4,5}) it is shown that the initial state shift is comparable to the measured XPS shift while the final state relaxation shift contributes only marginally to the binding energy shift. The cluster results differ from the negative surface core-level shift of crystalline copper which has been explained in terms of a final state relaxation effect.

  13. Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

    experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated the...... free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine....

  14. Binding energy of adsorbates on a noble-metal surface: exchange and correlation effects.

    Science.gov (United States)

    Rohlfing, Michael; Bredow, Thomas

    2008-12-31

    We discuss the adsorption of xenon and of PTCDA on the silver (111) surface within a first-principles approach, focusing on the adsorbate-substrate interaction energy as a function of distance. We combine exact exchange with correlation energy from the adiabatic-connection fluctuation-dissipation theorem. At a large distance Z from the surface, the correlation causes a van der Waals attraction [approximately -C3/(Z - Z0)3]. At a closer distance, the attraction deviates from its asymptotic form and, combined with the repulsive exact-exchange energy, yields an equilibrium in close agreement with experiment. PMID:19437654

  15. Predicting the binding free energy of the inclusion process of 2-hydroxypropyl-β-cyclodextrin and small molecules by means of the MM/3D-RISM method

    Science.gov (United States)

    Sugita, Masatake; Hirata, Fumio

    2016-09-01

    A protocol to calculate the binding free energy of a host–guest system is proposed based on the MM/3D-RISM method, taking cyclodextrin derivatives and their ligands as model systems. The protocol involves the procedure to identify the most probable binding mode (MPBM) of receptors and ligands by means of the umbrella sampling method. The binding free energies calculated by the MM/3D-RISM method for the complexes of the seven ligands with the MPBM of the cyclodextrin, and with the fluctuated structures around it, are in agreement with the corresponding experimental data in a semi-quantitative manner. It suggests that the protocol proposed here is promising for predicting the binding affinity of a small ligand to a relatively rigid receptor such as cyclodextrin.

  16. Predicting the binding free energy of the inclusion process of 2-hydroxypropyl-β-cyclodextrin and small molecules by means of the MM/3D-RISM method.

    Science.gov (United States)

    Sugita, Masatake; Hirata, Fumio

    2016-09-28

    A protocol to calculate the binding free energy of a host-guest system is proposed based on the MM/3D-RISM method, taking cyclodextrin derivatives and their ligands as model systems. The protocol involves the procedure to identify the most probable binding mode (MPBM) of receptors and ligands by means of the umbrella sampling method. The binding free energies calculated by the MM/3D-RISM method for the complexes of the seven ligands with the MPBM of the cyclodextrin, and with the fluctuated structures around it, are in agreement with the corresponding experimental data in a semi-quantitative manner. It suggests that the protocol proposed here is promising for predicting the binding affinity of a small ligand to a relatively rigid receptor such as cyclodextrin. PMID:27452185

  17. Binding Free Energies for Nicotine Analogs Inhibiting Cytochrome P450 2A6 by a Combined Use of Molecular Dynamics Simulations and QM/MM-PBSA Calculations

    OpenAIRE

    Lu, Haiting; Huang, Xiaoqin; AbdulHameed, Mohamed Diwan M.; Zhan, Chang-Guo

    2014-01-01

    Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been perforemd to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson-Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2...

  18. Stark effect of donor binding energy in a self-assembled GaAs quantum dot subjected to a tilted electric field

    International Nuclear Information System (INIS)

    We theoretically investigated the donor binding energy distribution with respect to the dopant positions in a self-assembled GaAs/AlGaAs quantum dot (QD) in the presence of a tilted electric field. It is found that there is a critical line in a doping plane, corresponding to zero Stark shift of the donor binding energy. At low electric fields, our work reveals that Stark shift of an on-center donor binding energy is a “purely” quadratic function of the electric field strength, irrespective of QD dimensions and field orientations. This scaling law permits us to indirectly estimate the impurity polarizability in a self-assembled QD. -- Highlights: ► There is a critical line corresponding to zero shift of the donor binding energy. ► Dot dimensions and applied electric field affect significantly the critical line. ► Stark shift of on center donor binding energy is a quadratic function of the field. ► An indirect way to estimate the impurity polarizability has been reported.

  19. Stark effect of donor binding energy in a self-assembled GaAs quantum dot subjected to a tilted electric field

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Zaiping [Materials Science Department, University of Patras, Rio 26504 (Greece); Garoufalis, Christos S. [Materials Science Department, University of Patras, Rio 26504 (Greece); Department of Environment Technology and Ecology, Technological Institute of Ionian Islands, 2 Kalvou Sq, 29100 Zakynthos (Greece); Baskoutas, Sotirios, E-mail: bask@upatras.gr [Materials Science Department, University of Patras, Rio 26504 (Greece); Terzis, Andreas F. [Physics Department, University of Patras, 26504 Patras (Greece)

    2012-09-03

    We theoretically investigated the donor binding energy distribution with respect to the dopant positions in a self-assembled GaAs/AlGaAs quantum dot (QD) in the presence of a tilted electric field. It is found that there is a critical line in a doping plane, corresponding to zero Stark shift of the donor binding energy. At low electric fields, our work reveals that Stark shift of an on-center donor binding energy is a “purely” quadratic function of the electric field strength, irrespective of QD dimensions and field orientations. This scaling law permits us to indirectly estimate the impurity polarizability in a self-assembled QD. -- Highlights: ► There is a critical line corresponding to zero shift of the donor binding energy. ► Dot dimensions and applied electric field affect significantly the critical line. ► Stark shift of on center donor binding energy is a quadratic function of the field. ► An indirect way to estimate the impurity polarizability has been reported.

  20. ADMET, Docking studies & binding energy calculations of some Novel ACE - inhibitors for the treatment of Diabetic Nephropathy

    Directory of Open Access Journals (Sweden)

    Gade Deepak Reddy

    2012-09-01

    Full Text Available Diabetic Nephropathy (DN is one of the major complications of diabetes mellitus, representing the leading of cause of chronic renal disease and a major cause of morbidity and mortality in both type 1 and type 2 diabetic patients. The Renin-Angiotensin-Aldosterone System (RAAS has been implicated in the pathophysiology of DN, and suggests a therapeutic target for blocking this system. Therefore, inhibition of RAAS plays a crucial role in the treatment of DN and therapeutic intervention mostly involves administration of angiotensin converting enzyme (ACE inhibitors and angiotensin AT1 receptor blockers. In this current study, we have used computational methods to design 37 novel ACE-inhibitors and evaluated them for the interaction with the enzyme ACE through insilico analysis. The obtained results were compared with the standard drug enalapril to find out the potential inhibitors. Here we report that ligand 4 exhibited strongest inhibitory activity among all. All the analogs are also screened for their ADME & Toxicity profiles using insilico tools and ligand 9 is having better binding affinity next to ligand 4, and also having better ADMET profile when compared to that of ligand 4. Post docking calculations were also performed for the docked complexes in order to identify the individual ligand binding energies by employing Multi-Ligand Bimolecular Association with Energetics (Embrace

  1. Hypernuclear interactions and the binding energies of Λ and ΛΛ hypernuclei

    International Nuclear Information System (INIS)

    By use of variational calculations a reasonable hadronic description is obtained of the s-shell hypernuclei, of /sub Λ/9Be, and of the well depth, with ΛN forces which are consistent with Λp scattering and which are quite strongly spin-dependent, with reasonable TPE ΛNN forces with strongly repulsive dispersive-type ΛNN forces. For the latter we also consider a spin-dependent version which is somewhat favored by our analysis. /sub Λ/9Be is treated as a 2α + Λ system and is significantly overbound, ≅1 MeV, if only αα and αΛ potentials are used. An ααΛ potential obtained from the ΛNN forces nicely accounts for this overbinding. The ΛΛ hypernuclei /sub ΛΛ/6He and /sub ΛΛ/10Be are treated as α + 2Λ and 2α + 2Λ systems. Use of the /sub ΛΛ/10Be event gives ≅1.5 MeV too little binding for /sub ΛΛ/6He. The 1S0 ΛΛ potential obtained from /sub ΛΛ/10Be is quite strongly attractive, comparable to the ΛN and also to the NN potential without OPE. 18 refs

  2. Study of the structure and energy of grain boundaries using an LMTO based tight-binding method

    International Nuclear Information System (INIS)

    A parametrized tight-binding (TB) method based on TB-LMTO approach in the atomic sphere approximation (ASA) [26] has been developed. The Hamiltonian is written in terms of the canonical structure matrix and potential parameters. The former is for a given configuration of atoms evaluated using a Dyson-type equation and the latter are those found self-consistently for the ideal lattice. A warping correction has been added to the scheme to be able to account for the effects of local straining which can not be included in the ASA. This is essential for applications in defect studies. Using this method the structure and energy of the Σ = 5 [001] twist boundary in cooper has been calculated

  3. Optical determination of phosphorus acceptor binding energy in bulk wide-gap II-VI semimagnetic semiconductors

    International Nuclear Information System (INIS)

    Zn1-xMnxTe and Cd1-xMnxTe semimagnetic semiconductors doped with phosphorus have been investigated by means of the resistivity, Hall effect, photoluminescence and reflectance measurements. The high p-type doping level of these materials was achieved using Zn3P2 and CdP2 as the sources of P-impurities. By applying a unique technology of high-pressure annealing we were able to overcome a self-compensation in Zn1-xMnxTe:P. As a result, the sample with high and controllable concentration of electrical active acceptors were produced. The ground state binding energy of phosphorus acceptors in both Zn1-xMnxTe and Cd1-xMnxTe as well as its variation with the phosphorus doping level were optically determined. (copyright 2004 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  4. MMPBSA Decomposition of the Binding Energy throughout a Molecular Dynamics Simulation of Amyloid-Beta (Aß10−35 Aggregation

    Directory of Open Access Journals (Sweden)

    Josep M. Campanera

    2010-04-01

    Full Text Available Recent experiments with amyloid-beta (Aβ peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer’s disease. The toxicity of Aβ oligomers depend on their structure, which is governed by assembly dynamics. However, a detailed knowledge of the structure of at the atomic level has not been achieved yet due to limitations of current experimental techniques. In this study, replica exchange molecular dynamics simulations are used to identify the expected diversity of dimer conformations of Aβ10−35 monomers. The most representative dimer conformation has been used to track the dimer formation process between both monomers. The process has been characterized by means of the evolution of the decomposition of the binding free energy, which provides an energetic profile of the interaction. Dimers undergo a process of reorganization driven basically by inter-chain hydrophobic and hydrophilic interactions and also solvation/desolvation processes.

  5. Orbital momentum distribution and binding energies for the complete valence shell of molecular chlorine by electron momentum spectroscopy

    International Nuclear Information System (INIS)

    The complete valence shell binding energy spectrum (10-50 eV) of Cl2 has been determined using electron momentum (binary (e,2e)) spectroscopy. The inner valence region, corresponding to 4σu and 4σg ionization, has been measured for the first time and shows extensive splitting of the ionization strength due to electron correlation effects. These measurements are compared with the results of many-body calculations using Green's function and CI methods employing unpolarised as well as polarised wave functions. Momentum distributions, measured in both the outer and inner valence regions, are compared with calculations using a range of unpolarised and polarised wave functions. Computed orbital density maps in momentum and position space for oriented Cl2 molecules are discussed in comparison with the measured and calculated spherically averaged momentum distributions

  6. THE GENERALIZED RIEMANN PROBLEM FOR A SCALAR NONCONVEX COMBUSTION MODEL-THE PERTURBATION ON INITIAL BINDING ENERGY

    Institute of Scientific and Technical Information of China (English)

    Pan Lijun; Sheng Wancheng

    2012-01-01

    In this article,we study the generalized Riemann problem for a scalar nonconvex Chapman-Jouguet combustion model in a neighborhood of the origin (t > 0) on the (x,t) plane.We focus our attention to the perturbation on initial binding energy.The solutions are obtained constructively under the entropy conditions.It can be found that the solutions are essentially different from the corresponding Piemann solutions for some cases.Especially,two important phenomena are observed:the transition from detonation to deflagration followed by a shock,which appears in the numerical simulations [7,27]; the transition from deflagration to detonation (DDT),which is one of the core problems in gas dynamic combustion.

  7. Simulation investigations in the binding energy and mechanical properties of HMX-based polymer-bonded explosives

    Institute of Scientific and Technical Information of China (English)

    XIAO Jijun; FANG Guoyong; JI Guangfu; XIAO Heming

    2005-01-01

    The molecular simulations of the well-known high explosive β-HMX (cyclotetramethylene tetranitramine) and its fluorine containing polymer-bonded explosives (PBXs) were carried out with the combination method of quantum mechanics, molecular mechanics and molecular dynamics. The atomic cluster model, containing the β-HMX molecule and the polymer molecule whose chain dimension was about the same as β-HMX's, was fully optimized by AM1 and PM3 semi-empirical molecular orbital and molecular mechanical methods using COMPASS and PCFF force field. Then the calculated binding energy is found to be linearly correlated to each other. Molecular dynamics simulations using COMPASS force field were performed for β-HMX crystal and the PBXs involving β-HMX and a series of fluorine containing polymers. Their elastic coefficients, moduli and Poisson's ratios were calculated. It is found that the mechanical properties of β-HMX can be effectively improved by blending with fluorine containing polymers in small amounts.

  8. Binding energy shift in photoemission spectroscopy study of Ni clusters deposited on rutile TiO2 surfaces

    International Nuclear Information System (INIS)

    Cluster-size-dependent binding energy (BE) shifts of Ni 2p3/2 spectra in Ni clusters with respect to bulk Ni metal have been studied as a function of Ni coverage on clean rutile TiO2(0 0 1) surfaces at room temperature. Auger parameter (AP) analysis of photoelectron spectra has been employed and revealed an obvious initial state contribution at the coverage of 0.5 monolayers (ML). The initial state effect was demonstrated to be strongly affected by the substrate and was assigned to a combination of eigenvalue shift in surface core-level shift (SCLS) and charge transfer between the metal clusters and substrates. The TiO2(0 0 1) surface stoichiometry was found to introduce different charge transfer behaviors. Our results experimentally present that the Ni clusters are charged positively on stoichiomtric TiO2 surface and less positively or even negatively on various reduced surfaces.

  9. Exactly solvable tight-binding model on the RAN: fractal energy spectrum and Bose–Einstein condensation

    International Nuclear Information System (INIS)

    The Regularized Apollonian Network (RAN) is defined starting from a tetrahedral structure with four nodes all connected (generation 0). At any successive generations, new nodes are added and connected with the surrounding three nodes. As a result, a power-law cumulative distribution of connectivity P(k) ∝ 1/k η with η = ln(3)/ln(2) ≈ 1.585 is obtained. We initially consider a single-particle tight-binding model on the RAN. The eigenvalues of the Hamiltonian are exactly computed by a recursive approach for any size of the network. In the infinite size limit, the density of states and the cumulative distribution of states (integrated density of states) are also exactly determined. The relevant scaling behavior of the cumulative distribution close to the band bottom is shown to be a power law with an exponent depending on the spectral dimension and not on the dimension of the embedding space. We then consider a gas made by an infinite number of non-interacting bosons, each of them described by the tight-binding Hamiltonian on the RAN and we prove that, for sufficiently large bosonic density and sufficiently small temperature, a macroscopic fraction of the particles occupies the lowest single-particle energy state forming the Bose–Einstein condensate. Not only do we determine the transition temperature as a function of the bosonic density, but also the fraction of condensed particles, the fugacity, the energy and the specific heat for any temperature and bosonic density. (paper)

  10. On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study

    International Nuclear Information System (INIS)

    Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments

  11. On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Juanjuan [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); Kara, Abdelkader, E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Department of Physics, University of Central Florida, Orlando, Florida 32816 (United States); Pasquali, Luca [Dipartimento di Ingegneria “E. Ferrari,” Università di Modena e Reggio Emilia, Via Vignolese 905, 41125 Modena (Italy); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy); Department of Physics, University of Johannesburg, P.O. Box 524, Auckland Park 2006 (South Africa); Bendounan, Azzedine; Sirotti, Fausto [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette Cedex (France); Esaulov, Vladimir A., E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy)

    2015-09-14

    Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments.

  12. A New Determination of the Binding Energy of Atomic Oxygen on Dust Grain Surfaces: Experimental Results and Simulations

    CERN Document Server

    He, Jiao; Hopkins, Tyler; Vidali, Gianfranco; Kaufman, Michael J

    2015-01-01

    The energy to desorb atomic oxygen from an interstellar dust grain surface, $E_{\\rm des}$, is an important controlling parameter in gas-grain models; its value impacts the temperature range over which oxygen resides on a dust grain. However, no prior measurement has been done of the desorption energy. We report the first direct measurement of $E_{\\rm des}$ for atomic oxygen from dust grain analogs. The values of $E_{\\rm des}$ are $1660\\pm 60$~K and $1850\\pm 90$~K for porous amorphous water ice and for a bare amorphous silicate film, respectively, or about twice the value previously adopted in simulations of the chemical evolution of a cloud. We use the new values to study oxygen chemistry as a function of depth in a molecular cloud. For $n=10^4$ cm$^{-3}$ and $G_0$=10$^2$ ($G_0$=1 is the average local interstellar radiation field), the main result of the adoption of the higher oxygen binding energy is that H$_2$O can form on grains at lower visual extinction $A_{\\rm V}$, closer to the cloud surface. A higher ...

  13. Size-dependent stability toward dissociation and ligand binding energies of phosphine-ligated gold cluster ions

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Grant E.; Priest, Thomas A.; Laskin, Julia

    2014-01-01

    The stability of sub-nanometer size gold clusters ligated with organic molecules is of paramount importance to the scalable synthesis of monodisperse size-selected metal clusters with highly tunable chemical and physical properties. For the first time, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) equipped with surface induced dissociation (SID) has been employed to investigate the time and collision energy resolved fragmentation behavior of cationic doubly charged gold clusters containing 7-9 gold atoms and 6-7 triphenylphosphine (TPP) ligands prepared by reduction synthesis in solution. The TPP ligated gold clusters are demonstrated to fragment through three primary dissociation pathways: (1) Loss of a neutral TPP ligand from the precursor gold cluster, (2) asymmetric fission and (3) symmetric fission and charge separation of the gold core resulting in formation of complementary pairs of singly charged fragment ions. Threshold energies and activation entropies of these fragmentation pathways have been determined employing Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental SID data. It is demonstrated that the doubly charged cluster ion containing eight gold atoms and six TPP ligands, (8,6)2+, exhibits exceptional stability compared to the other cationic gold clusters examined in this study due to its large ligand binding energy of 1.76 eV. Our findings demonstrate the dramatic effect of the size and extent of ligation on the gas-phase stability and preferred fragmentation pathways of small TPP-ligated gold clusters.

  14. Accurate computations of the structures and binding energies of the imidazole⋯benzene and pyrrole⋯benzene complexes

    International Nuclear Information System (INIS)

    Highlights: • We have computed accurate binding energies of two NH⋯π hydrogen bonds. • We compare to results from dispersion-corrected density-functional theory. • A double-hybrid functional with explicit correlation has been proposed. • First results of explicitly-correlated ring-coupled-cluster theory are presented. • A double-hybrid functional with random-phase approximation is investigated. - Abstract: Using explicitly-correlated coupled-cluster theory with single and double excitations, the intermolecular distances and interaction energies of the T-shaped imidazole⋯benzene and pyrrole⋯benzene complexes have been computed in a large augmented correlation-consistent quadruple-zeta basis set, adding also corrections for connected triple excitations and remaining basis-set-superposition errors. The results of these computations are used to assess other methods such as Møller–Plesset perturbation theory (MP2), spin-component-scaled MP2 theory, dispersion-weighted MP2 theory, interference-corrected explicitly-correlated MP2 theory, dispersion-corrected double-hybrid density-functional theory (DFT), DFT-based symmetry-adapted perturbation theory, the random-phase approximation, explicitly-correlated ring-coupled-cluster-doubles theory, and double-hybrid DFT with a correlation energy computed in the random-phase approximation

  15. Accurate computations of the structures and binding energies of the imidazole⋯benzene and pyrrole⋯benzene complexes

    Energy Technology Data Exchange (ETDEWEB)

    Ahnen, Sandra; Hehn, Anna-Sophia [Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe (Germany); Vogiatzis, Konstantinos D. [Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe (Germany); Center for Functional Nanostructures, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Straße 1a, D-76131 Karlsruhe (Germany); Trachsel, Maria A.; Leutwyler, Samuel [Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern (Switzerland); Klopper, Wim, E-mail: klopper@kit.edu [Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe (Germany); Center for Functional Nanostructures, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Straße 1a, D-76131 Karlsruhe (Germany)

    2014-09-30

    Highlights: • We have computed accurate binding energies of two NH⋯π hydrogen bonds. • We compare to results from dispersion-corrected density-functional theory. • A double-hybrid functional with explicit correlation has been proposed. • First results of explicitly-correlated ring-coupled-cluster theory are presented. • A double-hybrid functional with random-phase approximation is investigated. - Abstract: Using explicitly-correlated coupled-cluster theory with single and double excitations, the intermolecular distances and interaction energies of the T-shaped imidazole⋯benzene and pyrrole⋯benzene complexes have been computed in a large augmented correlation-consistent quadruple-zeta basis set, adding also corrections for connected triple excitations and remaining basis-set-superposition errors. The results of these computations are used to assess other methods such as Møller–Plesset perturbation theory (MP2), spin-component-scaled MP2 theory, dispersion-weighted MP2 theory, interference-corrected explicitly-correlated MP2 theory, dispersion-corrected double-hybrid density-functional theory (DFT), DFT-based symmetry-adapted perturbation theory, the random-phase approximation, explicitly-correlated ring-coupled-cluster-doubles theory, and double-hybrid DFT with a correlation energy computed in the random-phase approximation.

  16. Binding energies and scattering observables in the $^{4}He_{3}$ atomic system

    CERN Document Server

    Motovilov, A K; Sofianos, S A; Kolganova, E A

    2001-01-01

    The $^4$He$_3$ bound states and the scattering of a $^4$He atom off a $^4$He dimer at ultra-low energies are investigated using a hard-core version of the Faddeev differential equations. Various realistic $^4$He-$^4$He interactions were employed, amomg them the LM2M2 potential by Aziz and Slaman and the recent TTY potential by Tang, Toennies and Yiu. The ground state and the excited (Efimov) state obtained are compared with other results. The scattering lengths and the atom-diatom phase shifts were calculated for center of mass energies up to 2.45 mK. It was found that the LM2M2 and TTY potentials, although of quite different structure, give practically the same bound-state and scattering results.

  17. Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes

    Science.gov (United States)

    Chu, Wen-Ting; Wang, Jin

    2016-06-01

    Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the “hot-spot” within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design.

  18. Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

    Energy Technology Data Exchange (ETDEWEB)

    Nakano, C. Masato [Flintridge Preparatory School, La Canada Flintridge, California 91011 (United States); Ma, Heng; Wei, Tao, E-mail: twei@lamar.edu [Dan F. Smith Department of Chemical Engineering, Lamar University, Beaumont, Texas 77710 (United States)

    2015-04-13

    Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the other hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.

  19. Effects of the atomic environment on the electron binding energies in samarium

    Czech Academy of Sciences Publication Activity Database

    Inoyatov, A. K.; Kovalík, Alojz; Filosofov, D. V.; Ryšavý, Miloš; Vénos, Drahoslav; Yushkevich, Y. V.; Perevoshchikov, L. L.; Zhdanov, V. S.

    2016-01-01

    Roč. 207, FEB (2016), s. 38-49. ISSN 0368-2048 R&D Projects: GA ČR(CZ) GAP203/12/1896; GA MŠk LG14004 Institutional support: RVO:61389005 Keywords : Sm-149 * atomic environment * electron ginding energy * intermediate-valence state * chemical shift * natural atomic level width Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.436, year: 2014

  20. A Simple Efficient Method for Obtaining the Binding Energy of Lithium Nucleus under the Hulth\\'en and Inversely Quadratic Yukawa Potentials

    CERN Document Server

    Salehi, Nasrin

    2015-01-01

    In this paper, the binding energy of Lithium nucleus in a nonrelativistic model is obtained for the Hulth\\'en and the Inversely Quadratic Yukawa Potential. In order to that, we used the concept of supersymmetry to solving the Schr\\"odinger equation exact analytically. These potentials, due to their physical interpretations, are of interest within many areas of theoretical physics. The results of our model for all calculations show that the ground state binding energy of Lithium nucleus with these potentials are very close to the ones obtained in experiments.

  1. Structure of the nucleotide-binding subunit B of the energy producer A1A0 ATP synthase in complex with adenosine diphosphate.

    Science.gov (United States)

    Kumar, Anil; Manimekalai, Malathy Sony Subramanian; Grüber, Gerhard

    2008-11-01

    A1A0 ATP synthases are the major energy producers in archaea. Like the related prokaryotic and eukaryotic F1F0 ATP synthases, they are responsible for most of the synthesis of adenosine triphosphate. The catalytic events of A1A0 ATP synthases take place inside the A3B3 hexamer of the A1 domain. Recently, the crystallographic structure of the nucleotide-free subunit B of Methanosarcina mazei Gö1 A1A0 ATP synthase has been determined at 1.5 A resolution. To understand more about the nucleotide-binding mechanism, a protocol has been developed to crystallize the subunit B-ADP complex. The crystallographic structure of this complex has been solved at 2.7 A resolution. The ADP occupies a position between the essential phosphate-binding loop and amino-acid residue Phe149, which are involved in the binding of the antibiotic efrapeptin in the related F1F0 ATP synthases. This trapped ADP location is about 13 A distant from its final binding site and is therefore called the transition ADP-binding position. In the trapped ADP position the structure of subunit B adopts a different conformation, mainly in its C-terminal domain and also in the final nucleotide-binding site of the central alphabeta-domain. This atomic model provides insight into how the substrate enters into the nucleotide-binding protein and thereby into the catalytic A3B3 domain. PMID:19020348

  2. Binding Energies and Scattering Observables in the 4^He_3 Atomic System

    OpenAIRE

    Motovilov, A. K.; Sandhas, W.; Sofianos, S. A.; Kolganova, E. A.

    1999-01-01

    The ^4He_3 bound states and the scattering of a ^4He atom off a ^4He dimer at ultra-low energies are investigated using a hard-core version of the Faddeev differential equations. Various realistic ^4He-^4He interactions were employed, amomg them the LM2M2 potential by Aziz and Slaman and the recent TTY potential by Tang, Toennies and Yiu. The ground state and the excited (Efimov) state obtained are compared with other results. The scattering lengths and the atom-diatom phase shifts were calcu...

  3. A self-interaction-free local hybrid functional: Accurate binding energies vis-\\`a-vis accurate ionization potentials from Kohn-Sham eigenvalues

    CERN Document Server

    Schmidt, Tobias; Makmal, Adi; Kronik, Leeor; Kümmel, Stephan

    2014-01-01

    We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potent...

  4. Derivation of binding energies on the basis of fundamental nuclear theory

    International Nuclear Information System (INIS)

    An attempt to assess the degree of consistency between the underlying ideas of two different approaches to nuclear energy relations is described. The fundamental approach in the form of density dependent Hartree-Fock theory, as well as the method of renormalizing shell model energies have both met with fair success. Whereas the former method is based on nuclear matter theory, the latter's central idea is to combine shell structure with an average liquid drop behaviour. The shell smoothing procedure employed there has been subject to intense theoretical study. Only little attention has been paid to the liquid drop aspect of the method. It is purposed to derive the liquid drop mass formula by means of a model force fitted to results of some nuclear matter calculations. Moreover, the force is tested by applying it to finite nuclei. Because of this, the present work could also be regarded as an attempt to find a very direct way of relating nuclear matter properties to those of finite nuclei. As the results in this respect are worse than expected, we conclude with a discussion of possible directions of improvement. (author)

  5. Binding energy and optical properties of an off-center hydrogenic donor impurity in a spherical quantum dot placed at the center of a cylindrical nano-wire

    Energy Technology Data Exchange (ETDEWEB)

    Safarpour, Gh., E-mail: safarpour.ghasem@gmail.com [Young Researchers and Elite Club, Shiraz Branch, Islamic Azad University, Shiraz (Iran, Islamic Republic of); Marvdasht Branch, Islamic Azad University, Marvdasht (Iran, Islamic Republic of); Barati, M. [Department of Physics, Science and Research Branch, Islamic Azad University, Fars (Iran, Islamic Republic of); Zamani, A. [Young Researchers and Elite Club, Zarghan Branch, Islamic Azad University, Zarghan (Iran, Islamic Republic of); Niknam, E. [Marvdasht Branch, Islamic Azad University, Marvdasht (Iran, Islamic Republic of)

    2014-01-15

    The binding energy as well as the linear, third-order nonlinear and total optical absorption coefficient and refractive index changes of an off-center hydrogenic donor impurity in an InAs spherical quantum dot placed at the center of a GaAs cylindrical nano-wire have been investigated. In this regard, the effective-mass approximation approach is considered and eigenvalues and corresponding eigenfunctions are calculated via the finite element method. The binding energy is plotted as a function of the dot size and impurity position along with optical properties as a function of photon energy. In this study two different directions have been considered for impurity position, along the nano-wire axis and perpendicular to it. It has been found that the binding energy, absorption coefficient and refractive index changes are impressively affected not only by the dot radius but also by the position of the impurity and its direction. Additionally, the optical saturation can be tuned by the direction of the impurity and incident optical intensity. -- Highlights: • We consider spherical quantum dot located at the center of a cylindrical nano-wire. • An off-center hydrogenic donor impurity is considered in the system. • Binding energy is affected by orientation of impurity and its distance from center. • Saturation depends on the orientation of impurity position. • By shifting impurity position, orientation and dot radius blue- and red-shifts appear.

  6. Binding energy and optical properties of an off-center hydrogenic donor impurity in a spherical quantum dot placed at the center of a cylindrical nano-wire

    International Nuclear Information System (INIS)

    The binding energy as well as the linear, third-order nonlinear and total optical absorption coefficient and refractive index changes of an off-center hydrogenic donor impurity in an InAs spherical quantum dot placed at the center of a GaAs cylindrical nano-wire have been investigated. In this regard, the effective-mass approximation approach is considered and eigenvalues and corresponding eigenfunctions are calculated via the finite element method. The binding energy is plotted as a function of the dot size and impurity position along with optical properties as a function of photon energy. In this study two different directions have been considered for impurity position, along the nano-wire axis and perpendicular to it. It has been found that the binding energy, absorption coefficient and refractive index changes are impressively affected not only by the dot radius but also by the position of the impurity and its direction. Additionally, the optical saturation can be tuned by the direction of the impurity and incident optical intensity. -- Highlights: • We consider spherical quantum dot located at the center of a cylindrical nano-wire. • An off-center hydrogenic donor impurity is considered in the system. • Binding energy is affected by orientation of impurity and its distance from center. • Saturation depends on the orientation of impurity position. • By shifting impurity position, orientation and dot radius blue- and red-shifts appear

  7. New measurements of the sticking coefficient and binding energy of molecules on non-porous amorphous solid water in the submonolayer regime

    Science.gov (United States)

    He, Jiao; Acharyya, Kinsuk; Emtiaz, S. M.; Vidali, Gianfranco

    2016-06-01

    Sticking and adsorption of molecules on dust grains are two important processes in gas-grain interactions. We accurately measured both the sticking coefficient and the binding energy of several key molecules on the surface of amorphous solid water as a function of coverage.A time-resolved scattering technique was used to measure sticking coefficient of H2, D2, N2, O2, CO, CH4, and CO2 on non-porous amorphous solid water (np-ASW) in the low coverage limit over a wide range of surface temperatures. We found that the time-resolved scattering technique is advantageous over the conventional King-Wells method that underestimates the sticking coefficient. Based on the measured values we suggest a useful general formula of the sticking coefficient as a function of grain temperature and molecule-surface binding energy.We measured the binding energy of N2, CO, O2, CH4, and CO2 on np-ASW, and of N2 and CO on porous amorphous solid water (p-ASW). We were able to measure binding energies down to a fraction of 1% of a layer, thus making these measurements more appropriate for astrochemistry than the existing values. We found that CO2 forms clusters on np-ASW surface even at very low coverage; this may help in explaining the segregation of CO2 in ices. The binding energies of N2, CO, O2, and CH4 on np-ASW decrease with coverage in the submonolayer regime. Their values in the low coverage limit are much higher than what is commonly used in gas-grain models. An empirical formula was used to describe the coverage dependence of the binding energies. We used the newly determined binding energy distributions in a simulation of gas-grain chemistry for cold dense clouds and hot core models. We found that owing to the higher value of desorption energy in the sub-monlayer regime a fraction of all these ices stays much longer and to higher temperature on the grain surface compared to the case using single value energies as currently done in astrochemical models.This work was supported in

  8. The Binding Energy, Spin-Excitation Gap, and Charged Gap in the Boson-Fermion Model

    Institute of Scientific and Technical Information of China (English)

    YANG Kai-Hua; TIAN Guang-Shan; HAN Ru-Qi

    2003-01-01

    In this paper, by applying a simplified version of Lieb 's spin-refleetion-positivity method, which was recentlydeveloped by one of us [G.S. Tian and J.G. Wang, J. Phys. A: Math. Gen. 35 (2002) 941], we investigate some generalproperties of the boson-fermion Hamiltonian, which has been widely used as a phenomenological model to describe thereal-space pairing of electrons. On a mathematically rigorous basis, we prove that for either negative or positive couplingV, which represents the spontaneous decay and recombination process between boson and fermion in the model, thepairing energy of electrons is nonzero. Furthermore, we also show that the spin-excitation gap of the boson-fermionHamiltonian is always larger than its charged gap, as predicted by the pre-paired electron theory.

  9. The Binding Energy, Spin-Excitation Gap, and Charged Gap in the Boson-Fermion Model

    Institute of Scientific and Technical Information of China (English)

    YANGKai-Hua; Guang-Shan; HANRu-Qi

    2003-01-01

    In this paper, by applying a simplified version of Lieb's spin-reflection-positivity method, which was recently developed by one of us [G.S. Tian and J.G. Wang, J. Phys. A: Math. Gen. 35 (2002) 941], we investigate some general properties of the boeon-fermion Hamiltonlan, which has been widely used as a phenomenological model to describe the real-space pairing of electrons. On a mathematically rigorous basis, we prove that for either negative or positive couping V, which represents the spontaneous decay and recombination process between boson and fermion in the model, the pairing energy of electrons is nonzero. Furthermore, we also show that the spin-excitation gap of the boson-fermion Hamiltonian is always larger than its charged gap, as predicted by the pre-palred electron theory.

  10. Mechanism of adenylate kinase. Is there a relationship between local substrate dynamics, local binding energy, and the catalytic mechanism?

    International Nuclear Information System (INIS)

    Adenylyl (β,γ-methylene)diphosphonic acid (AMPPCP) labeled with deuterium at the adenine ring ([8-2H]AMPPCP) and at the β,γ-methylene group (AMPPCD2P), as well as adenosine 5'-monophosphate labeled at the adenine ring ([8-2H]AMP), was synthesized and used for deuterium nuclear magnetic resonance (NMR) determination of effective correlation times (τc) of the free nucleotide and the complexes with adenylate kinase (AK). Extensive and rigorous control experiments and theoretical analysis were performed to justify the validity of the experimental approaches, particularly the fast exchange condition, and the reliability of the τc values obtained. For the free nucleotide, the results suggest that the phosphonate group of free AMPPCP possesses appreciable local mobility relative to the adenine ring and that complexation with Mg2+ greatly reduced such a local mobility. These results suggest that the adenine ring of substrates is rigidly bound in all cases, that the phosphonate chain of AMPPCP possesses considerable local mobility, and that Mg2+ reduces such local mobility but does not totally immobilize it. The results suggest that no general correlation exists between the local rigidity of portions of a bound substrate and the corresponding (ground state) local binding energy contributed by these portions. The authors have found that the Ki values for the mixture, the Δ isomer, and the Λ isomer of CrATP are 16, 11, and 20 μM, respectively, which suggest that ground-state binding by AK is stereochemically permissive. The results of both problems fully support the conclusion that the phosphonate chain of AK-MgAMPPCP possesses considerable local mobility and illuminate the relationship between the dynamics of bound substrates and the catalytic mechanism

  11. Comparison between the classical interaction energy and periodic Hartree-Fock binding energies for the interaction between molecules and surfaces

    International Nuclear Information System (INIS)

    The energetics of the H2O/MgO(001), HCl/MgO(001), and NH3/MgO(001) interface were investigated using the ab initio periodic Hartree-Fock LCAO method and a classical interaction energy model. The QM calculations treated a system that was periodic in two dimensions with the adsorbate approaching a three-layer slab of MgO(001). The authors used an approximation to the classical interaction energy, where the surface is represented by its potential, electric field, and electric field derivatives at the positions of the molecule center of mass, and the molecule is described by its charge, electric dipole, electric quadrupole and polarizability. The potential, electric field and electric field gradient are obtained for the clean three-layer slab using the ab initio periodic Hartree-Fock LCAO method (CRYSTAL) and an optimized split valence basis 8-61G on Mg and 8-51G on O. The charge, electric dipole, and electric quadrupole are calculated using ab initio Hartree-Fock theory (GAUSSIAN-92) with a 6-31G* basis set while the SCF polarizability is determined analytically using the same basis set

  12. What can be learned from binding energy differences about nuclear structure: The example of δVpn

    International Nuclear Information System (INIS)

    We perform an analysis of a binding energy difference called δVpn(N,Z)≡-(1/4)[E(Z,N)-E(Z,N-2)-E(Z-2,N)+E(Z-2,N-2)] in the framework of a realistic nuclear model. It has been suggested that δVpn values provide a sensitive probe of nuclear structure, and it has been put forward as a primary motivation for the measurement of specific nuclear masses. Using the angular momentum and particle-number projected generator coordinate method and the Skyrme interaction SLy4, we analyze the contribution brought to δVpn by static deformation and dynamic fluctuations around the mean-field ground state. Our method gives a good overall description of δVpn throughout the chart of nuclei with the exception of the anomaly related to the Wigner energy along the N=Z line. The main conclusions of our analysis of δVpn, which are at variance with its standard interpretation, are that (i) the structures seen in the systematics of δVpn throughout the chart of nuclei can be easily explained combining a smooth background related to the symmetry energy and correlation energies due to deformation and collective fluctuations, (ii) the characteristic pattern of δVpn having a much larger size for nuclei that add only particles or only holes to a doubly magic nucleus than for nuclei that add particles for one nucleon species and holes for the other is a trivial consequence of the asymmetric definition of δVpn and not due to a the different structure of these nuclei, (iii) δVpn does not provide a very reliable indicator for structural changes, (iv)δVpn does not provide a reliable measure of the proton-neutron interaction in the nuclear energy density functional (EDF) or of that between the last filled orbits or of the one summed over all orbits, and (v) δVpn does not provide a conclusive benchmark for nuclear EDF methods that is superior or complementary to other mass filters such as two-nucleon separation energies or Q values.

  13. Diels-Alder addition of some 6-and 5-member ring aromatic compounds on the Si(001)-2×1 surface: dependence of the binding energy on the resonance energy of the aromatic compounds

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An energy decomposition scheme is proposed for understanding of the relative lowbinding energy of the [4+2] cycloaddition of benzene on the Si(001)-2×1 surface. By means ofdensity functional cluster model calculations, this scheme is demonstrated to be applicable tosome other 6-and 5-member ring aromatic compounds, giving a trend that the binding energy ofthe [4+2] cycloaddition products of those aromatic compounds on the Si(001) surface dependsstrongly on their resonance energy.

  14. Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.

    Directory of Open Access Journals (Sweden)

    Yuzhen Niu

    Full Text Available As a promising target for the treatment of lung cancer, the MutT Homolog 1 (MTH1 protein can be inhibited by crizotinib. A recent work shows that the inhibitory potency of (S-crizotinib against MTH1 is about 20 times over that of (R-crizotinib. But the detailed molecular mechanism remains unclear. In this study, molecular dynamics (MD simulations and free energy calculations were used to elucidate the mechanism about the effect of chirality of crizotinib on the inhibitory activity against MTH1. The binding free energy of (S-crizotinib predicted by the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA and Adaptive biasing force (ABF methodologies is much lower than that of (R-crizotinib, which is consistent with the experimental data. The analysis of the individual energy terms suggests that the van der Waals interactions are important for distinguishing the binding of (S-crizotinib and (R-crizotinib. The binding free energy decomposition analysis illustrated that residues Tyr7, Phe27, Phe72 and Trp117 were important for the selective binding of (S-crizotinib to MTH1. The adaptive biasing force (ABF method was further employed to elucidate the unbinding process of (S-crizotinib and (R-crizotinib from the binding pocket of MTH1. ABF simulation results suggest that the reaction coordinates of the (S-crizotinib from the binding pocket is different from (R-crizotinib. The results from our study can reveal the details about the effect of chirality on the inhibition activity of crizotinib to MTH1 and provide valuable information for the design of more potent inhibitors.

  15. Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin

    International Nuclear Information System (INIS)

    Multidimensional potential energy surfaces based on reproducing kernel-interpolation are employed to explore the energetics and dynamics of free and bound nitric oxide in myoglobin (Mb). Combining a force field description for the majority of degrees of freedom and the higher-accuracy representation for the NO ligand and the Fe out-of-plane motion allows for a simulation approach akin to a mixed quantum mechanics/molecular mechanics treatment. However, the kernel-representation can be evaluated at conventional force-field speed. With the explicit inclusion of the Fe-out-of-plane (Fe-oop) coordinate, the dynamics and structural equilibrium after photodissociation of the ligand are correctly described compared to experiment. Experimentally, the Fe-oop coordinate plays an important role for the ligand dynamics. This is also found here where the isomerization dynamics between the Fe–ON and Fe–NO state is significantly affected whether or not this co-ordinate is explicitly included. Although the Fe–ON conformation is metastable when considering only the bound 2A state, it may disappear once the 4A state is included. This explains the absence of the Fe–ON state in previous experimental investigations of MbNO

  16. Binding Energy of Ionized-Donor-Bound Excitons in the GaAs-AlxGa1-xAs Quantum Wells

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-Jun; ZHANG Shu-Fang; KONG Xiao-Jun; LI Shu-Shen

    2000-01-01

    The binding energy of an exciton bound to anionized donor impurity (D+, X) located at the center or the edgein GaAs-AlxGa1-xAs quantum wells is calculated variationally for the well width from 10 to 300 A by using atwo-parameter wave function, The theoretical results are discussed and compared with the previous experimentalresults.

  17. Binding energies of impurity states in strained wurtzite GaN/AlxGa1−xN heterojunctions with finitely thick potential barriers

    International Nuclear Information System (INIS)

    Ground state binding energies of donor impurities in a strained wurtzite GaN/AlxGa1−xN heterojunction with a potential barrier of finite thickness are investigated using a variational approach combined with a numerical computation. The built-in electric field due to the spontaneous and piezoelectric polarization, the strain modification due to the lattice mismatch near the interfaces, and the effects of ternary mixed crystals are all taken into account. It is found that the binding energies by using numerical wave functions are obviously greater than those by using variational wave functions when impurities are located in the channel near the interface of a heterojunction. Nevertheless, the binding energies using the former functions are obviously less than using the later functions when impurities are located in the channel far from an interface. The difference between our numerical method and the previous variational method is huge, showing that the former should be adopted in further work for the relevant problems. The binding energies each as a function of hydrostatic pressure are also calculated. But the change is unobvious in comparison with that obtained by the variational method

  18. Relativistic correlation correction to the binding energies of the ground configuration of Beryllium-like, Neon-like, Magnesium-like and Argon-like ions

    CERN Document Server

    Santos, J P; Marques, J P; Parente, F; Desclaux, J P; Indelicato, P J; Rodriges, Gustavo C.; Marques, Jos\\'{e} P.; Desclaux, Jean-Paul; Indelicato, Paul

    2005-01-01

    Total electronic correlation correction to the binding energies of the isoelectronic series of Beryllium, Neon, Magnesium and Argon, are calculated in the framework of relativistic multiconfiguration Dirac-Fock method. Convergence of the correlation energies is studied as the active set of orbitals is increased. The Breit interaction is treated fully self-consistently. The final results can be used in the accurately determination of atomic masses from highly charged ions data obtained in Penning-trap experiments.

  19. Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

    OpenAIRE

    Fernandez Pacios, Luis; Gomez Casado, Cristina; Tordesillas Villuendas, Leticia; Palacín Gómez, Aranzazu; Sanchez-Monge Laguna De Rins, Maria Rosa; Díaz Perales, Araceli

    2012-01-01

    Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a co...

  20. First-principles investigation on the electronic efficiency and binding energy of the contacts formed by graphene and poly-aromatic hydrocarbon anchoring groups

    International Nuclear Information System (INIS)

    The electronic efficiency and binding energy of contacts formed between graphene electrodes and poly-aromatic hydrocarbon (PAH) anchoring groups have been investigated by the non-equilibrium Green’s function formalism combined with density functional theory. Our calculations show that PAH molecules always bind in the interior and at the edge of graphene in the AB stacking manner, and that the binding energy increases following the increase of the number of carbon and hydrogen atoms constituting the PAH molecule. When we move to analyzing the electronic transport properties of molecular junctions with a six-carbon alkyne chain as the central molecule, the electronic efficiency of the graphene-PAH contacts is found to depend on the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the corresponding PAH anchoring group, rather than its size. To be specific, the smaller is the HOMO-LUMO gap of the PAH anchoring group, the higher is the electronic efficiency of the graphene-PAH contact. Although the HOMO-LUMO gap of a PAH molecule depends on its specific configuration, PAH molecules with similar atomic structures show a decreasing trend for their HOMO-LUMO gap as the number of fused benzene rings increases. Therefore, graphene-conjugated molecule-graphene junctions with high-binding and high-conducting graphene-PAH contacts can be realized by choosing appropriate PAH anchor groups with a large area and a small HOMO-LUMO gap

  1. Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA.

    Science.gov (United States)

    Carra, Claudio; Cucinotta, Francis A

    2012-06-01

    The eukaryotic replication protein A (RPA) has several pivotal functions in the cell metabolism, such as chromosomal replication, prevention of hairpin formation, DNA repair and recombination, and signaling after DNA damage. Moreover, RPA seems to have a crucial role in organizing the sequential assembly of DNA processing proteins along single stranded DNA (ssDNA). The strong RPA affinity for ssDNA, K(A) between 10(-9)-10(-10) M, is characterized by a low cooperativity with minor variation for changes on the nucleotide sequence. Recently, new data on RPA interactions was reported, including the binding free energy of the complex RPA70AB with dC(8) and dC(5), which has been estimated to be -10 ± 0.4 kcal mol(-1) and -7 ± 1 kcal mol(-1), respectively. In view of these results we performed a study based on molecular dynamics aimed to reproduce the absolute binding free energy of RPA70AB with the dC(5) and dC(8) oligonucleotides. We used several tools to analyze the binding free energy, rigidity, and time evolution of the complex. The results obtained by MM-PBSA method, with the use of ligand free geometry as a reference for the receptor in the separate trajectory approach, are in excellent agreement with the experimental data, with ±4 kcal mol(-1) error. This result shows that the MM-PB(GB)SA methods can provide accurate quantitative estimates of the binding free energy for interacting complexes when appropriate geometries are used for the receptor, ligand and complex. The decomposition of the MM-GBSA energy for each residue in the receptor allowed us to correlate the change of the affinity of the mutated protein with the ΔG(gas+sol) contribution of the residue considered in the mutation. The agreement with experiment is optimal and a strong change in the binding free energy can be considered as the dominant factor in the loss for the binding affinity resulting from mutation. PMID:22116609

  2. Thickness-Dependent Binding Energy Shift in Few-Layer MoS2 Grown by Chemical Vapor Deposition.

    Science.gov (United States)

    Lin, Yu-Kai; Chen, Ruei-San; Chou, Tsu-Chin; Lee, Yi-Hsin; Chen, Yang-Fang; Chen, Kuei-Hsien; Chen, Li-Chyong

    2016-08-31

    The thickness-dependent surface states of MoS2 thin films grown by the chemical vapor deposition process on the SiO2-Si substrates are investigated by X-ray photoelectron spectroscopy. Raman and high-resolution transmission electron microscopy suggest the thicknesses of MoS2 films to be ranging from 3 to 10 layers. Both the core levels and valence band edges of MoS2 shift downward ∼0.2 eV as the film thickness increases, which can be ascribed to the Fermi level variations resulting from the surface states and bulk defects. Grainy features observed from the atomic force microscopy topographies, and sulfur-vacancy-induced defect states illustrated at the valence band spectra imply the generation of surface states that causes the downward band bending at the n-type MoS2 surface. Bulk defects in thick MoS2 may also influence the Fermi level oppositely compared to the surface states. When Au contacts with our MoS2 thin films, the Fermi level downshifts and the binding energy reduces due to the hole-doping characteristics of Au and easy charge transfer from the surface defect sites of MoS2. The shift of the onset potentials in hydrogen evolution reaction and the evolution of charge-transfer resistances extracted from the impedance measurement also indicate the Fermi level varies with MoS2 film thickness. The tunable Fermi level and the high chemical stability make our MoS2 a potential catalyst. The observed thickness-dependent properties can also be applied to other transition-metal dichalcogenides (TMDs), and facilitates the development in the low-dimensional electronic devices and catalysts. PMID:27488185

  3. How Similar Are Protein Folding and Protein Binding Nuclei? Examination of Vibrational Motions of Energy Hot Spots and Conserved Residues

    OpenAIRE

    Haliloglu, Turkan; Keskin, Ozlem; Ma, Buyong; Nussinov, Ruth

    2004-01-01

    The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and experimental hot spots at intermolecular binding interfaces overlap residues that vibrate with high frequencies. Similarly, conserved residues and hot spots are found in protein cores and are also observed to vibrate with high frequencies. In both cases, these residues contribute significantly to t...

  4. Size dependent 2p3/2 binding-energy shift of Ni nanoclusters on SiO2 support: Skin-depth local strain and quantum trapping

    International Nuclear Information System (INIS)

    An in situ X-ray photoelectron emission investigation revealed that the size trend of the 2p3/2 binding-energy shift (BES) of Ni nanoclusters grown on SiO2 substrate follows the prediction of the bond order-length-strength (BOLS) correlation theory . Theoretical reproduction of the measurements turns out that the 2p3/2 binding energy of an isolated Ni atom is 850.51 eV and its intrinsic bulk shift is 2.70 eV. Findings confirmed that the skin-depth local strain and potential well quantum trapping induced by the shorter and stronger bonds between under-coordinated surface atoms provide perturbation to the Hamiltonian and hence dominate the size dependent BES.

  5. Effects of hydrostatic pressure on the donor binding energy and intra donor transition matrix elements in GaAs-GaAlAs quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Panahi, H. [Institutes for Studies in Theoretical Physics and Mathematics, Tehran 19395-1795 (Iran); Maleki, M. [Department of Physics, University of Guilan, Rasht 41335-1914 (Iran)

    2008-05-15

    The effects of hydrostatic pressure on the donor binding energy in GaAs-Ga{sub 0.7}Al{sub 0.3}As quantum wells have been studied in the effective mass approximation, using a variational approach for hydrogenic ground state 1s and excited states 2s, 2p{sub x}, 3p{sub x}. Results obtained show that the donor binding energy variation with the well width and the position of impurity under pressure is similar to that without pressure. The intra donor squared transition matrix elements are calculated as functions of impurity position in the presence of hydrostatic pressure. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  6. Binding energy of a holographic deuteron and tritium in anti-de-Sitter space/conformal field theory (AdS/CFT)

    CERN Document Server

    Pahlavani, M R; Morad, R

    2013-01-01

    In the large 't Hooft coupling limit, the hadronic size of baryon is small and nucleon-nucleon potential is obtained from massless pseudo-scalar exchanges and an infinite tower of spin one mesons exchanges. In this paper we use the holographic nucleon-nucleon interaction and obtain the corresponding potential and binding energy for deuteron and tritium nuclei. The obtained potentials are repulsive at short distances and clearly become zero by increasing distance as we expected.

  7. THEORETICAL-ANALYSIS OF THE O(1S) BINDING-ENERGY SHIFTS IN ALKALINE-EARTH OXIDES - CHEMICAL OR ELECTROSTATIC CONTRIBUTIONS

    NARCIS (Netherlands)

    PACCHIONI, G; BAGUS, PS

    1994-01-01

    We report results from ab initio cluster-model calculations on the O(1s) binding energy (BE) in the alkaline-earth oxides, MgO, CaO, SrO, and BaO; all these oxides have a cubic lattice structure. We have obtained values for both the initial- and final-state BE's. A simple point-charge model, where a

  8. Binding energy of a holographic deuteron and tritium in anti-de-Sitter space/conformal field theory (AdS/CFT)

    International Nuclear Information System (INIS)

    In the large 't Hooft coupling limit, the hadronic size of baryon is small and the nucleon-nucleon potential is obtained from massless pseudoscalar exchanges and an infinite tower of spin-one mesons exchanges. In this article we use the holographic nucleon-nucleon interaction and obtain the corresponding potential and binding energy for deuteron and tritium nuclei. The obtained potentials are repulsive at short distances and clearly become zero by increasing the distance as we expected.

  9. Binding Energies of the pi-Stacked Anisole Dimer: New Molecular Beam-Laser Spectroscopy Experiments and CCSD(T) Calculations

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Nachtigallová, Dana; Mazzoni, F.; Pasquini, M.; Pietraperzia, G.; Becucci, M.; Müller-Dethlefs, K.; Hobza, Pavel

    2015-01-01

    Roč. 21, č. 18 (2015), s. 6740-6746. ISSN 0947-6539 R&D Projects: GA ČR GBP208/12/G016 Grant ostatní: GA MŠk(CZ) ED2.1.00/03.0058 Institutional support: RVO:61388963 Keywords : binding energy * noncovalent interactions * pi stacking * laser spectroscopy * CCSD(T) calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.731, year: 2014

  10. Observation of core-level binding energy shifts between (100) surface and bulk atoms of epitaxial CuInSe2

    International Nuclear Information System (INIS)

    Core-level and valence band photoemission from semiconductors has been shown to exhibit binding energy differences between surface atoms and bulk atoms, thus allowing one to unambiguously distinguish between the two atomic positions. Quite clearly, surface atoms experience a potential different from the bulk due to the lower coordination number - a characteristic feature of any surface is the incomplete atomic coordination. Theoretical accounts of this phenomena are well documented in the literature for III-V and II-VI semiconductors. However, surface state energies corresponding to the equilibrium geometry of (100) and (111) surfaces of Cu-based ternary chalcopyrite semiconductors have not been calculated or experimental determined. These compounds are generating great interest for optoelectronic and photovoltaic applications, and are an isoelectronic analog of the II-VI binary compound semiconductors. Surface core-level binding energy shifts depend on the surface cohesive energies, and surface cohesive energies are related to surface structure. For ternary compound semiconductor surfaces, such as CuInSe2, one has the possibility of variations in surface stoichiometry. Applying standard thermodynamical calculations which consider the number of individual surface atoms and their respective chemical potentials should allow one to qualitatively determine the magnitude of surface core-level shifts and, consequently, surface state energies

  11. Observation of core-level binding energy shifts between (100) surface and bulk atoms of epitaxial CuInSe{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, A.J. [Colorado School of Mines, Golden, CO (United States); Berry, G.; Rockett, A. [Univ. of Illinois, Urbana-Champaign, IL (United States)] [and others

    1997-04-01

    Core-level and valence band photoemission from semiconductors has been shown to exhibit binding energy differences between surface atoms and bulk atoms, thus allowing one to unambiguously distinguish between the two atomic positions. Quite clearly, surface atoms experience a potential different from the bulk due to the lower coordination number - a characteristic feature of any surface is the incomplete atomic coordination. Theoretical accounts of this phenomena are well documented in the literature for III-V and II-VI semiconductors. However, surface state energies corresponding to the equilibrium geometry of (100) and (111) surfaces of Cu-based ternary chalcopyrite semiconductors have not been calculated or experimental determined. These compounds are generating great interest for optoelectronic and photovoltaic applications, and are an isoelectronic analog of the II-VI binary compound semiconductors. Surface core-level binding energy shifts depend on the surface cohesive energies, and surface cohesive energies are related to surface structure. For ternary compound semiconductor surfaces, such as CuInSe{sub 2}, one has the possibility of variations in surface stoichiometry. Applying standard thermodynamical calculations which consider the number of individual surface atoms and their respective chemical potentials should allow one to qualitatively determine the magnitude of surface core-level shifts and, consequently, surface state energies.

  12. Vacuum Referred Binding Energy of the Single 3d, 4d, or 5d Electron in Transition Metal and Lanthanide Impurities in Compounds

    OpenAIRE

    Rogers, E.G.; Dorenbos, P.

    2014-01-01

    The vacuum referred binding energy (VRBE) of the single electron in the lowest energy 3d level of Sc2 +, V4 +, Cr5 +, the lowest 4d level of Y2 +, Zr3 +, Nb4 +, Mo5 + and the lowest 5d level of Ta4 +, and W5 + in various compounds are determined by means of the chemical shift model. They will be compared with the VRBE in the already established lowest 3d level of Ti3 + and the lowest 5d level of Eu2 + and Ce3 +. Clear trends with changing charge of the transition metal (TM) cation and with ch...

  13. Relativistic correlation correction to the binding energies of the ground configuration of beryllium-like, neon-like, magnesium-like and argon-like ions

    International Nuclear Information System (INIS)

    Total electronic correlation corrections to the binding energies of the isoelectronic series of beryllium, neon, magnesium and argon, are calculated in the framework of relativistic multiconfiguration Dirac-Fock method. Convergence of the correlation energies is studied as the active set of orbitals is increased. The Breit interaction is treated fully self-consistently. We have shown that accurate results can be achieved if excitations to all shells up to the n = 6 shell are included. The final results can be used in the accurately determination of atomic masses from highly charged ions data obtained in Penning-trap experiments

  14. A combination of 3D-QSAR, docking, local-binding energy (LBE) and GRID study of the species differences in the carcinogenicity of benzene derivatives chemicals.

    Science.gov (United States)

    Fratev, Filip; Benfenati, Emilio

    2008-09-01

    A combination of 3D-QSAR, docking, local-binding energy (LBE) and GRID methods was applied as a tool to study and predict the mechanism of action of 100 carcinogenic benzene derivatives. Two 3D-QSAR models were obtained: (i) model of mouse carcinogenicity on the basis of 100 chemicals (model 1) and (ii) model of the differences in mouse and rat carcinogenicity on the basis of 73 compounds (model 2). 3D-QSAR regression maps indicated the important differences in species carcinogenicity, and the molecular positions associated with them. In order to evaluate the role of P450 metabolic process in carcinogenicity, the following approaches were used. The 3D models of CYP2E1 for mouse and rat were built up. A docking study was applied and the important ligand-protein residues interactions and oxidation positions of the molecules were identified. A new approach for quantitative assessment of metabolism pathways was developed, which enabled us to describe the species differences in CYP2E1 metabolism, and how it can be related to differences in the carcinogenic potential for a subset of compounds. The binding energies of the important substituents (local-binding energy-LBE) were calculated, in order to quantitatively demonstrate the contribution of the substituents in metabolic processes. Furthermore, a computational procedure was used for determining energetically favourable binding sites (GRID examination) of the enzymes. The GRID procedure allowed the identification of some important differences, related to species metabolism in CYP2E1. Comparing GRID, 3D-QSAR maps and LBE results, a similarity was identified, indicating a relationship between P450 metabolic processes and the differences in the carcinogenicity. PMID:18495507

  15. First-principles investigation on the electronic efficiency and binding energy of the contacts formed by graphene and poly-aromatic hydrocarbon anchoring groups

    KAUST Repository

    Li, Yang

    2015-04-28

    © 2015 AIP Publishing LLC. The electronic efficiency and binding energy of contacts formed between graphene electrodes and poly-aromatic hydrocarbon (PAH) anchoring groups have been investigated by the non-equilibrium Green\\'s function formalism combined with density functional theory. Our calculations show that PAH molecules always bind in the interior and at the edge of graphene in the AB stacking manner, and that the binding energy increases following the increase of the number of carbon and hydrogen atoms constituting the PAH molecule. When we move to analyzing the electronic transport properties of molecular junctions with a six-carbon alkyne chain as the central molecule, the electronic efficiency of the graphene-PAH contacts is found to depend on the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the corresponding PAH anchoring group, rather than its size. To be specific, the smaller is the HOMO-LUMO gap of the PAH anchoring group, the higher is the electronic efficiency of the graphene-PAH contact. Although the HOMO-LUMO gap of a PAH molecule depends on its specific configuration, PAH molecules with similar atomic structures show a decreasing trend for their HOMO-LUMO gap as the number of fused benzene rings increases. Therefore, graphene-conjugated molecule-graphene junctions with high-binding and high-conducting graphene-PAH contacts can be realized by choosing appropriate PAH anchor groups with a large area and a small HOMO-LUMO gap.

  16. Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies

    Directory of Open Access Journals (Sweden)

    Stegmaier Philip

    2010-05-01

    Full Text Available Abstract Background Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription factors in the literature, however, for many of them the corresponding DNA-binding motifs remain uncharacterized. Results The position weight matrices (PWMs of transcription factors from different structural classes have been determined using a knowledge-based statistical potential. The scoring function calibrated against crystallographic data on protein-DNA contacts recovered PWMs of various members of widely studied transcription factor families such as p53 and NF-κB. Where it was possible, extensive comparison to experimental binding affinity data and other physical models was made. Although the p50p50, p50RelB, and p50p65 dimers belong to the same family, particular differences in their PWMs were detected, thereby suggesting possibly different in vivo binding modes. The PWMs of p63 and p73 were computed on the basis of homology modeling and their performance was studied using upstream sequences of 85 p53/p73-regulated human genes. Interestingly, about half of the p63 and p73 hits reported by the Match algorithm in the altogether 126 promoters lay more than 2 kb upstream of the corresponding transcription start sites, which deviates from the common assumption that most regulatory sites are located more proximal to the TSS. The fact that in most of the cases the binding sites of p63 and p73 did not overlap with the p53 sites suggests that p63 and p73 could influence the p53 transcriptional activity cooperatively. The newly computed p50p50 PWM recovered 5 more experimental binding sites than the corresponding TRANSFAC matrix, while both PWMs showed comparable receiver operator characteristics. Conclusions A novel algorithm was developed to calculate position weight matrices from protein-DNA complex structures. The proposed algorithm was extensively validated

  17. Quarkonium Binding and Entropic Force

    CERN Document Server

    Satz, Helmut

    2015-01-01

    A Q-Qbar bound state represents a balance between repulsive kinetic and attractive potential energy. In a hot quark-gluon plasma, the interaction potential experiences medium effects. Color screening modifies the attractive binding force between the quarks, while the increase of entropy with Q-Qbar separation gives rise to a growing repulsion. We study the role of these phenomena for in-medium Q-Qbar binding and dissociation. It is found that the relevant potential for Q-Qbar binding is the free energy F; with increasing Q-Qbar separation, further binding through the internal energy U is compensated by repulsive entropic effects.

  18. Binding Procurement

    Science.gov (United States)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  19. Proton-bound dimers of nitrogen heterocyclic molecules: Substituent effects on the structures and binding energies of homodimers of diazine, triazine, and fluoropyridine

    International Nuclear Information System (INIS)

    The bonding energies of proton-bound homodimers BH+B were measured by ion mobility equilibrium studies and calculated at the DFT B3LYP/6-311++G** level, for a series of nitrogen heterocyclic molecules (B) with electron-withdrawing in-ring N and on-ring F substituents. The binding energies (ΔH°dissoc) of the proton-bound dimers (BH+B) vary significantly, from 29.7 to 18.1 kcal/mol, decreasing linearly with decreasing the proton affinity of the monomer (B). This trend differs significantly from the constant binding energies of most homodimers of other organic nitrogen and oxygen bases. The experimentally measured ΔH°dissoc for (1,3-diazine)2H+, i.e., (pyrimidine)2H+ and (3-F-pyridine)2H+ are 22.7 and 23.0 kcal/mol, respectively. The measured ΔH°dissoc for the pyrimidine·+(3-F-pyridine) radical cation dimer (19.2 kcal/mol) is signifcantly lower than that of the proton-bound homodimers of pyrimidine and 3-F-pyridine, reflecting the stronger interaction in the ionic H-bond of the protonated dimers. The calculated binding energies for (1,2-diazine)2H+, (pyridine)2H+, (2-F-pyridine)2H+, (3-F-pyridine)2H+, (2,6-di-F-pyridine)2H+, (4-F-pyridine)2H+, (1,3-diazine)2H+, (1,4-diazine)2H+, (1,3,5-triazine)2H+, and (pentafluoropyridine)2H+ are 29.7, 24.9, 24.8, 23.3, 23.2, 23.0, 22.4, 21.9, 19.3, and 18.1 kcal/mol, respectively. The electron-withdrawing substituents form internal dipoles whose electrostatic interactions contribute to both the decreased proton affinities of (B) and the decreased binding energies of the protonated dimers BH+B. The bonding energies also vary with rotation about the hydrogen bond, and they decrease in rotamers where the internal dipoles of the components are aligned efficiently for inter-ring repulsion. For compounds substituted at the 3 or 4 (meta or para) positions, the lowest energy rotamers are T-shaped with the planes of the two rings rotated by 90° about the hydrogen bond, while the planar rotamers are weakened by repulsion between the

  20. Proton-bound dimers of nitrogen heterocyclic molecules: Substituent effects on the structures and binding energies of homodimers of diazine, triazine, and fluoropyridine

    Energy Technology Data Exchange (ETDEWEB)

    Attah, Isaac K.; Platt, Sean P.; Meot-Ner, Michael; El-Shall, M. S., E-mail: mselshal@vcu.edu [Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006 (United States); Aziz, Saadullah G.; Alyoubi, Abdulrahman O. [Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589 (Saudi Arabia)

    2014-03-21

    The bonding energies of proton-bound homodimers BH{sup +}B were measured by ion mobility equilibrium studies and calculated at the DFT B3LYP/6-311++G{sup **} level, for a series of nitrogen heterocyclic molecules (B) with electron-withdrawing in-ring N and on-ring F substituents. The binding energies (ΔH°{sub dissoc}) of the proton-bound dimers (BH{sup +}B) vary significantly, from 29.7 to 18.1 kcal/mol, decreasing linearly with decreasing the proton affinity of the monomer (B). This trend differs significantly from the constant binding energies of most homodimers of other organic nitrogen and oxygen bases. The experimentally measured ΔH°{sub dissoc} for (1,3-diazine){sub 2}H{sup +}, i.e., (pyrimidine){sub 2}H{sup +} and (3-F-pyridine){sub 2}H{sup +} are 22.7 and 23.0 kcal/mol, respectively. The measured ΔH°{sub dissoc} for the pyrimidine{sup ·+}(3-F-pyridine) radical cation dimer (19.2 kcal/mol) is signifcantly lower than that of the proton-bound homodimers of pyrimidine and 3-F-pyridine, reflecting the stronger interaction in the ionic H-bond of the protonated dimers. The calculated binding energies for (1,2-diazine){sub 2}H{sup +}, (pyridine){sub 2}H{sup +}, (2-F-pyridine){sub 2}H{sup +}, (3-F-pyridine){sub 2}H{sup +}, (2,6-di-F-pyridine){sub 2}H{sup +}, (4-F-pyridine){sub 2}H{sup +}, (1,3-diazine){sub 2}H{sup +}, (1,4-diazine){sub 2}H{sup +}, (1,3,5-triazine){sub 2}H{sup +}, and (pentafluoropyridine){sub 2}H{sup +} are 29.7, 24.9, 24.8, 23.3, 23.2, 23.0, 22.4, 21.9, 19.3, and 18.1 kcal/mol, respectively. The electron-withdrawing substituents form internal dipoles whose electrostatic interactions contribute to both the decreased proton affinities of (B) and the decreased binding energies of the protonated dimers BH{sup +}B. The bonding energies also vary with rotation about the hydrogen bond, and they decrease in rotamers where the internal dipoles of the components are aligned efficiently for inter-ring repulsion. For compounds substituted at the 3 or 4

  1. Binding energies from diffusion Monte Carlo for the MB-pol H2O and D2O dimer: A comparison to experimental values

    International Nuclear Information System (INIS)

    The diffusion Monte Carlo (DMC) method is applied to compute the ground state energies of the water monomer and dimer and their D2O isotopomers using MB-pol; the most recent and most accurate ab inito-based potential energy surface (PES). MB-pol has already demonstrated excellent agreement with high level electronic structure data, as well as agreement with some experimental, spectroscopic, and thermodynamic data. Here, the DMC binding energies of (H2O)2 and (D2O)2 agree with the corresponding values obtained from velocity map imaging within, respectively, 0.01 and 0.02 kcal/mol. This work adds two more valuable data points that highlight the accuracy of the MB-pol PES

  2. Binding Energies from Diffusion Monte Carlo for the MB-pol H_2O and D_2O Dimer: A Comparison to Experimental Values

    CERN Document Server

    Mallory, Joel

    2015-01-01

    The Diffusion Monte Carlo (DMC) method is applied to compute the ground state energies of the water monomer and dimer and their D 2 O isotopomers using MB-pol; the most recent and most accurate ab inito- based potential energy surface (PES). MB-pol has already demonstrated excellent agreement with high level electronic structure data, as well as agreement with some experimental, spectroscopic, and thermodynamic data. Here, the DMC binding energies of (H 2 O) 2 and (D 2 O) 2 agree with the corresponding values obtained from velocity map imaging within, respectively, 0.01 and 0.02 kcal/mol. This work adds two more valuable data points that highlight the accuracy of the MB-pol PES.

  3. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method

    OpenAIRE

    Marharyta Petukh; Minghui Li; Emil Alexov

    2015-01-01

    Author Summary Developing methods for accurate prediction of effects of amino acid substitutions on protein-protein affinity is important for both understanding disease-causing mechanism of missense mutations and guiding protein engineering. For both purposes, there is a need for accurate methods primarily based on first principle calculations, while being fast enough to handle large number of cases. Here we report a new method, the Single Amino Acid Mutation based change in Binding free Ener...

  4. The effects of the hydrostatic pressure and temperature on binding energy and optical properties of a donor impurity in a spherical quantum dot under external electric field

    International Nuclear Information System (INIS)

    The effects of the hydrostatic pressure and temperature on the electronic and the linear and nonlinear optical properties (i.e., absorption coefficients and refractive indices) are investigated in a spherical quantum dot in the presence of the electric field. The energy levels and wave functions are calculated using the variational method within the effective-mass approximation. The results show that these external factors have a significant effect not only on the binding energy of the donor impurity but also on the optical characteristics of the system. Moreover, it is found that the total absorption coefficient is strongly affected by the existence of impurity, the incident optical intensity, and relaxation time. -- Highlights: ► The electronic and optical properties of a spherical quantum dot are investigated. ► The presence of electric field, pressure and temperature pressure has a great influence on the binding energy. ► The absorption coefficients and the refractive index changes are strongly dependent on the external factors. ► The incident optical intensity and relaxation time considerably change the optical properties

  5. Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface

    Science.gov (United States)

    Löytynoja, T.; Li, X.; Jänkälä, K.; Rinkevicius, Z.; Ågren, H.

    2016-07-01

    We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

  6. Scalar and Spinor Particles with Low Binding Energy in the Strong Stationary Magnetic Field Studied by Means of Two-and Three-Dimensional Models

    CERN Document Server

    Rodionov, V N

    2007-01-01

    On the basis of analytic solutions of Schrodinger and Pauli equations for a uniform magnetic field and a single attractive $\\delta({\\bf r})$-potential the equations for the bound one-active electron states are discussed. It is vary important that ground electron states in the magnetic field essentially different from the analog state of spin-0 particles that binding energy has been intensively studied at more then forty years ago. We show that binding energy equations for spin-1/2 particles can be obtained without using of a well-known language of boundary conditions in the model of $\\delta$-potential that has been developed in pioneering works. Obtained equations are used for the analytically calculation of the energy level displacements, which demonstrate nonlinear dependencies on field intensities. It is shown that in a case of the weak intensity a magnetic field indeed plays a stabilizing role in considering systems. However the strong magnetic field shows the opposite action. We are expected that these p...

  7. Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface.

    Science.gov (United States)

    Löytynoja, T; Li, X; Jänkälä, K; Rinkevicius, Z; Ågren, H

    2016-07-14

    We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered. PMID:27421423

  8. Estimating effective higher order terms in the post-Newtonian binding energy and gravitational-wave flux: Non-spinning compact binary inspiral

    CERN Document Server

    Kapadia, Shasvath J; Ajith, Parameswaran

    2016-01-01

    In the adiabatic post-Newtonian (PN) approximation, the phase evolution of gravitational waves (GWs) from inspiralling compact binaries in quasicircular orbits is computed by equating the change in binding energy with the GW flux. This energy balance equation can be solved in different ways, which result in multiple approximants of the PN waveforms. Due to the poor convergence of the PN expansion, these approximants tend to differ from each other during the late inspiral. Which of these approximants should be chosen as templates for detection and parameter estimation of GWs from inspiraling compact binaries is not obvious. In this paper, we present estimates of the effective higher order (beyond the currently available 4PN and 3.5PN) non-spinning terms in the PN expansion of the binding energy and the GW flux that minimize the difference of multiple PN approximants (TaylorT1, TaylorT2, TaylorT4, TaylorF2) with effective one body waveforms calibrated to numerical relativity (EOBNR). We show that PN approximant...

  9. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    Science.gov (United States)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

  10. Role of hydrophobic mutations on the binding affinity and stability of blood coagulation factor VIIIa: a computational molecular dynamics and free-energy analysis.

    Science.gov (United States)

    Venkateswarlu, Divi

    2014-07-18

    Factor VIIIa is a non-covalently bound hetero-trimer among A1, A2 and A3-C1-C2 domains and an essential co-factor for factor IXa enzyme during proteolytic activation of factor X zymogen. The relatively weak interactions between A2 and the interface A1/A3 domains dampen the functional stability of FVIIIa in plasma and results in rapid degradation. We studied the mutational effect of three charged residues (Asp519, Glu665 and Asp666) to several hydrophobic residues by molecular dynamics simulations. Analysis of the binding free energy by MM-PBSA and MM-GBSA methods shows that the mutation of Asp519 and Glu665 residues to either Val or Ala enhance the A2 domain binding affinity in agreement with the experimental site-specific mutagenesis data. Mutation of Asp666 to Val, Tyr, Met and Phe showed largest improvement in the A2-domain binding among the eight hydrophobic mutants studied. Our studies suggest that the enrichment of hydrophobic interactions in the buried surface regions of A2 domain plays crucial role in improving the overall stability of FVIIIa. PMID:24952158

  11. Involvement of the Acyl-CoA binding domain containing 7 in the control of food intake and energy expenditure in mice.

    Science.gov (United States)

    Lanfray, Damien; Caron, Alexandre; Roy, Marie-Claude; Laplante, Mathieu; Morin, Fabrice; Leprince, Jérôme; Tonon, Marie-Christine; Richard, Denis

    2016-01-01

    Acyl-CoA binding domain-containing 7 (Acbd7) is a paralog gene of the diazepam-binding inhibitor/Acyl-CoA binding protein in which single nucleotide polymorphism has recently been associated with obesity in humans. In this report, we provide converging evidence indicating that a splice variant isoform of the Acbd7 mRNA is expressed and translated by some POMC and GABAergic-neurons in the hypothalamic arcuate nucleus (ARC). We have demonstrated that the ARC ACBD7 isoform was produced and processed into a bioactive peptide referred to as nonadecaneuropeptide (NDN) in response to catabolic signals. We have characterized NDN as a potent anorexigenic signal acting through an uncharacterized endozepine G protein-coupled receptor and subsequently via the melanocortin system. Our results suggest that ACBD7-producing neurons participate in the hypothalamic leptin signalling pathway. Taken together, these data suggest that ACBD7-producing neurons are involved in the hypothalamic control exerted on food intake and energy expenditure by the leptin-melanocortin pathway. PMID:26880548

  12. Exploring the mechanism of how tvMyb2 recognizes and binds ap65-1 by molecular dynamics simulations and free energy calculations.

    Science.gov (United States)

    Li, Wei-Kang; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-01-01

    TvMyb2, one of the Myb-like transcriptional factors in Trichomonas vaginalis, binds to two closely spaced promoter sites, MRE-1/MRE-2r and MRE-2f, on the ap65-1 gene. However, detailed dynamical structural characteristics of the tvMyb2-ap65-1 complex and a detailed study of the protein in the complex have not been done. Focused on a specific tvMyb2-MRE-2-13 complex (PDB code: ) and a series of mutants K51A, R84A and R87A, we applied molecular dynamics (MD) simulation and molecular mechanics generalized Born surface area (MM-GBSA) free energy calculations to examine the role of the tvMyb2 protein in recognition interaction. The simulation results indicate that tvMyb2 becomes stable when it binds the DNA duplex. A series of mutants, K51A, R84A and R87A, have been followed, and the results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on recognition and binding to ap65-1 DNA. Our work gives important information to understand the interactions of tvMyb2 with ap65-1. PMID:26548411

  13. Simultaneous effects of external electric field and aluminum concentration on the binding energy of a laser-dressed donor impurity in a spherical quantum dot confined at the center of a cylindrical nano-wire

    International Nuclear Information System (INIS)

    Based on the effective-mass approximation, the effects of external electric field and laser radiation on the binding energy and Stark shifts of electronic energy levels of a system consist of an on-center hydrogenic donor impurity in a spherical quantum dot which is located at the center of a cylindrical nano-wire have been studied. The energy eigenvalues and corresponding wave functions are calculated using the finite difference approximation. The binding energy and Stark shifts dependencies are reported upon the electric field strength, aluminum concentration and laser radiation. The results reveal that Stark shifts of ground and first excited states are strongly affected by presence of impurity, laser radiation and Al concentration. Additionally, the binding energies decreases as the electric field increases and become negligible for large values of electric field; decreases as the laser radiation increases and increases as the Al concentration increases

  14. ATP–Binding Cassette Transporter Structure Changes Detected by Intramolecular Fluorescence Energy Transfer for High-Throughput Screening

    OpenAIRE

    Iram, Surtaj H.; Gruber, Simon J.; Raguimova, Olga N.; Thomas, David D.; Seth L Robia

    2015-01-01

    Multidrug resistance protein 1 (MRP1) actively transports a wide variety of drugs out of cells. To quantify MRP1 structural dynamics, we engineered a “two-color MRP1” construct by fusing green fluorescent protein (GFP) and TagRFP to MRP1 nucleotide–binding domains NBD1 and NBD2, respectively. The recombinant MRP1 protein expressed and trafficked normally to the plasma membrane. Two-color MRP1 transport activity was normal, as shown by vesicular transport of [3H]17β-estradiol-17-β-(d-glucuroni...

  15. Theoretical Study of the Structures and Binding Energies of Ca+-(CO)n and Ca+-(CO2)n (n=1,2)

    International Nuclear Information System (INIS)

    The optimized structures and vibrational frequencies for Ca+-(CO)n and Ca+-(CO2)n (n=1,2) complexes were calculated with MP2 and B3LYP methods employing 6-311++G(2d,p) basis sets. Also the binding energies were investigated for all complexes to compare the stabilities. For Ca+-(CO)n C-bonded complexes are more stable than O-bonded complexes. Two stable conformations, linear and C2v form, are possible for Ca+-(CO)2 complexes and the C2v form is more stable than the linear form. Ca+-(CO2)2 also has two possible conformations and linear form has slightly lower energy than C2v form

  16. Photoelectron spectroscopy of aqueous solutions: Streaming potentials of NaX (X = Cl, Br, and I) solutions and electron binding energies of liquid water and X−

    International Nuclear Information System (INIS)

    The streaming potentials of liquid beams of aqueous NaCl, NaBr, and NaI solutions are measured using soft X-ray, He(I), and laser multiphoton ionization photoelectron spectroscopy. Gaseous molecules are ionized in the vicinity of liquid beams and the photoelectron energy shifts are measured as a function of the distance between the ionization point and the liquid beam. The streaming potentials change their polarity with concentration of electrolytes, from which the singular points of concentration eliminating the streaming potentials are determined. The streaming currents measured in air also vanish at these concentrations. The electron binding energies of liquid water and I−, Br−, and Cl− anions are revisited and determined more accurately than in previous studies

  17. Formation and properties of astrophysical carbonaceous dust. I: ab-initio calculations of the configuration and binding energies of small carbon clusters

    CERN Document Server

    Mauney, Christopher; Lazzati, Davide

    2014-01-01

    The binding energies of n < 100 carbon clusters are calculated using the ab-initio density functional theory code Quantum Espresso. Carbon cluster geometries are determined using several levels of classical techniques and further refined using density functional theory. The resulting energies are used to compute the work of cluster formation and the nucleation rate in a saturated, hydrogen-poor carbon gas. Compared to classical calculations that adopt the capillary approximation, we find that nucleation of carbon clusters is enhanced at low temperatures and depressed at high temperatures. This difference is ascribed to the different behavior of the critical cluster size. We find that the critical cluster size is at n = 27 or n = 8 for a broad range of temperatures and saturations, instead of being a smooth function of such parameters. The results of our calculations can be used to follow carbonaceous cluster/grain formation, stability, and growth in hydrogen poor environments, such as the inner layers of c...

  18. Development of a fluorescence model for the determination of constants associated with binding, quenching, and Förster resonance energy transfer efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Casciato, Shelly L. [Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712 (United States); Sapling Learning, Austin, TX (United States); Liljestrand, Howard M. [Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX 78712 (United States); Holcombe, James A., E-mail: holcombe@mail.utexas.edu [Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712 (United States)

    2014-02-01

    Graphical abstract: - Highlights: • The development of a FRET signal is modeled. • Absorbance of acceptor and donor and K{sub D} of the complex are accounted for. • The FRET efficiency and quenching are included as adjustable parameters. • Software provided for fitting the parameters to the experimental data. • Simulations can also be performed to study the impact of the various parameters. - Abstract: Determining accurate dissociation constants for equilibrium processes involving a fluorescent mechanism can prove to be quite challenging. Typically, titration curves and nonlinear least squares fitting of the data using computer programs are employed to obtain such constants. However, these approaches only consider the total fluorescence signal and often ignore other energy transfer processes within the system. The current model considers the impact on fluorescence from equilibrium binding (viz., metal-ligand, ligand-substrate, etc.), quenching, and resonance energy transfer. This model should provide more accurate binding constant as well as insights into other photonic processes. The equations developed for this model are discussed and are applied to experimental data from titrimetric experiments. Since the experimental data are generally in excess of the number of parameters that are needed to define the system, fitting is operated in an overdetermined mode and employs error minimization (either absolute or relative) to define goodness of fit. Examples of how changes in certain parameters affect the shape of the titrimetric curve are also presented. The current model does not consider chelation-enhanced fluorescence.

  19. Dual inhibitors for aspartic proteases HIV-1 PR and renin: advancements in AIDS-hypertension-diabetes linkage via molecular dynamics, inhibition assays, and binding free energy calculations.

    Science.gov (United States)

    Tzoupis, Haralambos; Leonis, Georgios; Megariotis, Grigorios; Supuran, Claudiu T; Mavromoustakos, Thomas; Papadopoulos, Manthos G

    2012-06-28

    Human immunodeficiency virus type 1 protease (HIV-1 PR) and renin are primary targets toward AIDS and hypertension therapies, respectively. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free-energy calculations and inhibition assays for canagliflozin, an antidiabetic agent verified its effective binding to both proteins (ΔG(pred) = -9.1 kcal mol(-1) for canagliflozin-renin; K(i,exp)= 628 nM for canagliflozin-HIV-1 PR). Moreover, drugs aliskiren (a renin inhibitor) and darunavir (an HIV-1 PR inhibitor) showed high affinity for HIV-1 PR (K(i,exp)= 76.5 nM) and renin (K(i,pred)= 261 nM), respectively. Importantly, a high correlation was observed between experimental and predicted binding energies (r(2) = 0.92). This study suggests that canagliflozin, aliskiren, and darunavir may induce profound effects toward dual HIV-1 PR and renin inhibition. Since patients on highly active antiretroviral therapy (HAART) have a high risk of developing hypertension and diabetes, aliskiren-based or canagliflozin-based drug design against HIV-1 PR may eliminate these side-effects and also facilitate AIDS therapy. PMID:22621689

  20. Binding of quasi two-dimensional biexcitons

    DEFF Research Database (Denmark)

    Birkedal, Dan; Singh, J; Vadim, Lyssenko; Hvam, Jørn Märcher

    Summary form only given. In this presentation we report on a determination of the biexciton binding energies in GaAs-AlGaAs quantum wells of different widths and the results of a theoretical calculation of the ratio of the biexciton binding energy to that of the exciton. We determine the binding ...