WorldWideScience

Sample records for h-v binding energy

  1. Sm and DNA Binding by dual reactive B cells requires distinct V{sub H}, V{sub {kappa}}, and V{sub H} CDR3 structures

    Energy Technology Data Exchange (ETDEWEB)

    Retter, M.W.; Eisenberg, R.A.; Cohen, P.L. [Univ. of North Carolina, Chapel Hill, NC (United States)] [and others

    1995-08-15

    We have previously demonstrated an overlap of the anti-Sm and anti-DNA responses in MRL/Mp-Ipr/Ipr mice. The Ab produced by many anti-Sm hybridomas bind DNA and are encoded by Ig V genes used by anti-DNA hybridomas. In addition, some anti-Sm Ab that bind DNA have acquired mutations that improve DNA binding, indicating that DNA is a selecting Ag in the anti-Sm response. To gain insight into the basis for the dual binding ability of these Ab, we coexpressed the H chain from the anti-Sm hybridoma 2-12 with nine different L chains. Hybridoma 2-12 binds Sm but not DNA, yet expresses the same J558 V{sub H} gene as three anti-Sm hybridomas that bind ssDNA and at least one anti-DNA hybridoma that does not bind Sm. We found that most of the transfectoma Ab bind Sm, but their avidities vary over more than 3 orders of magnitude. Five of the nine transfectoma Ab bind ssDNA, and none bind dsDNA. In general, the ability to bind each Ag follows the binding ability of the hybridoma from which the L chain is derived. H Chain swapping experiments indicate that the H chain, V{sub H} CDR3 in particular contributes to the binding of both Sm and DNA. We conclude that Sm and DNA select for distinct features of V{sub H}, V{sub {kappa}}, and V{sub H} CDR3, suggesting selection by both Ag in the anti-Sm response.

  2. Binding Energy and Enzymatic Catalysis.

    Science.gov (United States)

    Hansen, David E.; Raines, Ronald T.

    1990-01-01

    Discussed is the fundamental role that the favorable free energy of binding of the rate-determining transition state plays in catalysis. The principle that all of the catalytic factors discussed are realized by the use of this binding energy is reviewed. (CW)

  3. 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...

  4. Binding energies of hypernuclei and hypernuclear interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R. [Argonne National Lab., IL (United States)]|[Univ. of Illinois, Chicago, IL (United States). Dept. of Physics; Murali, S.; Usmani, Q.N. [Jamia Millia Islamia, New Delhi (India). Dept. of Physics

    1996-05-01

    In part 1 the effect of nuclear core dynamics on the binding energies of {Lambda} hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the {Lambda} single-particle energy in terms of basic {Lambda}-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body {Lambda}NN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei.

  5. Binding energy of two-dimensional biexcitons

    DEFF Research Database (Denmark)

    Singh, Jai; Birkedal, Dan; Vadim, Lyssenko;

    1996-01-01

    Using a model structure for a two-dimensional (2D) biexciton confined in a quantum well, it is shown that the form of the Hamiltonian of the 2D biexciton reduces into that of an exciton. The binding energies and Bohr radii of a 2D biexciton in its various internal energy states are derived...... analytically using the fractional dimension approach. The ratio of the binding energy of a 2D biexciton to that of a 2D exciton is found to be 0.228, which agrees very well with the recent experimental value. The results of our approach are compared with those of earlier theories....

  6. The binding energy and bonding in dialane.

    Science.gov (United States)

    Goebbert, Daniel J; Hernandez, Heriberto; Francisco, Joseph S; Wenthold, Paul G

    2005-08-24

    The binding energy of dialane, Al2H6, has been measured using mass spectrometric techniques to be 33 +/- 5 kcal/mol. This represents the first measurement of the thermochemical properties of dialane, which has only recently been observed in low-temperature matricies. High-level quantum mechanical calculations give a binding energy in agreement with the measured value. Experimental and quantum mechanical calculations show that dialane is chemically similar to diborane, B2H6, even though the bonding for these two systems shows significant differences.

  7. Mesic retardation and the triton binding energy

    Energy Technology Data Exchange (ETDEWEB)

    Brandenburg, R.A.; Chulick, G.S.; Machleidt, R.; Picklesimer, A.; Thaler, R.M.

    1988-09-01

    The relationship between the apparently successful result for the triton binding energy obtained from the static Bonn potentials and the underlying meson theory is investigated. The triton binding is shown to be strongly dependent upon mesic retardation and associated explicit energy dependences in the meson theory of the nucleon-nucleon interaction. Because it is a much closer representation of the full interaction than are its energy-independent counterparts, the energy-dependent one-boson-exchange potential representation of the Bonn interaction is used to gauge the implications of the full interaction. This one-boson-exchange potential, with or without corrections to adapt it for use in conjunction with nonrelativistic (Schroedinger) three-body equations, predicts a triton binding of only approx.6.7 MeV, as compared to a result of about 8.4 MeV obtained with the energy-independent potentials. This difference is traced to the combination of the explicit energy-dependence and the implicit energy dependence introduced through the tensor force, especially in the /sup 3/S/sub 1/ partial wave. This provides a new perspective on the success of the static Bonn potentials relative to other realistic potentials and relative to the meson-theoretic framework. Implications, especially with regard to the need for investigations of consistent three-body forces, are discussed.

  8. Mesic retardation and the triton binding energy

    Science.gov (United States)

    Brandenburg, R. A.; Chulick, G. S.; Machleidt, R.; Picklesimer, A.; Thaler, R. M.

    1988-09-01

    The relationship between the apparently successful result for the triton binding energy obtained from the static Bonn potentials and the underlying meson theory is investigated. The triton binding is shown to be strongly dependent upon mesic retardation and associated explicit energy dependences in the meson theory of the nucleon-nucleon interaction. Because it is a much closer representation of the full interaction than are its energy-independent counterparts, the energy-dependent one-boson-exchange potential representation of the Bonn interaction is used to gauge the implications of the full interaction. This one-boson-exchange potential, with or without corrections to adapt it for use in conjunction with nonrelativistic (Schrödinger) three-body equations, predicts a triton binding of only ~6.7 MeV, as compared to a result of about 8.4 MeV obtained with the energy-independent potentials. This difference is traced to the combination of the explicit energy-dependence and the implicit energy dependence introduced through the tensor force, especially in the 3S1 partial wave. This provides a new perspective on the success of the static Bonn potentials relative to other realistic potentials and relative to the meson-theoretic framework. Implications, especially with regard to the need for investigations of consistent three-body forces, are discussed.

  9. 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.

  10. Divacancy binding energy, formation energy and surface energy of BCC transition metals using MEAM potentials

    Science.gov (United States)

    Uniyal, Shweta; Chand, Manesh; Joshi, Subodh; Semalty, P. D.

    2016-05-01

    The modified embedded atom method (MEAM) potential parameters have been employed to calculate the unrelaxed divacancy formation energy, binding energy and surface energies for low index planes in bcc transition metals. The calculated results of divacancy binding energy and vacancy formation energy compare well with experimental and other available calculated results.

  11. K- nuclear states: Binding energies and widths

    Science.gov (United States)

    Hrtánková, J.; Mareš, J.

    2017-07-01

    K- optical potentials relevant to calculations of K- nuclear quasibound states were developed within several chiral meson-baryon coupled-channels interaction models. The applied models yield quite different K- binding energies and widths. Then the K- multinucleon interactions were incorporated by a phenomenological optical potential fitted recently to kaonic atom data. Though the applied K- interaction models differ significantly in the K-N subthreshold region, our self-consistent calculations of kaonic nuclei across the periodic table lead to conclusions valid quite generally. Due to K- multinucleon absorption in the nuclear medium, the calculated widths of K- nuclear states are sizable, ΓK-≥90 MeV, and exceed substantially their binding energies in all considered nuclei.

  12. 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.

  13. Yukawa-dissociation and the deuteron binding energy

    Energy Technology Data Exchange (ETDEWEB)

    Jacobsen, T.

    1997-05-01

    It is shown that energy must be conserved by the dissociation of an elementary particle. The energy deficit by a dissociation behaves as a basic concept. The binding energy of the deuteron is reproduced. 4 refs.

  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...

  15. 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...

  16. Inversion of H/V ratio in layered systems

    Science.gov (United States)

    Pina Flores, J.; García-Jerez, A.; Luzon, F.; Perton, M.; Sanchez-Sesma, F. J.

    2014-12-01

    Both coda of earthquakes and microtremors are assumed to be diffuse fields resulting from multiple scattering. From the diffuse field theory, the average of the autocorrelation of displacement components at a given receiver measures the directional energy densities that are proportional to the imaginary parts of the Green's function for source and receiver at the same point. The directional energies have been recently related to the calculation of microtremor H/V spectral ratio (MHVSR). These ratios are widely used in the assessment of the dominant frequency of soil sites and their measurements are relatively simple as only one station is required. The H/V spectral ratios have also been interpreted as representing either directly the S wave amplification or the Rayleigh wave ellipticity. Moreover, the H/V ratios can be also used for a finer characterization of the site assuming horizontally layered media without lateral heterogeneities. In that case and for an appropriate noise normalization the experimental spectral ratios H2/V2 should correspond to their theoretical counterpart: the ratio 2 ImG11 / ImG33, where ImG11 and ImG33 are the imaginary parts of Green functions at the load point for horizontal and vertical components, respectively and for horizontally layered media. In order to guarantee a viable inversion, the imaginary part of the theoretical Green's functions must be efficiently computed using both an integral in the complex k plane (in terms of homogeneous plane waves) and the pole contributions due to Rayleigh and Love normal modes, which result from the (application of the) Cauchy residue theorem. ACKNOWLEDGEMENTS. This research has been partially supported by DGAPA-UNAM under Project IN104712 and the AXA Research Fund.

  17. 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)

  18. Atomic Mass and Nuclear Binding Energy for F-35 (Fluorine)

    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 F-35 (Fluorine, atomic number Z = 9, mass number A = 35).

  19. Binding energy of donors in symmetric triangular quantum wells

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ji-ye; LIANG Xi-xia

    2005-01-01

    Hydrogen-like donor impurity states in symmetric triangular quantum wells are investigated by using a variational method.Both the effects of the variable effective mass of electrons and the spatially dependent dielectric constant are considered in the calculation.The numerical results show that the binding energy depends on not only the effective mass and dielectric constant but also the spatial distribution of electron probability density.The binding energies of donor states get the maximums at the well-center.The results are also compared with those obtained in parabolic and square wells.It is seen that the triangular well support the highest binding energies for donor states.

  20. Predicting accurate absolute binding energies in aqueous solution

    DEFF Research Database (Denmark)

    Jensen, Jan Halborg

    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. In this paper I summarize some of the many factors that could easily contribute 1-3 kcal......-represented by continuum models. While I focus on binding free energies in aqueous solution the approach also applies (with minor adjustments) to any free energy difference such as conformational or reaction free energy differences or activation free energies in any solvent....

  1. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania

    2016-11-10

    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  2. Relativistic calculation of the triton binding energy and its implications

    CERN Document Server

    Stadler, A; Stadler, Alfred; Gross, Franz

    1996-01-01

    First results for the triton binding energy obtained from the relativistic spectator or Gross equation are reported. The Dirac structure of the nucleons is taken into account. Numerical results are presented for a family of realistic OBE models with off-shell scalar couplings. It is shown that these off-shell couplings improve both the fits to the two-body data and the predictions for the binding energy.

  3. Atomic Mass and Nuclear Binding Energy for Po-269 (Polonium)

    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 Po-269 (Polonium, atomic number Z = 84, mass number A = 269).

  4. Atomic Mass and Nuclear Binding Energy for Po-278 (Polonium)

    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 Po-278 (Polonium, atomic number Z = 84, mass number A = 278).

  5. Atomic Mass and Nuclear Binding Energy for Po-282 (Polonium)

    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 Po-282 (Polonium, atomic number Z = 84, mass number A = 282).

  6. Atomic Mass and Nuclear Binding Energy for Po-271 (Polonium)

    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 Po-271 (Polonium, atomic number Z = 84, mass number A = 271).

  7. Atomic Mass and Nuclear Binding Energy for Po-283 (Polonium)

    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 Po-283 (Polonium, atomic number Z = 84, mass number A = 283).

  8. Atomic Mass and Nuclear Binding Energy for Po-281 (Polonium)

    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 Po-281 (Polonium, atomic number Z = 84, mass number A = 281).

  9. Atomic Mass and Nuclear Binding Energy for Po-284 (Polonium)

    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 Po-284 (Polonium, atomic number Z = 84, mass number A = 284).

  10. Atomic Mass and Nuclear Binding Energy for Po-280 (Polonium)

    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 Po-280 (Polonium, atomic number Z = 84, mass number A = 280).

  11. Atomic Mass and Nuclear Binding Energy for Po-272 (Polonium)

    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 Po-272 (Polonium, atomic number Z = 84, mass number A = 272).

  12. Atomic Mass and Nuclear Binding Energy for Po-276 (Polonium)

    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 Po-276 (Polonium, atomic number Z = 84, mass number A = 276).

  13. Atomic Mass and Nuclear Binding Energy for Po-277 (Polonium)

    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 Po-277 (Polonium, atomic number Z = 84, mass number A = 277).

  14. Atomic Mass and Nuclear Binding Energy for Po-275 (Polonium)

    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 Po-275 (Polonium, atomic number Z = 84, mass number A = 275).

  15. Atomic Mass and Nuclear Binding Energy for Po-273 (Polonium)

    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 Po-273 (Polonium, atomic number Z = 84, mass number A = 273).

  16. Atomic Mass and Nuclear Binding Energy for Po-274 (Polonium)

    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 Po-274 (Polonium, atomic number Z = 84, mass number A = 274).

  17. Atomic Mass and Nuclear Binding Energy for Po-270 (Polonium)

    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 Po-270 (Polonium, atomic number Z = 84, mass number A = 270).

  18. Atomic Mass and Nuclear Binding Energy for Po-279 (Polonium)

    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 Po-279 (Polonium, atomic number Z = 84, mass number A = 279).

  19. Atomic Mass and Nuclear Binding Energy for Ra-226 (Radium)

    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 Ra-226 (Radium, atomic number Z = 88, mass number A = 226).

  20. Binding energies and modelling of nuclei in semiclassical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Perez-Garcia, M. Angeles [Departamento de Fisica Fundamental and Instituto Universitario de Fisica Fundamental y Matematicas, IUFFyM, Universidad de Salamanca, Plaza de la Merced s/n 37008 Salamanca (Spain)], E-mail: mperezga@usal.es; Tsushima, K. [Departamento de Fisica Fundamental and Instituto Universitario de Fisica Fundamental y Matematicas, IUFFyM, Universidad de Salamanca, Plaza de la Merced s/n 37008 Salamanca (Spain)], E-mail: tsushima@usal.es; Valcarce, A. [Departamento de Fisica Fundamental and Instituto Universitario de Fisica Fundamental y Matematicas, IUFFyM, Universidad de Salamanca, Plaza de la Merced s/n 37008 Salamanca (Spain)], E-mail: valcarce@usal.es

    2008-03-06

    We study the binding energies of spin-isospin saturated nuclei with nucleon number 8{<=}A{<=}100 in semiclassical Monte Carlo many-body simulations. The model Hamiltonian consists of (i) nucleon kinetic energy, (ii) a nucleon-nucleon interaction potential, and (iii) an effective Pauli potential which depends on density. The basic ingredients of the nucleon-nucleon potential are a short-range repulsion, and a medium-range attraction. Our results demonstrate that one can always expect to obtain the empirical binding energies for a set of nuclei by introducing a proper density dependent Pauli potential in terms of a single variable, the nucleon number, A. The present work shows that in the suggested procedure there is a delicate counterbalance of kinetic and potential energetic contributions allowing a good reproduction of the experimental nuclear binding energies. This type of calculations may be of interest in further reproduction of other properties of nuclei such as radii and also exotic nuclei.

  1. 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.

  2. Predicting accurate absolute binding energies in aqueous solution

    DEFF Research Database (Denmark)

    Jensen, Jan Halborg

    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. In this paper I summarize some of the many factors that could easily contribute 1-3 kcal...... mol(-1) 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 I focus on binding free energies in aqueous solution the approach also applies (with minor adjustments) to any free energy difference such as conformational or reaction free energy differences or activation free energies in any solvent....

  3. Binding Energy of Excitons in a Quantum Ring

    Institute of Scientific and Technical Information of China (English)

    XIE Wen-Fang

    2008-01-01

    The binding energy of excitons confined to a quantum ring under the influence of perpendicular homogeneous magnetic field is calculated as a function of the ring radius. Calculations are made by using the method of exact diagonalization within the effective-mass approximation. The feature of binding energy of the ground state as a function of the ring radius for several values of the magnetic field has been revealed. The interesting feature of our study is that, in a quantum ring, the geometric structure of excitons may reveal transition.

  4. Full microtremor H/V(z, f) inversion for shallow subsurface characterization

    Science.gov (United States)

    Lontsi, Agostiny Marrios; Sánchez-Sesma, Francisco José; Molina-Villegas, Juan Camillo; Ohrnberger, Matthias; Krüger, Frank

    2015-07-01

    The H/V spectral ratio has emerged as a single station method within the seismic ambient noise analysis field by its capability to quickly estimate the frequency of resonance at a site and through inversion the average profile information. Although it is easy to compute from experimental data, its counter theoretical part is not obvious when building a forward model which can help in reconstructing the derived H/V spectrum. This has led to the simplified assumption that the noise wavefield is mainly composed of Rayleigh waves and the derived H/V often used without further correction. Furthermore, only the right (and left) flank around the H/V peak frequency is considered in the inversion for the subsurface 1-D shear wave velocity profile. A new theoretical approach for the interpretation of the H/V spectral ratio has been presented by Sánchez-Sesma et al. In this paper, the fundamental idea behind their theory is presented as it applies to receivers at depth. A smooth H/V(z, f) spectral curve on a broad frequency range is obtained by considering a fine integration step which is in turn time consuming. We show that for practical purposes and in the context of inversion, this can be considerably optimized by using a coarse integration step combined with the smoothing of the corresponding directional energy density (DED) spectrum. Further analysis shows that the obtained H/V(z, f) spectrum computed by the mean of the imaginary part of Green's function method could also be recovered using the reflectivity method for a medium well illuminated by seismic sources. Inversion of synthetic H/V(z, f) spectral curve is performed for a single layer over a half space. The striking results allow to potentially use the new theory as a forward computation of the H/V(z, f) to fully invert the experimental H/V spectral ratio at the corresponding depth for the shear velocity profile (Vs) and additionally the compressional velocity profile (Vp) using receivers both at the surface and

  5. Binding energy and fine structure of the He- ion

    Institute of Scientific and Technical Information of China (English)

    ZHUO; Lin; ZHU; Jing-jing; GOU; Bing-cong

    2007-01-01

    The variational method using a multiconfiguration wavefunction is carried out on the core-excited state 1s2s2p 4P0 for helium negative ion, including mass polarization and relativistic corrections. Binding energy and fine structure are reported. The results are compared with other theoretical and experimental date in the literature.

  6. Core level photoemission of rotaxanes : A summary on binding energies

    NARCIS (Netherlands)

    Mendoza, S. M.; Berna, J.; Perez, E. M.; Kay, E. R.; Mateo-Alonso, A.; De Nadai, C.; Zhang, S.; Baggerman, J.; Wiering, P. G.; Leigh, D. A.; Prato, M.; Brouwer, A.M.; Rudolf, P.; Nadaï, C. De

    2008-01-01

    Several rotaxanes were studied by XPS in the form of thin films or monolayers on gold substrates. Here we report a database of photoemission spectra of the C 1s, N 1s and F 1s core levels. Binding energy ranges are summarized, classifying the core levels according to the chemical groups that form pa

  7. Core level photoemission of rotaxanes: A summary on binding energies

    Energy Technology Data Exchange (ETDEWEB)

    Mendoza, S.M. [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen (Netherlands); Berna, J.; Perez, E.M.; Kay, E.R. [School of Chemistry, University of Edinburgh, King' s Buildings, West Mains Road, Edinburgh EH9 3JJ (United Kingdom); Mateo-Alonso, A. [Dipartimento di Scienze Farmaceutiche, Universita di Trieste, Piazzale Europa 1, 34127 Trieste (Italy); De Nadai, C. [Laboratoire Interdisciplinaire de Spectroscopie Electronique, Facultes Universitaires Notre Dame de la Paix, 61 Rue de Bruxelles, B-5000 Namur (Belgium); Zhang, S. [School of Chemistry, University of Edinburgh, King' s Buildings, West Mains Road, Edinburgh EH9 3JJ (United Kingdom); Baggerman, J.; Wiering, P.G. [Van' t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, NL-1018 WS Amsterdam (Netherlands); Leigh, D.A. [School of Chemistry, University of Edinburgh, King' s Buildings, West Mains Road, Edinburgh EH9 3JJ (United Kingdom); Prato, M. [Dipartimento di Scienze Farmaceutiche, Universita di Trieste, Piazzale Europa 1, 34127 Trieste (Italy); Brouwer, A.M. [Van' t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, NL-1018 WS Amsterdam (Netherlands); Rudolf, P. [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen (Netherlands)], E-mail: P.Rudolf@rug.nl

    2008-09-15

    Several rotaxanes were studied by XPS in the form of thin films or monolayers on gold substrates. Here we report a database of photoemission spectra of the C 1s, N 1s and F 1s core levels. Binding energy ranges are summarized, classifying the core levels according to the chemical groups that form part of the rotaxanes.

  8. Mass renormalization and binding energies in quantum field theory

    Science.gov (United States)

    Lv, Q. Z.; Stefanovich, E.; Su, Q.; Grobe, R.

    2017-10-01

    We compare the predictions of two methods of determining the amount of binding energy between two distinguishable fermions that interact with each other through force-intermediating bosons. Both measures try to quantify this binding energy by the downward shift of the fully interacting two-fermion ground state energy relative to the sum of the corresponding two single-particle ground state energies. The first method computes this energy difference directly from the standard quantum field theoretical Hamiltonian. The second method uses the mass renormalized form of this Hamiltonian. In order to have a concrete example for this comparison, we employ a simple Yukawa-like model system in one spatial dimension. We find that both approaches lead to identical predictions in the second and fourth order perturbation of the coupling constant, and they remain remarkably close even in the strong coupling domain where perturbation theory diverges. This illustrates that there are field theoretical systems for which rather accurate binding energies can be obtained even without the mass renormalization procedure.

  9. Alternate Energy Sources for Thermalplastic Binding Agent Consolidation

    Energy Technology Data Exchange (ETDEWEB)

    Frame, B.J.

    1999-01-01

    A study was conducted to investigate microwave and electron beam technologies as alternate energy sources to consolidate fiber coated with a thermoplastic binding agent into preforms for composite molding applications. Bench experiments showed that both microwave and electron beam energy can produce heat sufficient to melt and consolidate a thermoplastic binding agent applied to fiberglass mat, and several two- and three-dimensional fiberglass preforms were produced with each method. In both cases, it is postulated that the heating was accomplished by the effective interaction of the microwave or electron beam energy with the combination of the mat preform and the tooling used to shape the preform. Both methods contrast with conventional thermal energy applied via infrared heaters or from a heated tool in which the heat to melt the thermoplastic binding agent must diffuse over time from the outer surface of the preform toward its center under a thermal gradient. For these reasons, the microwave and electron beam energy techniques have the potential to rapidly consolidate thick fiber preforms more efficiently than the thermal process. With further development, both technologies have the potential to make preform production more cost effective by decreasing cycle time in the preform tool, reducing energy costs, and by enabling the use of less expensive tooling materials. Descriptions of the microwave and electron beam consolidation experiments and a summary of the results are presented in this report.

  10. Core level binding energies of functionalized and defective graphene.

    Science.gov (United States)

    Susi, Toma; Kaukonen, Markus; Havu, Paula; Ljungberg, Mathias P; Ayala, Paola; Kauppinen, Esko I

    2014-01-01

    X-ray photoelectron spectroscopy (XPS) is a widely used tool for studying the chemical composition of materials and it is a standard technique in surface science and technology. XPS is particularly useful for characterizing nanostructures such as carbon nanomaterials due to their reduced dimensionality. In order to assign the measured binding energies to specific bonding environments, reference energy values need to be known. Experimental measurements of the core level signals of the elements present in novel materials such as graphene have often been compared to values measured for molecules, or calculated for finite clusters. Here we have calculated core level binding energies for variously functionalized or defected graphene by delta Kohn-Sham total energy differences in the real-space grid-based projector-augmented wave density functional theory code (GPAW). To accurately model extended systems, we applied periodic boundary conditions in large unit cells to avoid computational artifacts. In select cases, we compared the results to all-electron calculations using an ab initio molecular simulations (FHI-aims) code. We calculated the carbon and oxygen 1s core level binding energies for oxygen and hydrogen functionalities such as graphane-like hydrogenation, and epoxide, hydroxide and carboxylic functional groups. In all cases, we considered binding energy contributions arising from carbon atoms up to the third nearest neighbor from the functional group, and plotted C 1s line shapes by using experimentally realistic broadenings. Furthermore, we simulated the simplest atomic defects, namely single and double vacancies and the Stone-Thrower-Wales defect. Finally, we studied modifications of a reactive single vacancy with O and H functionalities, and compared the calculated values to data found in the literature.

  11. On the Computation of H/V and its Application to Microzonation and Seismic Design

    Science.gov (United States)

    Perton, M.; Martínez, J. A.; Lermo, J. F.; Sanchez-Sesma, F. J.

    2014-12-01

    The H/V ratio is the square root of the ratio of horizontal to vertical energies of ground motion. It has been observed that the frequency of the main peak is well suited for the characterization of site effects and had been widely used for micro-zonation and seismic structural design. Historically that ratio was made from the average of individual H/V ratios obtained from noise autocorrelations. Nevertheless, it has been recently pointed out that the H/V ratio should be calculated differently as the ratio of the average of H over the average of V. This calculation is based on the relation between the directional energies (the imaginary part of Green's function) and the noise autocorrelations. In general, the average of ratios is different from the ratio of averages. Although the frequency of the main response was correctly obtained, the associated amplification factor has generally been badly predicted, having little matching with the amplification observed during strong earthquakes. The unexpected decay behavior of such ratios at high frequency and the lack of stability and reproducibility of the H/V ratios are other problems that face the method. These problems are addressed here from the point of view of normalization of noise correlations. In fact, several normalization techniques have already been proposed in order to correctly retrieve the Green's function. Some of them are well suited for the retrieval of the surface wave contribution, while others are more appropriate for bulk wave incidence. Since the H/V ratio may be used for various purposes like surface wave tomography, micro-zonation or seismic design, different normalizations are discussed in functions of the objectives. The H/V obtained from local historical earthquakes on top or far away from the subduction zone are also discussed. ACKNOWLEDGEMENT This research has been partially supported by DGAPA-UNAM under Project IN104712 and the AXA Research Fund.

  12. Bose polaron problem: Effect of mass imbalance on binding energy

    Science.gov (United States)

    Ardila, L. A. Peña; Giorgini, S.

    2016-12-01

    By means of quantum Monte Carlo methods we calculate the binding energy of an impurity immersed in a Bose-Einstein condensate at T =0 . The focus is on the attractive branch of the Bose polaron and on the role played by the mass imbalance between the impurity and the surrounding particles. For an impurity resonantly coupled to the bath, we investigate the dependence of the binding energy on the mass ratio and on the interaction strength within the medium. In particular, we determine the equation of state in the case of a static (infinite mass) impurity, where three-body correlations are irrelevant and the result is expected to be a universal function of the gas parameter. For the mass ratio corresponding to 40K impurities in a gas of 87Rb atoms, we provide an explicit comparison with the experimental findings of a recent study carried out at JILA.

  13. 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.

  14. Exciton and Biexciton Binding Energies in Rectangular Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    LIU Yong-Hui; KONG Xiao-Jun

    2005-01-01

    @@ In the effective mass approximation, using the variational technology and a method of expanding the wavefunctions of exciton in terms of the eigenfunctions of the noninteracting electron-hole system, we calculate the exciton and biexciton ground state binding energies for rectangular quantum dots (QDs). In the calculation, a three-dimensional Fourier expansion of Coulomb potential is used to remove the numerical difficulty with the 1/r singularity, and it considerably reduces the computational effort. Our results agree fairly well with the previous results. It is found that the binding energies are highly correlated to the size of QDs. The quantum confinement effect of spherical QDs about biexciton is obviously larger than that of rectangular QDs when the well width is narrower than 2.0aB.

  15. 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.

  16. Binding energy of the $X(3872)$ at unphysical pion masses

    CERN Document Server

    Baru, V; Filin, A A; Gegelia, J; Nefediev, A V

    2015-01-01

    Chiral extrapolation of the $X(3872)$ binding energy is investigated using the modified Weinberg formulation of chiral effective field theory for the $D \\bar{D}^*$ scattering. Given its explicit renormalisability, this approach is particularly useful to explore the interplay of the long- and short-range $D \\bar{D}^*$ forces in the $X(3872)$ from studying the light-quark (pion) mass dependence of its binding energy. In particular, the parameter-free leading-order calculation shows that the $X$-pole disappears for unphysical large pion masses. On the other hand, without contradicting the naive dimensional analysis, the higher-order pion-mass-dependent contact interaction can change the slope of the binding energy at the physical point yielding the opposite scenario of a stronger bound $X$ at pion masses larger than its physical value. An important role of the pion dynamics and of the 3-body $D\\bar{D}\\pi$ effects for chiral extrapolations of the $X$-pole is emphasised. The results of the present study should be ...

  17. 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.

  18. Binding Energy Calculations for Novel Ternary Ionic Lattices

    Science.gov (United States)

    Rodríguez-Mijangos, Ricardo; Vazquez-Polo, Gustavo

    2002-03-01

    Theoretical calculations for the binding energy between metalic ions and negative ions on a novel ternary ionic lattice is carried out for several solid solutions prepared with different concentrations and characterized recently (1). The ternary lattices that reach a good miscibility are: KCl(x)KBr(y)RbCl(z) in three different concentrations: (x=y=z=0.33), (x=0.5, y=0.25, z=0.25) and (x=0.33, y=0.07, z=0.60). The binding energy for these novel structures is calculated from the lattice constants obtained by X ray diffractometry analysis performed on the samples and the Vegard law (2). For the repulsive force exponent m, an average of the m values was considered. The energy values obtained by the Born´expression are compared with corresponding energy values from the lattice with more complex expressions, such as the Born Mayer, Born-Van der Walls. There is a good aggreement between all these calculations. (1)R. R. Mijangos, A. Cordero-Borboa, E. Alvarez, M. Cervantes, Physics Letters A 282 (2001) 195-200. (2) G. Vazquez-Polo, R. R. Mijangos et al. Revista Mexicana de Fisica, 47, Diciembre 2001. In Press.

  19. Phosphate binding energy and catalysis by small and large molecules.

    Science.gov (United States)

    Morrow, Janet R; Amyes, Tina L; Richard, John P

    2008-04-01

    Catalysis is an important process in chemistry and enzymology. The rate acceleration for any catalyzed reaction is the difference between the activation barriers for the uncatalyzed (Delta G(HO)(#)) and catalyzed (Delta G(Me)(#)) reactions, which corresponds to the binding energy (Delta G(S)(#) = Delta G(Me)(#)-Delta G(HO)(#)) for transfer of the reaction transition state from solution to the catalyst. This transition state binding energy is a fundamental descriptor of catalyzed reactions, and its evaluation is necessary for an understanding of any and all catalytic processes. We have evaluated the transition state binding energies obtained from interactions between low molecular weight metal ion complexes or high molecular weight protein catalysts and the phosphate group of bound substrate. Work on catalysis by small molecules is exemplified by studies on the mechanism of action of Zn2(1)(H2O). A binding energy of Delta G(S)(#) = -9.6 kcal/mol was determined for Zn2(1)(H2O)-catalyzed cleavage of the RNA analogue HpPNP. The pH-rate profile for this cleavage reaction showed that there is optimal catalytic activity at high pH, where the catalyst is in the basic form [Zn2(1)(HO-)]. However, it was also shown that the active form of the catalyst is Zn2(1)(H2O) and that this recognizes the C2-oxygen-ionized substrate in the cleavage reaction. The active catalyst Zn2(1)(H2O) shows a high affinity for oxyphosphorane transition state dianions and a stable methyl phosphate transition state analogue, compared with the affinity for phosphate monoanion substrates. The transition state binding energies, Delta G(S)(#), for cleavage of HpPNP catalyzed by a variety of Zn2+ and Eu3+ metal ion complexes reflect the increase in the catalytic activity with increasing total positive charge at the catalyst. These values of Delta G(S)(#) are affected by interactions between the metal ion and its ligands, but these effects are small in comparison with Delta G(S)(#) observed for catalysis

  20. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors.

    Science.gov (United States)

    Peón, Antonio; Coderch, Claire; Gago, Federico; González-Bello, Concepción

    2013-05-01

    Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.

  1. DFT calculation of core-electron binding energies

    Energy Technology Data Exchange (ETDEWEB)

    Takahata, Yuji; Chong, Delano P. E-mail: chong@chem.ubc.ca

    2003-11-01

    A total of 59 core-electron binding energies (CEBEs) were studied with the Amsterdam Density Functional Program (ADF) program and compared with the observed values. The results indicate that a polarized triple-zeta basis set of Slater-type orbitals is adequate for routine assessment of the performance of each method of computation. With such a basis set, seven density functionals were tested. In addition, the performance of 21 energy density functionals were computed from the density calculated with the statistical average of orbital potentials (SAOP). Among all the choices tested, the best density functional for core-electron binding energies of C to F turns out to be the combination of Perdew-Wang (1986) functional for exchange and the Perdew-Wang (1991) functional for correlation, confirming earlier studies based on contracted Gaussian-type orbitals. For this best functional, five Slater-type orbital basis sets were examined, ranging from polarized double-zeta quality to the largest set available in the ADF package. For the best functional with the best basis set, the average absolute deviation (AAD) of the calculated value from experiment is only 0.16 eV.

  2. Binding energies of CO2 with some ionic liquids

    Science.gov (United States)

    Eucker, William; Bendler, John

    2007-03-01

    Room temperature ionic liquids (RTILs), a novel class of materials with negligible vapor pressures and potentiality as benign solvents, may be an ideal chemical for carbon dioxide (CO2) gas sequestration. Ab initio computational modeling was used to investigate the molecular interactions of simple RTIL anions hexafluorophosphate (PF6^-) and tetrafluoroborate (BF4^-) with CO2. Electronic potential energy surface (PES) scans of a comprehensive sampling of 1:1 anion-CO2 orientations were computed using Spartan '02 with Dunning's correlation consistent basis sets. Qualitatively, the PES scans yielded deeper, more numerous and radially closer active sites surrounding BF4^- anion as compared with the PF6^- anion. Quantitatively, the binding energies of 17.87 kJ/mol and 25.24 kJ/mol were extracted from the identified global energy minima for the PF6^- and BF4^- systems, respectively. The smaller BF4^- anion was concluded to bind more strongly to the CO2. However, literature-reported experimental Henry's law constants for CO2 dissolved in imidizolium based RTILs show greater gas solvation in the PF6^- system. The discrepancy between the energetics calculation results and the experimental solvation data will be discussed.

  3. Many-body approximations for atomic binding energies

    CERN Document Server

    Schuster, Micah D; Staker, Joshua T

    2011-01-01

    We benchmark three approximations for the many-body problem -- the Hartree-Fock, projected Hartree-Fock, and random phase approximations -- against full numerical configuration-interaction calculations of the electronic structure of atoms, from Li through to Ne. Each method uses exactly the same input, i.e., the same single-particle basis and Coulomb matrix elements, so any differences are strictly due to the approximation itself. Although it consistently overestimates the ground state binding energy, the random phase approximation has the smallest overall errors; furthermore, we suggest it may be useful as a method for efficient optimization of single-particle basis functions.

  4. 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}-...

  5. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

    Science.gov (United States)

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

    2015-06-09

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  6. La- binding energies by analysis of its photodetachment spectra

    Science.gov (United States)

    Pan, Lin; Beck, Donald R.

    2016-06-01

    This study reinterprets an earlier experimental photoelectron kinetic energy spectrum of the negative ion of lanthanum [A. M. Covington, D. Calabrese, J. S. Thompson, and T. J. Kvale, J. Phys. B 31, L855 (1998), 10.1088/0953-4075/31/20/002] by carrying out relativistic configuration interaction (RCI) photodetachment calculations. The results confirm the earlier RCI calculation for the electron affinity of lanthanum (0.545 eV) [S. M. O'Malley and D. R. Beck, Phys. Rev. A 79, 012511 (2009), 10.1103/PhysRevA.79.012511] and revise it to a slightly larger value of 0.550 eV, thus modifying the experimental interpretation of 0.47 ±0.02 eV. The calculation also yields the binding energies of the other thirteen bound states of La-. Good agreement has been found when these energies are compared to the results of a recent experimental study on La- [C. W. Walter, N. D. Gibson, D. J. Matyas, C. T. Crocker, K. A. Dungan, B. R. Matola, and J. Rohlén, Phys. Rev. Lett. 113, 063001 (2014), 10.1103/PhysRevLett.113.063001]. Finally, our analysis confirms the transition energy for the potential laser cooling transition of 3F2e→3D1o in La-.

  7. 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.

  8. Relative Binding Free Energy Calculations Applied to Protein Homology Models.

    Science.gov (United States)

    Cappel, Daniel; Hall, Michelle Lynn; Lenselink, Eelke B; Beuming, Thijs; Qi, Jun; Bradner, James; Sherman, Woody

    2016-12-27

    A significant challenge and potential high-value application of computer-aided drug design is the accurate prediction of protein-ligand binding affinities. Free energy perturbation (FEP) using molecular dynamics (MD) sampling is among the most suitable approaches to achieve accurate binding free energy predictions, due to the rigorous statistical framework of the methodology, correct representation of the energetics, and thorough treatment of the important degrees of freedom in the system (including explicit waters). Recent advances in sampling methods and force fields coupled with vast increases in computational resources have made FEP a viable technology to drive hit-to-lead and lead optimization, allowing for more efficient cycles of medicinal chemistry and the possibility to explore much larger chemical spaces. However, previous FEP applications have focused on systems with high-resolution crystal structures of the target as starting points-something that is not always available in drug discovery projects. As such, the ability to apply FEP on homology models would greatly expand the domain of applicability of FEP in drug discovery. In this work we apply a particular implementation of FEP, called FEP+, on congeneric ligand series binding to four diverse targets: a kinase (Tyk2), an epigenetic bromodomain (BRD4), a transmembrane GPCR (A2A), and a protein-protein interaction interface (BCL-2 family protein MCL-1). We apply FEP+ using both crystal structures and homology models as starting points and find that the performance using homology models is generally on a par with the results when using crystal structures. The robustness of the calculations to structural variations in the input models can likely be attributed to the conformational sampling in the molecular dynamics simulations, which allows the modeled receptor to adapt to the "real" conformation for each ligand in the series. This work exemplifies the advantages of using all-atom simulation methods with

  9. Binding Energies of a Positively Charged Exciton in a Quantum Disc

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The binding energies of the lowest singlet and triplet states of positively charged excitons confined to a quantum disc are studied using exact diagonalization techniques. We investigate the dependence of the binding energies on the confinement strength and on the effective electron-to-hole mass ratio. The results we have obtained show that the binding energies are closely correlated to the strength of the confinement potential and the effective electron-to-hole mass ratio.

  10. 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.

  11. Determination of energies and sites of binding of PFOA and PFOS to human serum albumin.

    Science.gov (United States)

    Salvalaglio, Matteo; Muscionico, Isabella; Cavallotti, Carlo

    2010-11-25

    Structure and energies of the binding sites of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) to human serum albumin (HSA) were determined through molecular modeling. The calculations consisted of a compound approach based on docking, followed by molecular dynamics simulations and by the estimation of the free binding energies adopting WHAM-umbrella sampling and semiempirical methodologies. The binding sites so determined are common either to known HSA fatty acids sites or to other HSA sites known to bind to pharmaceutical compounds such as warfarin, thyroxine, indole, and benzodiazepin. Among the PFOA binding sites, five have interaction energies in excess of -6 kcal/mol, which become nine for PFOS. The calculated binding free energy of PFOA to the Trp 214 binding site is the highest among the PFOA complexes, -8.0 kcal/mol, in good agreement with literature experimental data. The PFOS binding site with the highest energy, -8.8 kcal/mol, is located near the Trp 214 binding site, thus partially affecting its activity. The maximum number of ligands that can be bound to HSA is 9 for PFOA and 11 for PFOS. The calculated data were adopted to predict the level of complexation of HSA as a function of the concentration of PFOA and PFOS found in human blood for different levels of exposition. The analysis of the factors contributing to the complex binding energy permitted to outline a set of guidelines for the rational design of alternative fluorinated surfactants with a lower bioaccumulation potential.

  12. 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.

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

    DEFF Research Database (Denmark)

    Wagner, Hans-Peter; Langbein, Wolfgang; Hvam, Jørn Märcher

    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...

  14. The Effect of Chemical Composition and Structure on XPS Binding Energies in Zeolites

    NARCIS (Netherlands)

    Weckhuysen, B.M.; Gijzeman, O.L.J.; Mens, A.J.M.; Lenthe, J.H. van; Mortier, W.J.

    2003-01-01

    The effect of zeolite composition and structure on XPS core level binding energies has been studied for a large class of zeolites (FAU, MFI, MOR, LTA) differing in their counterions (Na, K, Rb, Ca, Mg, Ba) and Si:Al ratio (1 to 160). Whereas absolute binding energies cannot be determined to any reas

  15. Determining binding energies of valence-band electrons in insulators and semiconductors via lanthanide spectroscopy

    NARCIS (Netherlands)

    Dorenbos, P.

    2013-01-01

    Models and methods to determine the absolute binding energy of 4f-shell electrons in lanthanide dopants will be combined with data on the energy of electron transfer from the valence band to a lanthanide dopant. This work will show that it provides a powerful tool to determine the absolute binding e

  16. The Effect of Chemical Composition and Structure on XPS Binding Energies in Zeolites

    NARCIS (Netherlands)

    Weckhuysen, B.M.; Gijzeman, O.L.J.; Mens, A.J.M.; Lenthe, J.H. van; Mortier, W.J.

    2003-01-01

    The effect of zeolite composition and structure on XPS core level binding energies has been studied for a large class of zeolites (FAU, MFI, MOR, LTA) differing in their counterions (Na, K, Rb, Ca, Mg, Ba) and Si:Al ratio (1 to 160). Whereas absolute binding energies cannot be determined to any

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

    Directory of Open Access Journals (Sweden)

    Manuela Maurer

    2016-04-01

    Full Text Available 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.

  18. CLiBE: a database of computed ligand binding energy for ligand-receptor complexes.

    Science.gov (United States)

    Chen, X; Ji, Z L; Zhi, D G; Chen, Y Z

    2002-11-01

    Consideration of binding competitiveness of a drug candidate against natural ligands and other drugs that bind to the same receptor site may facilitate the rational development of a candidate into a potent drug. A strategy that can be applied to computer-aided drug design is to evaluate ligand-receptor interaction energy or other scoring functions of a designed drug with that of the relevant ligands known to bind to the same binding site. As a tool to facilitate such a strategy, a database of ligand-receptor interaction energy is developed from known ligand-receptor 3D structural entries in the Protein Databank (PDB). The Energy is computed based on a molecular mechanics force field that has been used in the prediction of therapeutic and toxicity targets of drugs. This database also contains information about ligand function and other properties and it can be accessed at http://xin.cz3.nus.edu.sg/group/CLiBE.asp. The computed energy components may facilitate the probing of the mode of action and other profiles of binding. A number of computed energies of some PDB ligand-receptor complexes in this database are studied and compared to experimental binding affinity. A certain degree of correlation between the computed energy and experimental binding affinity is found, which suggests that the computed energy may be useful in facilitating a qualitative analysis of drug binding competitiveness.

  19. Free energy of binding of a small molecule to an amorphous polymer in a solvent.

    Science.gov (United States)

    Chunsrivirot, Surasak; Trout, Bernhardt L

    2011-06-01

    Crystallization is a commonly used purification process in industrial practice. It usually begins with heterogeneous nucleation on a foreign surface. The complicated mechanism of heterogeneous nucleation is not well understood, but we hypothesize that a possible correlation between binding affinity to a surface and nucleation enhancement might exist. Amorphous polymers have been used in controlling crystallization. However, to our knowledge, no attempt has been made to calculate the free energy of binding of a small molecule to an amorphous polymer in a solvent, and to characterize the binding sites/conformations of this system at a molecular level. We developed a two-step approach, first using Adsorption Locator to identify probable binding sites and molecular dynamics to screen for the best binding sites and then using the Blue-Moon Ensemble method to compute the free energy of binding. A system of ethylene glycol, polyvinyl alcohol (PVA), and heavy water (D(2)O) was used for validation, since experimental data exists on a related system. Looking at four independently constructed surfaces, we found that ethylene glycol binds to an indentation on the surface or in a hole beneath the surface. We focused on the indentation binding sites because they are easily accessible and do not have large free energy barriers. The closest system for which experimental data on binding energetics exists is ethylene glycol on PVA in aqueous solutions/gels, and the magnitudes of the free energy of binding to the three best indentation binding sites are close to the experimental value, 0.4-3.7 kcal/mol higher. Our approach offers a way to compute the free energy of binding and characterize the binding sites/conformations, and is general enough to apply to other small molecule/amorphous polymer/solvent systems.

  20. A Prediction Method of Binding Free Energy of Protein and Ligand

    Science.gov (United States)

    Yang, Kun; Wang, Xicheng

    2010-05-01

    Predicting the binding free energy is an important problem in bimolecular simulation. Such prediction would be great benefit in understanding protein functions, and may be useful for computational prediction of ligand binding strengths, e.g., in discovering pharmaceutical drugs. Free energy perturbation (FEP)/thermodynamics integration (TI) is a classical method to explicitly predict free energy. However, this method need plenty of time to collect datum, and that attempts to deal with some simple systems and small changes of molecular structures. Another one for estimating ligand binding affinities is linear interaction energy (LIE) method. This method employs averages of interaction potential energy terms from molecular dynamics simulations or other thermal conformational sampling techniques. Incorporation of systematic deviations from electrostatic linear response, derived from free energy perturbation studies, into the absolute binding free energy expression significantly enhances the accuracy of the approach. However, it also is time-consuming work. In this paper, a new prediction method based on steered molecular dynamics (SMD) with direction optimization is developed to compute binding free energy. Jarzynski's equality is used to derive the PMF or free-energy. The results for two numerical examples are presented, showing that the method has good accuracy and efficiency. The novel method can also simulate whole binding proceeding and give some important structural information about development of new drugs.

  1. On the binding energies of excitons in polar quantum well structures in a weak electric field

    Institute of Scientific and Technical Information of China (English)

    Wu Yun-Feng; Liang Xi-Xia; K. K. Bajaj

    2005-01-01

    The binding energies of excitons in quantum well structures subjected to an applied uniform electric field by taking into account the exciton longitudinal optical phonon interaction is calculated. The binding energies and corresponding Stark shifts for Ⅲ-Ⅴ and Ⅱ-Ⅵ compound semiconductor quantum well structures have been numerically computed.The results for GaAs/AlGaAs and ZnCdSe/ZnSe quantum wells are given and discussed. Theoretical results show that the exciton-phonon coupling reduces both the exciton binding energies and the Stark shifts by screening the Coulomb interaction. This effect is observable experimentally and cannot be neglected.

  2. Exciton binding energy in GaAsBiN spherical quantum dot heterostructures

    Science.gov (United States)

    Das, Subhasis; Dhar, S.

    2017-03-01

    The ground state exciton binding energies (EBE) of heavy hole excitons in GaAs1-x-yBixNy - GaAs spherical quantum dots (QD) are calculated using a variational approach under 1s hydrogenic wavefunctions within the framework of effective mass approximation. Both the nitrogen and the bismuth content in the material are found to affect the binding energy, in particular for larger nitrogen content and lower dot radii. Calculations also show that the ground state exciton binding energies of heavy holes increase more at smaller dot sizes as compared to that for the light hole excitons.

  3. Binding Energy of Biexcitons in GaAs Quantum-Well Wires

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-Jun; CHEN Xiao-Fang; LI Shu-Shen

    2004-01-01

    @@ The binding energy of a biexciton in GaAs quantum-well wires is calculated variationally by use ofa two-parameter trial wavefunction and a one-dimensional equivalent potential model. There is no artificial parameter added in our calculation. Our results agree fairly well with the previous results. It is found that the binding energies are closely correlative to the size of wire. The binding energy of biexcitons is smaller than that of neutral bound excitons in GaAs quantum-well wires when the dopant is located at the centre of the wires.

  4. Subsite binding energies of an exo-polygalacturonase using isothermal titration calorimetry

    Energy Technology Data Exchange (ETDEWEB)

    Mertens, Jeffrey A., E-mail: Jeffrey.Mertens@ars.usda.gov [Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604 (United States); Hector, Ronald E.; Bowman, Michael J. [Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604 (United States)

    2012-01-10

    Highlights: Black-Right-Pointing-Pointer Thermodynamics of (GalpA){sub n} oligomers binding to an exo-polygalacturonase. Black-Right-Pointing-Pointer Energetics of binding (GalpA){sub n} were determined by ITC. Black-Right-Pointing-Pointer Thermodynamic parameters attributable to individual subsites were determined. - Abstract: 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 process that is enthalpically driven and results in extremely tight binding of the substrate to RPG16. Binding energies in combination with prior biochemical data suggests that RPG16 has the potential for five subsites, -1 to +4, with the greatest contribution to binding energies arising from subsite -1/+1. While the enthalpic contribution to binding decreases substantially for subsites +2 to +4, beneficial entropic effects occur in subsites +3 and +4 leading to increased total free energy as the length of oligomer increases. This information will be useful for additional studies in determining the binding contributions of specific amino acids with mutant enzymes.

  5. Imaging the crustal structure of the valley of Mexico and higher mode identification using H/V spectral ratio

    Science.gov (United States)

    Rivet, D.; Campillo, M.; Sanchez-Sesma, F.; Singh, S. K.

    2012-04-01

    We reconstruct Rayleigh and Love waves from cross-correlations of ambient seismic noise recorded at 19 broad-band stations of the MesoAmerica Seismic Experiment (MASE) and Valley of Mexico Experiment (VMEX). The cross-correlations are computed over 2 years of noise records for the 8 MASE stations and over 1 year for the 11 VMEX stations. We use surface waves with sufficient signal-to-noise ratio to measure group velocity dispersion curves at period of 0.5 to 3 seconds. For paths within the soft quaternary sediments basin, the maximum energy is observed at velocity higher than expected for the fundamental mode. This observation suggests the importance of higher modes as the main vectors of energy in such complex structures. To perform a reliable inversion of the velocity structure beneath the valley, an identification of these dominants modes is required. To identify the modes of surface waves we use the spectral ratio of the horizontal components over the vertical component (H/V) measured on seismic coda. We compare the observed values with the theoretical H/V for the velocity model deduced from surface wave dispersion when assuming a particular mode. H/V ratio in the coda is computed under the hypothesis of equipartition of a diffuse field in a layered medium following Margerin et al. [2009] and Sánchez-Sesma et al. [2011]. We processed several events to ensure that the observed H/V is stable. The comparison of the modelled dispersion and H/V ratio allows for mode identification, and consequently to recover the velocity model of the structure. We conclude on the predominance of higher modes in our observations. The excitation of higher modes is key element of explanation for the long duration and amplification of the seismic signals observed in the Valley of Mexico.

  6. Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy.

    Science.gov (United States)

    Payne, Christina M; Jiang, Wei; Shirts, Michael R; Himmel, Michael E; Crowley, Michael F; Beckham, Gregg T

    2013-12-18

    Many glycoside hydrolase (GH) enzymes act via a processive mechanism whereby an individual carbohydrate polymer chain is decrystallized and hydrolyzed along the chain without substrate dissociation. Despite considerable structural and biochemical studies, a molecular-level theory of processivity that relates directly to structural features of GH enzymes does not exist. Here, we hypothesize that the degree of processivity is directly linked to the ability of an enzyme to decrystallize a polymer chain from a crystal, quantified by the binding free energy of the enzyme to the cello-oligosaccharide. We develop a simple mathematical relationship formalizing this hypothesis to quantitatively relate the binding free energy to experimentally measurable kinetic parameters. We then calculate the absolute ligand binding free energy of cellulose chains to the biologically and industrially important GH Family 7 processive cellulases with free energy perturbation/replica-exchange molecular dynamics. Taken with previous observations, our results suggest that degree of processivity is directly correlated to the binding free energy of cello-oligosaccharide ligands to GH7s. The observed binding free energies also suggest candidate polymer morphologies susceptible to enzyme action when compared to the work required to decrystallize cellulose chains. We posit that the ligand binding free energy is a key parameter in comparing the activity and function of GHs and may offer a molecular-level basis toward a general theory of carbohydrate processivity in GHs and other enzymes able to process linear carbohydrate polymers, such as cellulose and chitin synthases.

  7. Constraints on the variable subglacial structure of Whillans Ice Stream from ambient noise Rayleigh wave H/V ratios

    Science.gov (United States)

    Pratt, M. J.; Shen, W.; Wiens, D.; Winberry, J. P.; Anandakrishnan, S.

    2016-12-01

    Horizontal-to-vertical (H/V) ellipticity ratios of Rayleigh waves have been used to determine shallow (reflection imaging showing a deeper sedimentary package that extends to an unknown depth. It is also known that the frictional properties of the WIS ice-bed interface at 700 m depth are highly heterogeneous, including stick-spots of high friction, possibly as a result of compacted sediment or bedrock, and active subglacial lakes where frictional coefficients are effectively zero. Ambient noise cross-correlations are calculated between all station pairs, restricting the minimum interstation distance to 20 km, as well as constraining valid H/V ratios of radial and vertical sources between the same station pair to wave energy with good signal-to-noise between 6 s and 20 s that are sensitive to the shear velocity of the shallowest sedimentary layers beneath the ice stream and is combined with average phase and group velocity of the area to help constrain the inversion. H/V ratio modeling results suggest that ratios are highly susceptible to sedimentary layer thickness. Ratios also increase over the observed frequency band with the presence of a shallow, saturated sedimentary layer with high Vp/Vs. In preliminary results, we observe an increase in H/V ratio towards the grounding line as well as at stations where hydro-potential surface is high. These higher ratios can be attributed to higher water content within sediments, or an increase in the sedimentary layer thickness.

  8. Fragmentation cross sections and binding energies of neutron-rich nuclei

    Science.gov (United States)

    Tsang, M. B.; Lynch, W. G.; Friedman, W. A.; Mocko, M.; Sun, Z. Y.; Aoi, N.; Cook, J. M.; Delaunay, F.; Famiano, M. A.; Hui, H.; Imai, N.; Iwasaki, H.; Motobayashi, T.; Niikura, M.; Onishi, T.; Rogers, A. M.; Sakurai, H.; Suzuki, H.; Takeshita, E.; Takeuchi, S.; Wallace, M. S.

    2007-10-01

    An exponential dependence of the fragmentation cross section on the average binding energy is observed and reproduced with a statistical model. The observed functional dependence is robust and allows the extraction of binding energies from measured cross sections. From the systematics of Cu isotope cross sections, the binding energies of Cu76,77,78,79 have been extracted. They are 636.94±0.4,647.1±0.4,651.6±0.4, and 657.8±0.5 MeV, respectively. Specifically, the uncertainty of the binding energy of Cu75 is reduced from 980 keV, as listed in the 2003 mass table of Audi, Wapstra, and Thibault to 400 keV. The predicted cross sections of two near drip-line nuclei, Na39 and Mg40 from the fragmentation of Ca48 are discussed.

  9. In Silico Docking, Molecular Dynamics and Binding Energy Insights into the Bolinaquinone-Clathrin Terminal Domain Binding Site

    Directory of Open Access Journals (Sweden)

    Mohammed K. Abdel-Hamid

    2014-05-01

    Full Text Available Clathrin-mediated endocytosis (CME is a process that regulates selective internalization of important cellular cargo using clathrin-coated vesicles. Perturbation of this process has been linked to many diseases including cancer and neurodegenerative conditions. Chemical proteomics identified the marine metabolite, 2-hydroxy-5-methoxy-3-(((1S,4aS,8aS-1,4a,5-trimethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-2-ylmethylcyclohexa- 2,5-diene-1,4-dione (bolinaquinone as a clathrin inhibitor. While being an attractive medicinal chemistry target, the lack of data about bolinaquinone’s mode of binding to the clathrin enzyme represents a major limitation for its structural optimization. We have used a molecular modeling approach to rationalize the observed activity of bolinaquinone and to predict its mode of binding with the clathrin terminal domain (CTD. The applied protocol started by global rigid-protein docking followed by flexible docking, molecular dynamics and linear interaction energy calculations. The results revealed the potential of bolinaquinone to interact with various pockets within the CTD, including the clathrin-box binding site. The results also highlight the importance of electrostatic contacts over van der Waals interactions for proper binding between bolinaquinone and its possible binding sites. This study provides a novel model that has the potential to allow rapid elaboration of bolinaquinone analogues as a new class of clathrin inhibitors.

  10. A general scheme for the estimation of oxygen binding energies on binary transition metal surface alloys

    DEFF Research Database (Denmark)

    Greeley, Jeffrey Philip; Nørskov, Jens Kehlet

    2005-01-01

    A simple scheme for the estimation of oxygen binding energies on transition metal surface alloys is presented. It is shown that a d-band center model of the alloy surfaces is a convenient and appropriate basis for this scheme; variations in chemical composition, strain effects, and ligand effects...... for the estimation of oxygen binding energies on a wide variety of transition metal alloys. (c) 2005 Elsevier B.V. All rights reserved....

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

    Science.gov (United States)

    Petukh, Marharyta; Dai, Luogeng; Alexov, Emil

    2016-04-12

    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/.

  12. Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies.

    Science.gov (United States)

    Chaudhary, Neha; Aparoy, Polamarasetty

    2017-03-01

    COX-2 is a well-known drug target in inflammatory disorders. COX-1/COX-2 selectivity of NSAIDs is crucial in assessing the gastrointestinal side effects associated with COX-1 inhibition. Celecoxib, rofecoxib, and valdecoxib are well-known specific COX-2 inhibiting drugs. Recently, polmacoxib, a COX-2/CA-II dual inhibitor has been approved by the Korean FDA. These COXIBs have similar structure with diverse activity range. Present study focuses on unraveling the mechanism behind the 10-fold difference in the activities of these sulfonamide-containing COXIBs. In order to obtain insights into their binding with COX-2 at molecular level, molecular dynamics simulations studies, and MM-PBSA approaches were employed. Further, per-residue decomposition of these energies led to the identification of crucial amino acids and interactions contributing to the differential binding of COXIBs. The results clearly indicated that Leu338, Ser339, Arg499, Ile503, Phe504, Val509, and Ser516 (Leu352, Ser353, Arg513, Ile517, Phe518, Val523, and Ser530 in PGHS-1 numbering) were imperative in determining the activity of these COXIBs. The binding energies and energy contribution of various residues were similar in all the three simulations. The results suggest that hydrogen bond interaction between the hydroxyl group of Ser516 and five-membered ring of diarylheterocycles augments the affinity in COXIBs. The SAR of the inhibitors studied and the per-residue energy decomposition values suggested the importance of Ser516. Additionally, the positive binding energy obtained with Arg106 explains the binding of COXIBs in hydrophobic channel deep in the COX-2 active site. The findings of the present work would aid in the development of potent COX-2 inhibitors.

  13. Accurate determination of the binding energy of the formic acid dimer: The importance of geometry relaxation

    Science.gov (United States)

    Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

    2014-02-01

    The formic acid dimer in its C2h-symmetrical cyclic form is stabilized by two equivalent H-bonds. The currently accepted interaction energy is 18.75 kcal/mol whereas the experimental binding energy D0 value is only 14.22 ±0.12 kcal/mol [F. Kollipost, R. W. Larsen, A. V. Domanskaya, M. Nörenberg, and M. A. Suhm, J. Chem. Phys. 136, 151101 (2012)]. Calculation of the binding energies De and D0 at the CCSD(T) (Coupled Cluster with Single and Double excitations and perturbative Triple excitations)/CBS (Complete Basis Set) level of theory, utilizing CCSD(T)/CBS geometries and the frequencies of the dimer and monomer, reveals that there is a 3.2 kcal/mol difference between interaction energy and binding energy De, which results from (i) not relaxing the geometry of the monomers upon dissociation of the dimer and (ii) approximating CCSD(T) correlation effects with MP2. The most accurate CCSD(T)/CBS values obtained in this work are De = 15.55 and D0 = 14.32 kcal/mol where the latter binding energy differs from the experimental value by 0.1 kcal/mol. The necessity of employing augmented VQZ and VPZ calculations and relaxing monomer geometries of H-bonded complexes upon dissociation to obtain reliable binding energies is emphasized.

  14. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.

    Science.gov (United States)

    Jo, Sunhwan; Jiang, Wei; Lee, Hui Sun; Roux, Benoît; Im, Wonpil

    2013-01-28

    Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly Web interface, CHARMM-GUI Ligand Binder ( http://www.charmm-gui.org/input/gbinding ), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently set up the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three nonpolar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). Therefore, CHARMM-GUI Ligand Binder provides a convenient and reliable way to set up the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems.

  15. Sensitivity Analysis of Grain Surface Chemistry to Binding Energies of Ice Species

    Science.gov (United States)

    Penteado, E. M.; Walsh, C.; Cuppen, H. M.

    2017-07-01

    Advanced telescopes, such as ALMA and the James Webb Space Telescope, are likely to show that the chemical universe may be even more complex than currently observed, requiring astrochemical modelers to improve their models to account for the impact of new data. However, essential input information for gas-grain models, such as binding energies of molecules to the surface, have been derived experimentally only for a handful of species, leaving hundreds of species with highly uncertain estimates. We present in this paper a systematic study of the effect of uncertainties in the binding energies on an astrochemical two-phase model of a dark molecular cloud, using the rate equations approach. A list of recommended binding energy values based on a literature search of published data is presented. Thousands of simulations of dark cloud models were run, and in each simulation a value for the binding energy of hundreds of species was randomly chosen from a normal distribution. Our results show that the binding energy of H2 is critical for the surface chemistry. For high binding energies, H2 freezes out on the grain forming an H2 ice. This is not physically realistic, and we suggest a change in the rate equations. The abundance ranges found are in reasonable agreement with astronomical ice observations. Pearson correlation coefficients revealed that the binding energy of HCO, HNO, CH2, and C correlate most strongly with the abundance of dominant ice species. Finally, the formation route of complex organic molecules was found to be sensitive to the branching ratios of H2CO hydrogenation.

  16. 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.

  17. 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...

  18. A STUDY ON THE INTERPRETATION OF WAVE COMPONENTS IN MICROTREMOR H/V SPECTRUM

    Science.gov (United States)

    Nagao, Takashi; Yamada, Masayuki; Nozu, Atsushi

    The peak information in microtremor H/V spectrum is often used in the evaluation of amplification characteristics of earthquake ground motion. Although characteristics of microtremor H/V spectrum can be generally explained by those of surface waves, the assumption that microtremor only consists of surface wave is hardly valid considering the fact that peak amplification is finite and often correlates with amplification characteristics of earthquake ground motion. This study presents a new in terpretation of wave components of microtremor H/V spectrum using medium response analysis. Mixture rates of surface wave and body wave that well explain microtremor H/V spectrum was studied.

  19. Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking.

    Science.gov (United States)

    Minh, David D L

    2012-09-14

    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 calorimetry measurements. Implicit ligand theory provides guidance on how to improve existing molecular docking algorithms and insight into the concepts of induced fit and conformational selection in noncovalent macromolecular recognition.

  20. Binding Energy of an Off-Center D- in a Spherical Quantum Dot

    Institute of Scientific and Technical Information of China (English)

    LIU Dong-Ming; XIE Wen-Fang

    2009-01-01

    Using the method of matrix diagonalization, we investigate an off-center D- in a spherical quantum dot (QD) subjected to a parabolic potential confinement. We discuss the effect of the position of an impurity in the QD on the binding energy of the D- system. Furthermore, we compare a negatively charged donor D- with a neutral donor D0 confined by a spherical QD with a parabolic potential. The results have dearly demonstrate the so-called quantum size effect. The binding energy/s dependent on the confining potential hω0 and the impurity ion distance D.

  1. Binding energies of hydrogen molecules to isoreticular metal-organic framework materials

    Science.gov (United States)

    Sagara, Tatsuhiko; Klassen, James; Ortony, Julia; Ganz, Eric

    2005-07-01

    Recently, several novel isoreticular metal-organic framework (IRMOF) structures have been fabricated and tested for hydrogen storage applications. To improve our understanding of these materials, and to promote quantitative calculations and simulations, the binding energies of hydrogen molecules to the MOF have been studied. High-quality second-order Møller-Plesset (MP2) calculations using the resolution of the identity approximation and the quadruple zeta QZVPP basis set were used. These calculations use terminated molecular fragments from the MOF materials. For H2 on the zinc oxide corners, the MP2 binding energy using Zn4O(HCO2)6 molecule is 6.28kJ/mol. For H2 on the linkers, the binding energy is calculated using lithium-terminated molecular fragments. The MP2 results with coupled-cluster singles and doubles and noniterative triples method corrections and charge-transfer corrections are 4.16kJ/mol for IRMOF-1, 4.72kJ/mol for IRMOF-3, 4.86kJ/mol for IRMOF-6, 4.54kJ/mol for IRMOF-8, 5.50 and 4.90kJ/mol for IRMOF-12, 4.87 and 4.84kJ/mol for IRMOF-14, 5.42kJ/mol for IRMOF-18, and 4.97 and 4.66kJ/mol for IRMOF-993. The larger linkers are all able to bind multiple hydrogen molecules per side. The linkers of IRMOF-12, IRMOF-993, and IRMOF-14 can bind two to three, three, and four hydrogen molecules per side, respectively. In general, the larger linkers have the largest binding energies, and, together with the enhanced surface area available for binding, will provide increased hydrogen storage. We also find that adding up NH2 or CH3 groups to each linker can provide up to a 33% increase in the binding energy.

  2. Hypernuclear interactions and the binding energies of and hypernuclei

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R.; Usmani, Q.N.

    1988-01-01

    By use of variational calculations a reasonable hadronic description is obtained of the s-shell hypernuclei, of /sub /ZBe, and of the well depth, with N forces which are consistent with p scattering and which are quite strongly spin-dependent, with reasonable TPE NN forces with strongly repulsive dispersive-type NN forces. For the latter we also consider a spin-dependent version which is somewhat favored by our analysis. /sub /ZBe is treated as a 2ed + system and is significantly overbound, approx. =1 MeV, if only ed ed and ed potentials are used. An ed ed potential obtained from the NN forces nicely accounts for this overbinding. The hypernuclei /sub /WHe and /sub / Be are treated as ed + 2 and 2ed + 2 systems. Use of the /sub / Be event gives approx. =1.5 MeV too little binding for /sub /WHe. The S0 potential obtained from /sub / Be is quite strongly attractive, comparable to the N and also to the NN potential without OPE. 18 refs.

  3. Theoretical studies on the binding energy of β-sheet models

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In this paper,B3LYP and MP2 methods are used to investigate the binding energy of seventeen antiparallel and parallel β-sheet models. The results indicate that the binding energy obtained from B3LYP calculations is weaker than that obtained from MP2 calculations but the relative binding energy yielded by B3LYP is almost the same as that by MP2. For the antiparallel β-sheets in which two N―H···O═C hydrogen bonds can form either a large hydrogen-bonded ring or a small hydrogen-bonded ring,the binding energy increases obviously when one large ring unit is added,whereas it only changes slightly when one small ring unit is added because of the secondary electrostatic repulsive interaction existing in the small ring unit which is estimated to be about 20 kJ/mol. For the parallel β-sheet models,the binding energy increases almost exactly linearly with the increase of the chain length.

  4. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

    Science.gov (United States)

    Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

    2016-01-01

    We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations.

  5. Binding energies of hypernuclei and. lambda. -nuclear interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R.; Usmani, Q.N.

    1985-01-01

    Variational Monte Carlo calculations have been made for the s-shell hypernuclei and also of /sup 9/Be hypernuclei with a 2..cap alpha.. + ..lambda.. model. The well depth is calculated variationally with the Fermi hypernetted chain method. A satisfactory description of all the relevant experimental ..lambda.. separation energies and also of the ..lambda..p scattering can be obtained with reasonable TPE ..lambda..N and ..lambda..NN forces and strongly repulsive dispersive ..lambda..NN forces which are preferred to be spin dependent. We discuss variational calculations for /sup 6/He and /sup 10/Be hypernuclei with ..cap alpha.. + 2..lambda.. and 2..cap alpha.. + 2..lambda.. models, and the results obtained for the ..lambda lambda.. interaction and for /sup 6/He hypernuclei from analysis of /sup 10/Be hypernuclei Coulomb effects and charge symmetry breaking in the A = 4 hypernuclei are discussed. 24 refs., 5 figs.

  6. H v Council: Another Court breakthrough in the Common Foreign and Security Policy

    DEFF Research Database (Denmark)

    Butler, Graham

    2016-01-01

    , Tanzania (Case C-263/14) and H v. Council (Case C-455/14 P) address different questions, and with a third, Rosneft (Case C-72/15), being delivered later in the year. This sequence of judgments demonstrates the fluidity of CFSP dynamics. In this blog post, analysis will focus on the H v. Council judgment...

  7. H v Council: Another Court breakthrough in the Common Foreign and Security Policy

    DEFF Research Database (Denmark)

    Butler, Graham

    2016-01-01

    , Tanzania (Case C-263/14) and H v. Council (Case C-455/14 P) address different questions, and with a third, Rosneft (Case C-72/15), being delivered later in the year. This sequence of judgments demonstrates the fluidity of CFSP dynamics. In this blog post, analysis will focus on the H v. Council judgment...

  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. 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.

  11. Evaluation of atomic electron binding energies for Monte Carlo particle transport

    CERN Document Server

    Pia, Maria Grazia; Batic, Matej; Begalli, Marcia; Kim, Chan Hyeong; Quintieri, Lina; Saracco, Paolo

    2011-01-01

    A survey of atomic binding energies used by general purpose Monte Carlo systems is reported. Various compilations of these parameters have been evaluated; their accuracy is estimated with respect to experimental data. Their effects on physics quantities relevant to Monte Carlo particle transport are highlighted: X-ray fluorescence emission, electron and proton ionization cross sections, and Doppler broadening in Compton scattering. The effects due to different binding energies are quantified with respect to experimental data. The results of the analysis provide quantitative ground for the selection of binding energies to optimize the accuracy of Monte Carlo simulation in experimental use cases. Recommendations on software design dealing with these parameters and on the improvement of data libraries for Monte Carlo simulation are discussed.

  12. Fragmentation cross-sections and binding energies of neutron-rich nuclei

    CERN Document Server

    Tsang, M B; Friedman, W A; Mocko, M; Sun, Z Y; Aoi, N; Cook, J M; Delaunay, F; Famiano, M A; Hui, H; Imai, N; Iwasaki, H; Motobayashi, T; Niikura, M; Onishi, T; Rogers, A M; Sakuraï, H; Suzuki, H; Takeshita, E; Takeuchi, S; Wallace, M S

    2007-01-01

    An exponential dependence of the fragmentation cross-section on the average binding energy is observed and reproduced with a statistical model. The observed functional dependence is robust and allows the extraction of binding energies from measured cross-sections. From the systematics of 75,77,78,79Cu isotope cross-sections have been extracted. They are 636.94 +/- 0.40 MeV, 647.1 +/- 0.4 MeV, 651.6 +/- 0.4 MeV and 657.8 +/- 0.5 MeV, respectively. Specifically, the uncertainty of the binding energy of 75Cu is reduced from 980 keV (listed value in the 2003 mass table of Audi and Wapstra) to 400 keV. The predicted cross-sections of two near drip-line nuclei, 39Na and 40Mg, from the fragmentation of 48Ca are discussed.

  13. 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.

  14. Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions.

    Science.gov (United States)

    Singh, Nidhi; Warshel, Arieh

    2010-05-15

    Calculating the absolute binding free energies is a challenging task. Reliable estimates of binding free energies should provide a guide for rational drug design. It should also provide us with deeper understanding of the correlation between protein structure and its function. Further applications may include identifying novel molecular scaffolds and optimizing lead compounds in computer-aided drug design. Available options to evaluate the absolute binding free energies range from the rigorous but expensive free energy perturbation to the microscopic linear response approximation (LRA/beta version) and related approaches including the linear interaction energy (LIE) to the more approximated and considerably faster scaled protein dipoles Langevin dipoles (PDLD/S-LRA version) as well as the less rigorous molecular mechanics Poisson-Boltzmann/surface area (MM/PBSA) and generalized born/surface area (MM/GBSA) to the less accurate scoring functions. There is a need for an assessment of the performance of different approaches in terms of computer time and reliability. We present a comparative study of the LRA/beta, the LIE, the PDLD/S-LRA/beta, and the more widely used MM/PBSA and assess their abilities to estimate the absolute binding energies. The LRA and LIE methods perform reasonably well but require specialized parameterization for the nonelectrostatic term. The PDLD/S-LRA/beta performs effectively without the need of reparameterization. Our assessment of the MM/PBSA is less optimistic. This approach appears to provide erroneous estimates of the absolute binding energies because of its incorrect entropies and the problematic treatment of electrostatic energies. Overall, the PDLD/S-LRA/beta appears to offer an appealing option for the final stages of massive screening approaches.

  15. Protein:Ligand binding free energies: A stringent test for computational protein design.

    Science.gov (United States)

    Druart, Karen; Palmai, Zoltan; Omarjee, Eyaz; Simonson, Thomas

    2016-02-01

    A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl-tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate l-tyrosine (l-Tyr), compared to the analogs d-Tyr, p-acetyl-, and p-azido-phenylalanine (ac-Phe, az-Phe). We simulate l- and d-Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous "MD/GBSA" procedure: molecular dynamics with explicit solvent for structures and a Generalized Born + Surface Area model for binding free energies. Next, we consider l-Tyr, ac- and az-Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either l-Tyr or d-Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when l-Tyr is the ligand and a d-Tyr specific mutant when d-Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln.

  16. Nuclear charge symmetry breaking and the /sup 3/H-/sup 3/He binding energy difference

    Energy Technology Data Exchange (ETDEWEB)

    Brandenburg, R.A.; Chulick, G.S.; Kim, Y.E.; Klepacki, D.J.; Machleidt, R.; Picklesimer, A.; Thaler, R.M.

    1988-02-01

    We study the /sup 3/H- /sup 3/He binding energy difference, taking into account the Coulomb interaction and charge symmetry breaking of the nuclear force consistent with recent NN experimental data. Realistic interactions are generated which describe the charge symmetry violations reflected in the different nucleon-nucleon scattering lengths. The influence of nuclear charge symmetry breaking on the perturbative Coulomb contribution to the /sup 3/He binding energy is discussed. It is shown that the experimental mass difference can be explained by these and theoretical estimates of other known effects.

  17. Nuclear charge symmetry breaking and the 3H-3He binding energy difference

    Science.gov (United States)

    Brandenburg, R. A.; Chulick, G. S.; Kim, Y. E.; Klepacki, D. J.; Machleidt, R.; Picklesimer, A.; Thaler, R. M.

    1988-02-01

    We study the 3H- 3He binding energy difference, taking into account the Coulomb interaction and charge symmetry breaking of the nuclear force consistent with recent NN experimental data. Realistic interactions are generated which describe the charge symmetry violations reflected in the different nucleon-nucleon scattering lengths. The influence of nuclear charge symmetry breaking on the perturbative Coulomb contribution to the 3He binding energy is discussed. It is shown that the experimental mass difference can be explained by these and theoretical estimates of other known effects.

  18. External electric field effect on exciton binding energy in InGaAsP/InP cylindrical quantum wires

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hailong, E-mail: hlwang@mail.qfnu.edu.cn [College of Physics and Engineering, Qufu Normal University, Qufu 273165 (China); Wang, Wenjuan [College of Physics and Engineering, Qufu Normal University, Qufu 273165 (China); Gong, Qian; Wang, Shumin [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050 (China)

    2016-12-15

    Exciton binding energies in InGaAsP/InP cylindrical quantum wires are calculated through variational method under the framework of effective-mass envelope-function approximation. It is shown that the variation of exciton binding energy is highly dependent on radius of the wire, material composition and external electric field. Exciton binding energy is a non-monotonic function of wire radius. It increases until it reaches a maximum, and then decreases as the wire radius decreases. With the increase of In composition, the wire radius need increase to reach the maximum value of exciton binding energy. It is also found that the external electric field has little effect on exciton binding energy. However, the excitonic effect will be destroyed when external electric field is large enough. In addition, the Stark shift of exciton binding energy is also calculated.

  19. Does alpha-helix folding necessarily provide an energy source for the protein-lipid binding?

    Science.gov (United States)

    Gursky, Olga

    2007-01-01

    Lipid-induced alpha-helix folding, which occurs in many lipid surface-binding proteins and peptides such as apolipoproteins and synucleins, has been proposed to provide an energy source for protein-lipid interactions. We propose that in a system comprised of a phospholipid surface and a small polypeptide that is unfolded in solution and binds reversibly to lipid surface, helical folding involves expenditure of free energy as compared to a similar polypeptide that is alpha-helical in solution. This is a consequence of the entropic cost of helix folding that is illustrated in a simple thermodynamic model and exemplifies the general "key-into-lock" paradigm of protein-ligand binding. Even though this simple model does not explicitly address the protein-induced lipid re-arrangement and may not directly apply to large proteins that undergo significant tertiary structural changes upon lipid binding, it suggests that the notion of helix folding as an energy source for lipid binding should be treated with caution.

  20. 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.

  1. Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations

    Science.gov (United States)

    Ngo, Son Tung; Nguyen, Minh Tung; Nguyen, Minh Tho

    2017-05-01

    The absolute binding free energy of an inhibitor to HIV-1 Protease (PR) was determined throughout evaluation of the non-bonded interaction energy difference between the two bound and unbound states of the inhibitor and surrounding molecules by the fast pulling of ligand (FPL) process using non-equilibrium molecular dynamics (NEMD) simulations. The calculated free energy difference terms help clarifying the nature of the binding. Theoretical binding affinities are in good correlation with experimental data, with R = 0.89. The paradigm used is able to rank two inhibitors having the maximum difference of ∼1.5 kcal/mol in absolute binding free energies.

  2. Seismic ambient noise H/V spectral ratio using the ACA (autocorrelations of coda of autocorrelations) approach

    Science.gov (United States)

    Sanchez-Sesma, F. J.; Piña, J.; Campillo, M.; Luzón, F.; García-Jerez, A.; Albarello, D.; Lunedei, E.

    2012-12-01

    The seismic ambient noise horizontal-to-vertical spectral ratios (NHVSR) are valuable for microzonation, and seismic prospecting. This is particularly true for low-cost dense spatial sampling projects. Arai and Tokimatsu (2004) proposed to use average energy densities to compose the ratios. It means that H/V comes from the square root of the ratio of averages. On the other hand, a popular approach makes the average of spectral ratios. For ergodic processes peak values are usually the same using these two approaches. Sometimes however, the observations are insufficient and computed values for low frequencies display large variability and the corresponding H/V estimates may be inaccurate. The bias caused by localized sources may be the source of errors in the estimates. In this work we propose to compute the NHVSR using the Autocorrelations of Coda of Autocorrelations. This ACA approach is inspired in the work by Stehly et al. (2008). They used the Correlations of Coda of Correlations (C3) to isotropize the field. In our ACA approach the whole time series, say of 30 minutes, for each component is autocorrelated and the averages of the spectral density of selected windows (late coda windows are eliminated) are then improved estimates of directional energy densities. The computation of NHVSR using ACA appears more stable and free of transient effects. It remains to establish how this may be accounted for in forward calculation of H/V spectral ratios for models like a layered medium (e.g. Sánchez-Sesma et al., 2011; Albarello and Lunedei, 2011). This will require further scrutiny. References. Albarello, D. & E. Lunedei (2011). Structure of ambient vibration wavefield in the frequency range of engineering interest ([0.5, 20] Hz): insights from numerical modelling. Near Surface Geophysics 9, 543-559. Arai, H. & K. Tokimatsu (2004). S-wave velocity profiling by inversion of microtremor H/V spectrum, Bull. Seismol. Soc. Am. 94, 53-63. Sánchez-Sesma, F. J., M. Rodr

  3. Increased binding energy of impurities near a semiconductor-vacuum interface

    Energy Technology Data Exchange (ETDEWEB)

    Wijnheijmer, A.P.; Garleff, J.K.; Koenraad, P.M. [PSN, Eindhoven University of Technology (Netherlands); Teichmann, K.; Wenderoth, M.; Loth, S.; Ulbrich, R.G. [IV. Phys. Inst., Georg-August Univ. Goettingen (Germany)

    2008-07-01

    We have recently shown that a STM tip can be used as a tool to manipulate the charge state of individual impurities below the cleavage surface of a semiconductor. This manipulation allowed us to determine the binding energy of single donors and acceptors as a function of their depth (up to 1 nm) below the surface. We found that the binding energy strongly increases near the surface. In the case of a Si-donor in GaAs the binding energy increases continuously from 5.6 meV in the bulk to about 150 meV close to the surface. Our STM techniques also allowed for the determination of the size and shape of the Coulomb field of single ionized donors. We found that the range of the potential is strongly reduced relative to the bulk value. Both the reduced range of the Coulomb potential and the increased binding energy can be related to a reduced dielectric constant and increased effective mass near the surface. We discuss the implications of these findings.

  4. Comparison of experimental and theoretical binding and transition energies in the actinide region. [Review

    Energy Technology Data Exchange (ETDEWEB)

    Krause, M.O.; Nestor, C.W. Jr.

    1977-01-01

    The status of experimental and theoretical binding and transition energy determinations is reviewed extending the comparison between experiment and theory to encompass representative series of data for all actinides. This comprehensive comparison reveals areas where improvements may be indicated, showing whether theoretical treatments including all known contributions to the lowest order would be adequate in all instances. 45 references. (JFP)

  5. Modeling the chemical shift of lanthanide 4f electron binding energies

    NARCIS (Netherlands)

    Dorenbos, P.

    2012-01-01

    Lanthanides in compounds can adopt the tetravalent [Xe]4fn−1 (like Ce4+, Pr4+, Tb4+), the trivalent [Xe]4fn (all lanthanides), or the divalent [Xe]4f n+1 configuration (like Eu2+, Yb2+, Sm2+, Tm2+). The 4f-electron binding energy depends on the charge Q of the lanthanide ion and its chemical environ

  6. The effect of chemical composition and structure on XPS binding energies in zeolites

    NARCIS (Netherlands)

    Gijzeman, O.L.J.; Mens, A.J.M.; Lenthe, J.H. van; Mortier, W.J.; Weckhuysen, B.M.

    2004-01-01

    The effect of the composition and structure of zeolites on the XPS core level binding energies has been studied for a large class of zeolites, viz. FAU, MFI, MOR and LTA with Si:Al ratio chabging from 1 to 160. Also the effect of the difference in the counter ions (Na, K, Rb, Ca, Mg, Ba, La) was

  7. A new interpretation of the proton-neutron bound state The calculation of the binding energy

    CERN Document Server

    Mandache, N

    1996-01-01

    We treat the old problem of the proton-neutron bound state (the deuteron). Using a new concept of incomplete (partial) annihilation process we derive a formula for the binding energy of the deuteron, which does not contain any new constant. Some implications of this new approach are discussed.

  8. Improving the LIE Method for Binding Free Energy Calculations of Protein-Ligand Complexes.

    Science.gov (United States)

    Miranda, Williams E; Noskov, Sergei Yu; Valiente, Pedro A

    2015-09-28

    In this work, we introduced an improved linear interaction energy (LIE) method parameterization for computations of protein–ligand binding free energies. The protocol, coined LIE-D, builds on the linear relationship between the empirical coefficient γ in the standard LIE scheme and the D parameter, introduced in our work. The D-parameter encompasses the balance (difference) between electrostatic (polar) and van der Waals (nonpolar) energies in protein–ligand complexes. Leave-one-out cross-validation showed that LIE-D reproduced accurately the absolute binding free energies for our training set of protein–ligand complexes ( = 0.92 kcal/mol, SDerror = 0.66 kcal/mol, R(2) = 0.90, QLOO(2) = 0.89, and sPRESS(LOO) = 1.28 kcal/mol). We also demonstrated LIE-D robustness by predicting accurately the binding free energies for three different protein–ligand systems outside the training data set, where the electrostatic and van der Waals interaction energies were calculated with different force fields.

  9. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

    Science.gov (United States)

    Jiang, Wei; Roux, Benoît

    2010-07-01

    Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

  10. 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.

  11. Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics

    Science.gov (United States)

    Bhakat, Soumendranath; Söderhjelm, Pär

    2017-01-01

    The funnel metadynamics method enables rigorous calculation of the potential of mean force along an arbitrary binding path and thereby evaluation of the absolute binding free energy. A problem of such physical paths is that the mechanism characterizing the binding process is not always obvious. In particular, it might involve reorganization of the solvent in the binding site, which is not easily captured with a few geometrically defined collective variables that can be used for biasing. In this paper, we propose and test a simple method to resolve this trapped-water problem by dividing the process into an artificial host-desolvation step and an actual binding step. We show that, under certain circumstances, the contribution from the desolvation step can be calculated without introducing further statistical errors. We apply the method to the problem of predicting host-guest binding free energies in the SAMPL5 blind challenge, using two octa-acid hosts and six guest molecules. For one of the hosts, well-converged results are obtained and the prediction of relative binding free energies is the best among all the SAMPL5 submissions. For the other host, which has a narrower binding pocket, the statistical uncertainties are slightly higher; longer simulations would therefore be needed to obtain conclusive results.

  12. RPM3: a multifunctional microporous MOF with recyclable framework and high H2 binding energy.

    Science.gov (United States)

    Lan, Anjian; Li, Kunhao; Wu, Haohan; Kong, Lingzhu; Nijem, Nour; Olson, David H; Emge, Thomas J; Chabal, Yves J; Langreth, David C; Hong, Maochun; Li, Jing

    2009-08-03

    A microporous metal organic framework structure, Zn(2)(bpdc)(2)(bpee).2DMF (DMF: N,N-dimethylformamide), has been synthesized via solvothermal reactions. The compound is a new member of the RPM series (RPM = Rutgers Recyclable Porous Material) that possesses a flexible and recyclable three-dimensional framework containing one-dimensional channels. It exhibits interesting and multifold functionality, including porosity, commensurate adsorption for hydrocarbons, high hydrogen binding energy (determined by isosteric heats of hydrogen adsorption and confirmed by van der Waals density functional calculations) as a result of multifold binding to aromatic ligands (determined by IR spectroscopy), strong photoluminescence emission, and reversible fluorescence quenching properties.

  13. Precision Measurement of the 29Si, 33S, and 36Cl Binding Energies

    CERN Document Server

    Dewey, M S; Deslattes, R D; Doll, C; Jentschel, M; Mutti, P

    2006-01-01

    The binding energies of 29Si, 33S, and 36Cl have been measured with a relative uncertainty $< 0.59 \\times 10^{-6}$ using a flat-crystal spectrometer. The unique features of these measurements are 1) nearly perfect crystals whose lattice spacing is known in meters, 2) a highly precise angle scale that is derived from first principles, and 3) a gamma-ray measurement facility that is coupled to a high flux reactor with near-core source capability. The binding energy is obtained by measuring all gamma-rays in a cascade scheme connecting the capture and ground states. The measurements require the extension of precision flat-crystal diffraction techniques to the 5 to 6 MeV energy region, a significant precision measurement challenge. The binding energies determined from these gamma-ray measurements are consistent with recent highly accurate atomic mass measurements within a relative uncertainty of $4.3 \\times 10^{-7}$. The gamma-ray measurement uncertainties are the dominant contributors to the uncertainty of th...

  14. 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...

  15. Orbital momentum profiles and binding energy spectra for the complete valence shell of molecular fluorine

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y.; Brion, C.E. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Chemistry; Brunger, M.J.; Zhao, K.; Grisogono, A.M.; Braidwood, S.; Weigold, E. [Flinders Univ. of South Australia, Adelaide, SA (Australia). Electronic Structure of Materials Centre; Chakravorty, S.J.; Davidson, E.R. [Indiana Univ., Bloomington, IN (United States). Dept. of Chemistry; Sgamellotti, A. [Univ di Perugia (Italy). Dipartimento di Chimica; von Niessen, W. [Technische Univ. Braunschweig (Germany). Inst fuer Physikalische

    1996-01-01

    The first electronic structural study of the complete valence shell binding energy spectrum of molecular fluorine, encompassing both the outer and inner valence regions, is reported. These binding energy spectra as well as the individual orbital momentum profiles have been measured using an energy dispersive multichannel electron momentum spectrometer at a total energy of 1500 eV, with an energy resolution of 1.5 eV and a momentum resolution of 0.1 a.u. The measured binding energy spectra in the energy range of 14-60 eV are compared with the results of ADC(4) many-body Green`s function and also direct-Configuration Interaction (CI) and MRSD-CI calculations. The experimental orbital electron momentum profiles are compared with SCF theoretical profiles calculated using the target Hartree-Fock approximation with a range of basis sets and with Density Functional Theory predictions in the target Kohn-Sham approximation with non-local potentials. The truncated (aug-cc-pv5z) Dunning basis sets were used for the Density Functional Theory calculations which also include some treatment of correlation via the exchange and correlation potentials. Comparisons are also made with the full ion-neutral overlap amplitude calculated with MRSD-CI wave functions. Large, saturated basis sets (199-GTO) were employed for both the high level SCF near Hartree-Fock limit and MRSD-CI calculations to investigate the effects of electron correlation and relaxation. 66 refs., 9 tabs., 9 figs.

  16. Free-energy analysis of enzyme-inhibitor binding: aspartic proteinase-pepstatin complexes.

    Science.gov (United States)

    Kalra, P; Das, A; Jayaram, B

    2001-01-01

    Expeditious in silico determinations of the free energies of binding of a series of inhibitors to an enzyme are of immense practical value in structure-based drug design efforts. Some recent advances in the field of computational chemistry have rendered a rigorous thermodynamic treatment of biologic molecules feasible, starting from a molecular description of the biomolecule, solvent, and salt. Pursuing the goal of developing and making available a software for assessing binding affinities, we present here a computationally rapid, albeit elaborate, methodology to estimate and analyze the molecular thermodynamics of enzyme-inhibitor binding with crystal structures as the point of departure. The complexes of aspartic proteinases with seven inhibitors have been adopted for this study. The standard free energy of complexation is considered in terms of a thermodynamic cycle of six distinct steps decomposed into a total of 18 well-defined components. The model we employed involves explicit all-atom accounts of the energetics of electrostatic interactions, solvent screening effects, van der Waals components, and cavitation effects of solvation combined with a Debye-Huckel treatment of salt effects. The magnitudes and signs of the various components are estimated using the AMBER parm94 force field, generalized Born theory, and solvent accessibility measures. Estimates of translational and rotational entropy losses on complexation as well as corresponding changes in the vibrational and configurational entropy are also included. The calculated standard free energies of binding at this stage are within an order of magnitude of the observed inhibition constants and necessitate further improvements in the computational protocols to enable quantitative predictions. Some areas such as inclusion of structural adaptation effects, incorporation of site-dependent amino acid pKa shifts, consideration of the dynamics of the active site for fine-tuning the methodology are easily

  17. Self-consistent determination of fullerene binding energies BE (C+n-C2), n=58ṡ ṡ ṡ44

    Science.gov (United States)

    Wörgötter, R.; Dünser, B.; Scheier, P.; Märk, T. D.; Foltin, M.; Klots, C. E.; Laskin, J.; Lifshitz, C.

    1996-01-01

    Using recently measured accurate relative partial ionization cross section functions for production of the C60 fragment ions C+58 through C+44 by electron impact ionization, we have determined the respective binding energies BE(C+n-C2), with n=58,...,44, using a novel self-consistent procedure. Appearance energies were determined from ionization efficiency curves. Binding energies were calculated from the corresponding appearance energies with the help of the finite heat bath theory. Then using these binding energies we calculated with transition state theory (TST), the corresponding breakdown curves, and compared these calculated ones with the ones derived from the measured cross sections. The good agreement between these breakdown curves proves the consistency of this multistep calculation scheme. As the only free parameter in this procedure is the binding energy C+58-C2, we studied the influence of different transition states chosen in the determination of this binding energy via TST theory and iterative comparison with breakdown curve measurements. Based on this study we can conclude that extremely loose transition states can be confidently excluded, and that somewhat looser transition states than those used earlier result in an upward change of the binding energy of less than 10% yielding an upper limit for the binding energy C+58-C2 of approximately 7.6 eV.

  18. Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids

    Science.gov (United States)

    Anatole von Lilienfeld, O.; Tkatchenko, Alexandre

    2010-06-01

    We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C6 and C9, are computed "on the fly" from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang-Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiricially determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C60 dimer, a peptide (Ala10), an intercalated drug-DNA model [ellipticine-d(CG)2], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.

  19. The Microtremor H/V Spectral Ratio: The Physical Basis of the Diffuse Field Assumption

    Science.gov (United States)

    Sanchez-Sesma, F. J.

    2016-12-01

    The microtremor H/V spectral ratio (MHVSR) is popular to obtain the dominant frequency at a site. Despite the success of MHVSR some controversy arose regarding its physical basis. One approach is the Diffuse Field Assumption, DFA. It is then assumed that noise diffuse features come from multiple scattering within the medium. According to theory, the average of the autocorrelation is proportional to directional energy density (DED) and to the imaginary part of the Green's function for same source and receiver. Then, the square of MHVSR is a ratio of DEDs which, in a horizontally layered system, is 2xImG11/ImG33, where ImG11 and ImG33 are the imaginary parts of Green's functions for horizontal and vertical components. This has physical implications that emerge from the duality DED-force, implicit in the DFA. Consider a surface force at a half-space. The radiated energy is carried away by various wave types and the proportions of each one are precisely the fractions of the energy densities of a diffuse elastic wave field at the free surface. Thus, some properties of applied forces are also characteristics of DEDs. For example, consider a Poisson solid. For a normal point load, 67 per cent of energy is carried away by Rayleigh waves. For the tangential case, it is less well known that, 77 per cent of energy goes as shear waves. In a full space, 92 per cent of the energy is emitted as shear waves. The horizontal DED at the half-space surface implies significant emission of down-going shear waves that explains the curious stair-like resonance spectrum of ImG11. Both ImG11 and ImG33 grow linearly versus frequency and this represents wave emission. For a layered medium, besides wave emission, the ensuing variations correspond to reflected waves. For high frequencies, ImG33 depends on the properties of the top layer. Reflected body waves are very small and Rayleigh waves behave in the top layer as in a kind of mini half-space. From HVSR one can invert the velocity model

  20. Calculation of positron binding energies using the generalized any particle propagator theory

    Energy Technology Data Exchange (ETDEWEB)

    Romero, Jonathan; Charry, Jorge A. [Department of Chemistry, Universidad Nacional de Colombia, Av. Cra. 30 #45-03, Bogotá (Colombia); Flores-Moreno, Roberto [Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal., C. P. 44430 (Mexico); Varella, Márcio T. do N. [Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP (Brazil); Reyes, Andrés, E-mail: areyesv@unal.edu.co [Department of Chemistry, Universidad Nacional de Colombia, Av. Cra. 30 #45-03, Bogotá (Colombia); Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP (Brazil)

    2014-09-21

    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.

  1. Binding free energy calculations on E-selectin complexes with sLe(x) oligosaccharide analogs.

    Science.gov (United States)

    Barra, Pabla A; Ribeiro, António J M; Ramos, Maria J; Jiménez, Verónica A; Alderete, Joel B; Fernandes, Pedro A

    2017-01-01

    Molecular dynamics simulations and binding free energy calculations were employed to examine the interaction between E-selectin and six structurally related oligosaccharides including the physiological ligand sialyl Lewis x. Molecular dynamics simulations revealed that sialyl Lewis x and its mimics share a common binding region and similar interactions with E-selectin involving the formation of hydrogen bonds with Glu80, Asn82, Asn83, Arg97, Asn105, Asp106, and Glu107 residues and electrostatic contacts with Ca(2+) and the positively charged Lys111 and Lys 113 residues. Regarding binding free energy calculations, the performance of the rigorous but computationally expensive pathway methods TI, BAR, and MBAR was compared to the less rigorous but faster end-point methods MM/PBSA and MM/GBSA aimed at identifying a suitable approach to deal with the very subtle binding free energy differences within the ligands under study. All methods succeeded in predicting increased binding affinities for sialyl Lewis x analogs compared to the native ligand with absolute errors <1 kcal/mol. The best correlation with experimental data was obtained by TI (r(2)  = 0.84), followed by MBAR (r(2)  = 0.80), BAR (r(2)  = 0.73), MM/PBSA (r(2)  = 0.73) and MM/GBSA (r(2)  = 0.47). These results provide valuable information to increase understanding about E-selectin-oligosaccharide interactions and conduct further research aimed at designing novel ligands targeting this protein. © 2016 John Wiley & Sons A/S.

  2. Calculation of positron binding energies using the generalized any particle propagator theory

    Science.gov (United States)

    Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto; Varella, Márcio T. do N.; Reyes, Andrés

    2014-09-01

    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.

  3. Modelling of binding free energy of targeted nanocarriers to cell surface

    Science.gov (United States)

    Liu, Jin; Ayyaswamy, Portonovo S.; Eckmann, David M.; Radhakrishnan, Ravi

    2014-03-01

    We have developed a numerical model based on Metropolis Monte Carlo and the weighted histogram analysis method that enables the calculation of the absolute binding free energy between functionalized nanocarriers (NC) and endothelial cell (EC) surfaces. The binding affinities are calculated according to the free energy landscapes. The model predictions quantitatively agree with the analogous measurements of specific antibody coated NCs (100 nm in diameter) to intracellular adhesion molecule-1 (ICAM-1) expressing EC surface in in vitro cell culture experiments. The model also enables an investigation of the effects of a broad range of parameters that include antibody surface coverage of NC, glycocalyx in both in vivo and in vitro conditions, shear flow and NC size. Using our model we explore the effects of shear flow and reproduce the shear-enhanced binding observed in equilibrium measurements in collagen-coated tube. Furthermore, our results indicate that the bond stiffness, representing the specific antibody-antigen interaction, significantly impacts the binding affinities. The predictive success of our computational protocol represents a sound quantitative approach for model driven design and optimization of functionalized NC in targeted vascular drug delivery.

  4. Excitonic fine structure and binding energies of excitonic complexes in single InAs quantum dashes

    Science.gov (United States)

    Mrowiński, P.; Zieliński, M.; Świderski, M.; Misiewicz, J.; Somers, A.; Reithmaier, J. P.; Höfling, S.; Sek, G.

    2016-09-01

    The fundamental electronic and optical properties of elongated InAs nanostructures embedded in quaternary InGaAlAs barrier are investigated by means of high-resolution optical spectroscopy and many-body atomistic tight-binding theory. These wire-like shaped, self-assembled nanostructures are known as quantum dashes and are typically formed during the molecular beam epitaxial growth on InP substrates. In this paper, we study properties of excitonic complexes confined in quantum dashes emitting in a broad spectral range from below 1.2 to 1.55 μm. We find peculiar trends for the biexciton and negative trion binding energies, with pronounced trion binding in smaller size quantum dashes. These experimental findings are then compared and qualitatively explained by atomistic theory. The theoretical analysis shows a fundamental role of correlation effects for the absolute values of excitonic binding energies. Eventually, we determine the bright exciton fine structure splitting (FSS), where both the experiment and theory predict a broad distribution of the splitting varying from below 50 to almost 180 μeV. We identify several key factors determining the FSS values in such nanostructures, including quantum dash size variation and composition fluctuations.

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

    Science.gov (United States)

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

    2008-08-26

    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 by direct cross-species comparison between four yeast species. We find ubiquitous compensatory mutations within functional sites, such that the energy phenotype and the function of a site evolve in a significantly more constrained way than does its sequence. We also find evidence for substantial evolution of regulatory function involving point mutations as well as sequence insertions and deletions within binding sites. Genes lose their regulatory link to a given transcription factor at a rate similar to the neutral point mutation rate, from which we infer a moderate average fitness advantage of functional over nonfunctional sites. In a wider context, this study provides an example of inference of selection acting on a quantitative molecular trait.

  6. 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

  7. Simulative Calculation of Mechanical Property, Binding Energy and Detonation Property of TATB/Fluorine-polymer PBX

    Institute of Scientific and Technical Information of China (English)

    MA, Xiu-Fang; XIAO, Ji-Jun; HUANG, Hui; JU, Xue-Hai; LI, Jin-Shan; XIAO, He-Ming

    2006-01-01

    Molecular dynamics (MD) method was used to simulate 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) coated with fluorine containing polymers. The mechanical properties and binding energies of PBXs were obtained. It was found that when the number of chain monomers of fluorine containing polymers was the same, the elasticity of TATB/F2314 was increased more greatly than others and the binding energy of TATB/F2311 was the largest among four PBXs. Detonation heat and velocity of such four PBXs were calculated according to theoretical and empirical formulas. The results show that the order of detonation heat is TATB>TATB/PVDF>TATB/F2311 >TATB/F2314>TATB/PCTFE while the order of detonation velocity is TATB/PVDF<TATB/F2311 <TATB/F2314<TATB/PCTFE<TATB.

  8. 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.

  9. Binding Energy of an Exciton in the Quantum Dot Under a Magnetic Field

    Institute of Scientific and Technical Information of China (English)

    XIE Wen-nng

    2001-01-01

    The author reports on a calculation of the binding energy of the ground and some excited states of excitons in parabolic quantum dots in the presence of an external magnetic field. Calculations are made by using the method of few-body physics within the effective-mass approximation. The results are obtained for several strength values of the magnetic field as a function of the quantum dot radius.

  10. Binding energies of an exciton in a Gaussian potential quantum dot

    Institute of Scientific and Technical Information of China (English)

    Xie Wen-Fang

    2006-01-01

    In this paper, an exciton trapped by a Gaussian confining potential quantum dot has been investigated. Calculations are made by using the method of numerical diagonalization of Hamiltonian in the effective-mass approximation. The dependences of binding energies of the ground state and the first excited state on the size of the confining potential and the strength of the magnetic field are analysed explicitly.

  11. Binding energy of exciton in a nanowire superlattice in magnetic and electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Galvan-Moya, J E; Gutierrez, W [Escuela de Fisica, Universidad Industrial de Santander, Bucaramanga, Colombia A.A. 678 (Colombia); Moscoso, C, E-mail: edogalvan@gmail.co [Departamento de Fisica, Universidad Nacional de Colombia, Bogota, Colombia A.A. 5997 (Colombia)

    2010-02-01

    We study the binding energy of excitons in a cylindrical GaAs/Ga{sub 1-x}Al{sub x}As nanowire superlattice, embedded in Ga{sub 1-y}Al{sub y}As matrix, in the presence of magnetic and electric fields applied parallel to the growth direction. We express the exciton trial function as a product of one-particle wave functions of the electron and the hole with variationally determined envelope function, which describes the exciton intrinsic properties and depends only on the electron-hole separation. By using a functional derivative technique, we derive a differential equation for this envelope function, which we solve numerically. By varying the wire radius, interwell barrier width and well sizes we obtain binding energies ranging in character from one for strongly coupled superlattice to that for a system of stack of isolated disks. The behaviour of the binding energies and the charge distributions as functions of the interwell coupling, well sizes, and the external fields is consistently described with our simple formalism.

  12. Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

    Directory of Open Access Journals (Sweden)

    Bodee Nutho

    2014-11-01

    Full Text Available In the present study, our aim is to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nano-pore of β-cyclodextrin (β-CD at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD simulations and binding free energy calculations. The molecular docking suggested four possible fisetin orientations in the cavity through its chromone or phenyl ring with two different geometries of fisetin due to the rotatable bond between the two rings. From the multiple MD results, the phenyl ring of fisetin favours its inclusion into the β-CD cavity, whilst less binding or even unbinding preference was observed in the complexes where the larger chromone ring is located in the cavity. All MM- and QM-PBSA/GBSA free energy predictions supported the more stable fisetin/β-CD complex of the bound phenyl ring. Van der Waals interaction is the key force in forming the complexes. In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system.

  13. 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.

  14. First-principles calculation of core-level binding energy shift in surface chemical processes

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Combined with third generation synchrotron radiation light sources, X-ray photoelectron spectroscopy (XPS) with higher energy resolution, brilliance, enhanced surface sensitivity and photoemission cross section in real time found extensive applications in solid-gas interface chemistry. This paper reports the calculation of the core-level binding energy shifts (CLS) using the first-principles density functional theory. The interplay between the CLS calculations and XPS measurements to uncover the structures, adsorption sites and chemical reactions in complex surface chemical processes are highlight. Its application on clean low index (111) and vicinal transition metal surfaces, molecular adsorption in terms of sites and configuration, and reaction kinetics are domonstrated.

  15. Formation Mechanism and Binding Energy for Body-Centered Cubic Structure of He+9 Cluster

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jian-Ping; GOU Qing-Quan; LI Ping

    2004-01-01

    The formation mechanism for the body-centered cubic structure of He+9 cluster is proposed and its total energy curve is calculated by the method of a Modified Arrangement Channel Quantum Mechanics. The energy is the function of separation R between the nuclei at the center and an apex of the body-centered cubic structure. The result of the calculation shows that the curve has a minimal energy -25.6669 (a.u.) at R = 2.550ao. The binding energy of He+9 with respect to He+ + 8He was calculated to be 0.8857 a.u. This means that the cluster of He+9 may be formed in the body-centered cubic structure of R = 2.55a0.

  16. Design of protein-ligand binding based on the molecular-mechanics energy model.

    Science.gov (United States)

    Boas, F Edward; Harbury, Pehr B

    2008-07-04

    While the molecular-mechanics field has standardized on a few potential energy functions, computational protein design efforts are based on potentials that are unique to individual laboratories. Here we show that a standard molecular-mechanics potential energy function without any modifications can be used to engineer protein-ligand binding. A molecular-mechanics potential is used to reconstruct the coordinates of various binding sites with an average root-mean-square error of 0.61 A and to reproduce known ligand-induced side-chain conformational shifts. Within a series of 34 mutants, the calculation can always distinguish between weak (K(d)>1 mM) and tight (K(d)mechanics potential is used to redesign a ribose-binding site. Out of a search space of 2 x 10(12) sequences, the calculation selects a point mutant of the native protein as the top solution (experimental K(d)=17 microM) and the native protein as the second best solution (experimental K(d)=210 nM). The quality of the predictions depends on the accuracy of the generalized Born electrostatics model, treatment of protonation equilibria, high-resolution rotamer sampling, a final local energy minimization step, and explicit modeling of the bound, unbound, and unfolded states. The application of unmodified molecular-mechanics potentials to protein design links two fields in a mutually beneficial way. Design provides a new avenue for testing molecular-mechanics energy functions, and future improvements in these energy functions will presumably lead to more accurate design results.

  17. Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.

    Science.gov (United States)

    Chakavorty, Arghya; Li, Lin; Alexov, Emil

    2016-10-30

    Macromolecular interactions are essential for understanding numerous biological processes and are typically characterized by the binding free energy. Important component of the binding free energy is the electrostatics, which is frequently modeled via the solutions of the Poisson-Boltzmann Equations (PBE). However, numerous works have shown that the electrostatic component (ΔΔGelec ) of binding free energy is very sensitive to the parameters used and modeling protocol. This prompted some researchers to question the robustness of PBE in predicting ΔΔGelec . We argue that the sensitivity of the absolute ΔΔGelec calculated with PBE using different input parameters and definitions does not indicate PBE deficiency, rather this is what should be expected. We show how the apparent sensitivity should be interpreted in terms of the underlying changes in several numerous and physical parameters. We demonstrate that PBE approach is robust within each considered force field (CHARMM-27, AMBER-94, and OPLS-AA) once the corresponding structures are energy minimized. This observation holds despite of using two different molecular surface definitions, pointing again that PBE delivers consistent results within particular force field. The fact that PBE delivered ΔΔGelec values may differ if calculated with different modeling protocols is not a deficiency of PBE, but natural results of the differences of the force field parameters and potential functions for energy minimization. In addition, while the absolute ΔΔGelec values calculated with different force field differ, their ordering remains practically the same allowing for consistent ranking despite of the force field used. © 2016 Wiley Periodicals, Inc.

  18. Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.

    Science.gov (United States)

    Tsai, Min-Yeh; Zheng, Weihua; Balamurugan, D; Schafer, Nicholas P; Kim, Bobby L; Cheung, Margaret S; Wolynes, Peter G

    2016-01-01

    While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes.

  19. The influence of solutes on the enthalpy/entropy change of the actinomycin D binding to DNA: hydration, energy compensation and long-range deformation on DNA.

    Science.gov (United States)

    Galo, André L; Rugiero Neto, João; Brognaro, Dulcinea P; Caetano, Renato C; Souza, Fátima P; Colombo, Márcio F

    2011-07-21

    The effects of the changes in the temperature and in the water chemical potential on the energetic of the actinomycin D (ACTD) interaction with natural DNA are studied. At reduced water chemical potential, induced by the addition of neutral solute (sucrose), the ACTD-to-DNA binding isotherms show that the drug accesses two types of binding sites: strong and weak. The binding constants to the stronger sites are sensitive to changes in the temperature and in the water chemical potential, while the weak sites are practically insensitive to these changes. The van't Hoff analyses of the binding in different water chemical potential shows that the binding process to the more specific sites is endothermic in phosphate buffer (ΔH(vH) ∼ 1 kcal/mol) and becomes exothermic when the water chemical potential decreases (ΔH(vH) = -11 kcal/mol in sucrose 30%). The number of water molecules released on the binding to the stronger sites, obtained from the slopes of linkage plots in different temperatures, increases with the decrease in the temperature. Ring closure reactions in the presence of neutral solutes have shown that the reduction in the water activity induces DNA unwinding. It was observed that both reduced water chemical potential and small ratios of daunomycin bound per base pairs have the same effects on the ACTD binding isotherms and consequently on the binding thermodynamic parameters. The results presented indicate that the ACTD binding to the recognition site is enthalpycally unfavorable, which should be compensated by the deformation in the DNA. This compensation would probably be the origin of the synergism observed for these two drugs.

  20. Elaboration and research of planetary precessional multiplier type K-H-V

    Science.gov (United States)

    Bostan, I.; Dulgheru, V.; Ciobanu, R.

    2016-08-01

    The multiplier is an indispensable part of the micro hydropower plant and high power wind turbine. It helps to increase rotor low speeds limited by the water flow small velocity and by the relative big placement diameter of the blades that participate in the energy conversion. For example, the microhydrostation rotor's speed is (2 - 3) min'1 for water flow velocity V= (1...1,6) m/s and for blade placement diameter D = 4 m. Diversity of requirements forwarded by the beneficiaries of mechanical transmissions consists, in particular, in increasing reliability, efficiency and lifting capacity, and in reducing the mass and dimensions. It becomes more and more difficult to satisfy the mentioned demands by partial updating of traditional transmissions. The target problem can be solved with special effects by developing new types of multipliers based on precessional planetary transmissions with multiple gear, that were developed by the authors. Absolute multiplicity of precessional gear (up to 100% pairs of teeth simultaneously involved in gearing, compared to 5%-7% - in classical gearings) provides increased lifting capacity and small mass and dimensions. To mention that until now precessional planetary transmissions have been researched and applied mainly in reducers. Therefore it was necessary to carry out theoretical research to determine the geometrical parameters of the precessional gear that operates in multiplier mode. Also, it was necessary to develop new conceptual diagrams of precessional transmissions that function under multiplier regime. The majority of precessional planetary transmissions diagrams developed previously operate efficiently in reducer's regime. Depending on the structural diagram, precessional transmissions fall into two main types - K-H-V and 2K-H, from which a wide range of constructive solutions with wide kinematical and functional options that operate in multiplier regime.

  1. Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies.

    Science.gov (United States)

    Nguyen, Duc D; Wang, Bao; Wei, Guo-Wei

    2017-05-15

    Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of ΔGel obtained at the grid spacing of 1.0 Å compared to ΔGel at 0.2 Å averaged over 153 molecules is less than 0.2%. Our results indicate that the use of grid spacing 0.6 Å ensures accuracy and reliability in ΔΔGel calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  2. Two and three-body interatomic dispersion energy contributions to binding in molecules and solids

    Science.gov (United States)

    von Lilienfeld, Anatole; Tkatchenko, Alexandre

    2010-03-01

    Numerical estimates of the leading two and three body dispersion energy terms in van der Waals (vdW) interactions are presented for a broad variety of molecules and solids. The calculations employ London and Axilrod-Teller-Muto expressions damped at short interatomic distances, where the required interatomic dispersion energy coefficients, C6 and C9, are computed from first-principles. The investigated systems include the S22 database of non-covalent interactions, benzene and ice crystals, bilayer graphene, fullerene dimer, a poly peptide (Ala10), an intercalated drug-DNA model (Ellipticine-d(CG)2), 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and molecular crystals from a crystal structure blind test. We find that the 2 and 3-body interatomic dispersion energies contribute significantly to binding and cohesive energies, for some systems they can reach up to 50% of experimental estimates of absolute binding. Our results suggest that interatomic 3-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.

  3. Locating Temporal Functional Dynamics of Visual Short-Term Memory Binding using Graph Modular Dirichlet Energy

    Science.gov (United States)

    Smith, Keith; Ricaud, Benjamin; Shahid, Nauman; Rhodes, Stephen; Starr, John M.; Ibáñez, Augustin; Parra, Mario A.; Escudero, Javier; Vandergheynst, Pierre

    2017-02-01

    Visual short-term memory binding tasks are a promising early marker for Alzheimer’s disease (AD). To uncover functional deficits of AD in these tasks it is meaningful to first study unimpaired brain function. Electroencephalogram recordings were obtained from encoding and maintenance periods of tasks performed by healthy young volunteers. We probe the task’s transient physiological underpinnings by contrasting shape only (Shape) and shape-colour binding (Bind) conditions, displayed in the left and right sides of the screen, separately. Particularly, we introduce and implement a novel technique named Modular Dirichlet Energy (MDE) which allows robust and flexible analysis of the functional network with unprecedented temporal precision. We find that connectivity in the Bind condition is less integrated with the global network than in the Shape condition in occipital and frontal modules during the encoding period of the right screen condition. Using MDE we are able to discern driving effects in the occipital module between 100–140 ms, coinciding with the P100 visually evoked potential, followed by a driving effect in the frontal module between 140–180 ms, suggesting that the differences found constitute an information processing difference between these modules. This provides temporally precise information over a heterogeneous population in promising tasks for the detection of AD.

  4. Absolute binding free energies for octa-acids and guests in SAMPL5

    Science.gov (United States)

    Tofoleanu, Florentina; Lee, Juyong; Pickard, Frank C., IV; König, Gerhard; Huang, Jing; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

    2017-01-01

    As part of the SAMPL5 blind prediction challenge, we calculate the absolute binding free energies of six guest molecules to an octa-acid (OAH) and to a methylated octa-acid (OAMe). We use the double decoupling method via thermodynamic integration (TI) or Hamiltonian replica exchange in connection with the Bennett acceptance ratio (HREM-BAR). We produce the binding poses either through manual docking or by using GalaxyDock-HG, a docking software developed specifically for this study. The root mean square deviations for our most accurate predictions are 1.4 kcal mol-1 for OAH with TI and 1.9 kcal mol-1 for OAMe with HREM-BAR. Our best results for OAMe were obtained for systems with ionic concentrations corresponding to the ionic strength of the experimental solution. The most problematic system contains a halogenated guest. Our attempt to model the σ-hole of the bromine using a constrained off-site point charge, does not improve results. We use results from molecular dynamics simulations to argue that the distinct binding affinities of this guest to OAH and OAMe are due to a difference in the flexibility of the host. We believe that the results of this extensive analysis of host-guest complexes will help improve the protocol used in predicting binding affinities for larger systems, such as protein-substrate compounds.

  5. Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase.

    Directory of Open Access Journals (Sweden)

    Daniel R Ripoll

    Full Text Available Quantitatively predicting changes in drug sensitivity associated with residue mutations is a major challenge in structural biology. By expanding the limits of free energy calculations, we successfully identified mutations in influenza neuraminidase (NA that confer drug resistance to two antiviral drugs, zanamivir and oseltamivir. We augmented molecular dynamics (MD with Hamiltonian Replica Exchange and calculated binding free energy changes for H274Y, N294S, and Y252H mutants. Based on experimental data, our calculations achieved high accuracy and precision compared with results from established computational methods. Analysis of 15 micros of aggregated MD trajectories provided insights into the molecular mechanisms underlying drug resistance that are at odds with current interpretations of the crystallographic data. Contrary to the notion that resistance is caused by mutant-induced changes in hydrophobicity of the binding pocket, our simulations showed that drug resistance mutations in NA led to subtle rearrangements in the protein structure and its dynamics that together alter the active-site electrostatic environment and modulate inhibitor binding. Importantly, different mutations confer resistance through different conformational changes, suggesting that a generalized mechanism for NA drug resistance is unlikely.

  6. Binding Energy of an Exciton Bound to Ionized Acceptor in Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    XIE Wen-Fang

    2001-01-01

    Binding energiesfor an exciton (X ) trapped in the two-dimensional quantum dot by a negative ion located on the z axis at a distance from the dot plane are calculated by using the method of few-body physics.This configuration is called a barrier (A-,X) center.The dependence of the binding energy of the ground state of the barrier (A-,X)center on the electron-to-hole mass ratio for a few values of the distance d between the fixed negative ion on the z axis and the dot plane is obtained.We find that when d → 0,the barrier (A-,X) center has not any bound state.We also studied the stability and binding energy of the ground state of the barrier (A-,X) center in a parabolic quantum dot as a function of the distance d between the fixed negative ion on the z axis and the dot plane.``

  7. Hyperon binding energy in Λ6He and Λ7He

    Directory of Open Access Journals (Sweden)

    Filikhin Igor

    2016-01-01

    Full Text Available The three-body approach based on the configuration space Faddeev equations for systems of non-identical particles is proposed to describe light hypernuclei (A=6,7, S=-1 with α particle clustering. We focus on the model (α +Λ + n + n for Λ7He hypernucleus for which the first experimental data have been recently reported. New evaluation for hyperon binding energy in Λ7He is done by using a relation between energies of the spin doublet (1−,2− of Λ6He and the Λ7He ground state. Energies of low-lying levels of Λ6He hypernucleus are calculated within the cluster α + Λ + n model.

  8. Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel

    2014-07-03

    Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is

  9. AIScore chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes.

    Science.gov (United States)

    Raub, Stephan; Steffen, Andreas; Kämper, Andreas; Marian, Christel M

    2008-07-01

    In this work we report on a novel scoring function that is based on the LUDI model and focuses on the prediction of binding affinities. AIScore extends the original FlexX scoring function using a chemically diverse set of hydrogen-bonded interactions derived from extensive quantum chemical ab initio calculations. Furthermore, we introduce an algorithmic extension for the treatment of multifurcated hydrogen bonds (XFurcate). Charged and resonance-assisted hydrogen bond energies and hydrophobic interactions as well as a scaling factor for implicit solvation were fitted to experimental data. To this end, we assembled a set of 101 protein-ligand complexes with known experimental binding affinities. Tightly bound water molecules in the active site were considered to be an integral part of the binding pocket. Compared to the original FlexX scoring function, AIScore significantly improves the prediction of the binding free energies of the complexes in their native crystal structures. In combination with XFurcate, AIScore yields a Pearson correlation coefficient of R P = 0.87 on the training set. In a validation run on the PDBbind test set we achieved an R P value of 0.46 for 799 attractively scored complexes, compared to a value of R P = 0.17 and 739 bound complexes obtained with the FlexX original scoring function. The redocking capability of AIScore, on the other hand, does not fully reach the good performance of the original FlexX scoring function. This finding suggests that AIScore should rather be used for postscoring in combination with the standard FlexX incremental ligand construction scheme.

  10. Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA.

    Science.gov (United States)

    Xiao, Xingqing; Hung, Michelle E; Leonard, Joshua N; Hall, Carol K

    2016-10-15

    Our previously developed peptide-design algorithm was improved by adding an energy minimization strategy which allows the amino acid sidechains to move in a broad configuration space during sequence evolution. In this work, the new algorithm was used to generate a library of 21-mer peptides which could substitute for λ N peptide in binding to boxB RNA. Six potential peptides were obtained from the algorithm, all of which exhibited good binding capability with boxB RNA. Atomistic molecular dynamics simulations were then conducted to examine the ability of the λ N peptide and three best evolved peptides, viz. Pept01, Pept26, and Pept28, to bind to boxB RNA. Simulation results demonstrated that our evolved peptides are better at binding to boxB RNA than the λ N peptide. Sequence searches using the old (without energy minimization strategy) and new (with energy minimization strategy) algorithms confirm that the new algorithm is more effective at finding good RNA-binding peptides than the old algorithm. © 2016 Wiley Periodicals, Inc.

  11. Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation.

    Science.gov (United States)

    Tsujikawa, Hiroto; Sato, Kenta; Wei, Cao; Saad, Gul; Sumikoshi, Kazuya; Nakamura, Shugo; Terada, Tohru; Shimizu, Kentaro

    2016-09-01

    We present a new method for predicting protein-ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure database, LigASite. Ligand-bound structure prediction (bound prediction) indicated that 74.0 % of predicted ligand-binding sites overlapped with real ligand-binding sites by over 25 % of their volume. Ligand-unbound structure prediction (unbound prediction) indicated that 73.9 % of predicted ligand-binding residues overlapped with real ligand-binding residues. The amino acid conservation score improved the average prediction accuracy by 17.0 and 17.6 points for the bound and unbound predictions, respectively. These results demonstrate the effectiveness of the combined use of the interaction energy and amino acid conservation in the ligand-binding site prediction.

  12. 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.

  13. Binding Energies of Excitons in Square Quantum-Well Wires in the Presence of a Magnetic Field

    Institute of Scientific and Technical Information of China (English)

    张迎涛; 邸冰; 谢尊; 李有成

    2004-01-01

    The binding energies of the ground state of excitons in the GaAs/Ga1-xAlxAs square quantum-well wire in the presence of a magnetic field are investigated by using the variational method. It is assumed that the magnetic field is applied parallel to the axis of the wire. The calculations of the binding energy as a function of the wire size have been performed for infinite and finite confinement potentials. The contribution of the magnetic field makes the binding energy larger obviously, particularly for the wide wire, and the magnetic field is much more pronounced for the binding energy in a square quantum wire than that in a cylindrical quantum wire. The mismatch of effective masses between the well and the barrier is also considered in the calculation.

  14. 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.

  15. Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane

    Science.gov (United States)

    Vivcharuk, Victor; Tomberli, Bruno; Tolokh, Igor S.; Gray, C. G.

    2008-03-01

    Molecular dynamics (MD) simulations are used to study the interaction of a zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with POPC is used as a model system for studying the details of membrane-peptide interactions, with the peptide selected because of its antimicrobial nature. Seventy-two 3 ns MD simulations, with six orientations of LFCinB at 12 different distances from a POPC membrane, are carried out to determine the potential of mean force (PMF) or free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the PMF for this relatively large system a new variant of constrained MD and thermodynamic integration is developed. A simplified method for relating the PMF to the LFCinB-membrane binding free energy is described and used to predict a free energy of adsorption (or binding) of -1.05±0.39kcal/mol , and corresponding maximum binding force of about 20 pN, for LFCinB-POPC. The contributions of the ions-LFCinB and the water-LFCinB interactions to the PMF are discussed. The method developed will be a useful starting point for future work simulating peptides interacting with charged membranes and interactions involved in the penetration of membranes, features necessary to understand in order to rationally design peptides as potential alternatives to traditional antibiotics.

  16. 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.

  17. Fabrication of CuCl quantum dots and the size dependence of the biexciton binding energy

    CERN Document Server

    Park, S T; Kim, H Y; Kim, I G

    2000-01-01

    We fabricated CuCl quantum dots (QDs) in an aluminoborosilicate glass matrix. The photoluminescence of the CuCl QDs was surveyed by using the band-to-band excitation and the site selective luminescence methods. The excitation density dependence of the exciton and the biexciton luminescence was measured, and the saturation effects of the luminescence intensities were observed. The biexciton binding energies measured using the site selective luminescence method increased with decreasing QD size. The data were well fitted by a function resulting from the numerical matrix-diagonalization method.

  18. 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.

  19. Transition between quasi 2 and 3D behaviour of the binding energy of screened excitons in semiconductor quantum well structures

    CERN Document Server

    Vazquez, G J; Reyes, J A; Lee, J; Spector, H N

    2003-01-01

    We have calculated the binding energy of screened excitons in a semiconducting quantum well structure as a function of screening parameter and the width of the quantum well using variational wave functions to obtain upper bounds for the energy. The binding energy decreases with increasing values of the screening parameter and with increasing well width. However, as long as the well width is narrow enough so the electrons and holes occupy their lowest-energy subbands, the exciton remains bound even for large values of the screening parameter whenever the electron gas remains nondegenerate. (Author)

  20. Estimation of the Binding Free Energy of AC1NX476 to HIV-1 Protease Wild Type and Mutations Using Free Energy Perturbation Method.

    Science.gov (United States)

    Ngo, Son Tung; Mai, Binh Khanh; Hiep, Dinh Minh; Li, Mai Suan

    2015-10-01

    The binding mechanism of AC1NX476 to HIV-1 protease wild type and mutations was studied by the docking and molecular dynamics simulations. The binding free energy was calculated using the double-annihilation binding free energy method. It is shown that the binding affinity of AC1NX476 to wild type is higher than not only ritonavir but also darunavir, making AC1NX476 become attractive candidate for HIV treatment. Our theoretical results are in excellent agreement with the experimental data as the correlation coefficient between calculated and experimentally measured binding free energies R = 0.993. Residues Asp25-A, Asp29-A, Asp30-A, Ile47-A, Gly48-A, and Val50-A from chain A, and Asp25-B from chain B play a crucial role in the ligand binding. The mutations were found to reduce the receptor-ligand interaction by widening the binding cavity, and the binding propensity is mainly driven by the van der Waals interaction. Our finding may be useful for designing potential drugs to combat with HIV.

  1. Pion tensor force and nuclear binding energy in the relativistic Hartree-Fock formalism

    Science.gov (United States)

    Marcos, S.; López-Quelle, M.; Niembro, R.; Savushkin, L. N.

    2014-03-01

    The binding energies of several isotopic families are studied within the relativistic Hartree-Fock approximation with the pseudovector coupling for the πN vertex, to find out a suitable strength for the effective pion tensor force (EPTF). An approximation for determining separately the contributions of the central and tensor forces generated by pion is considered. The results for heavy nuclei indicate that a realistic strength for the EPTF is smaller than a half of that appearing in the OPEP. This conclusion also applies to the results for the single-particle energies. Besides, it has been found that there is a genuine relativistic contribution of the EPTF in nuclear matter which is small but significant.

  2. 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...

  3. 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.

  4. CaFE: a tool for binding affinity prediction using end-point free energy methods.

    Science.gov (United States)

    Liu, Hui; Hou, Tingjun

    2016-07-15

    Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters. CaFE source code and documentation are freely available under the GNU General Public License via GitHub at https://github.com/huiliucode/cafe_plugin It is a VMD plugin written in Tcl and the usage is platform-independent. tingjunhou@zju.edu.cn. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. 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...

  6. Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP.

    Science.gov (United States)

    Bayden, Alexander S; Moustakas, Demetri T; Joseph-McCarthy, Diane; Lamb, Michelle L

    2015-08-24

    The SZMAP method computes binding free energies and the corresponding thermodynamic components for water molecules in the binding site of a protein structure [ SZMAP, 1.0.0 ; OpenEye Scientific Software Inc. : Santa Fe, NM, USA , 2011 ]. In this work, the ability of SZMAP to predict water structure and thermodynamic stability is examined for the X-ray crystal structures of a series of protein-ligand complexes. SZMAP results correlate with higher-level replica exchange thermodynamic integration double decoupling calculations of the absolute free energy of bound waters in the test set complexes. In addition, SZMAP calculations show good agreement with experimental data in terms of water conservation (across multiple crystal structures) and B-factors over a subset of the test set. In particular, the SZMAP neutral entropy difference term calculated at crystallographic water positions within each of the complex structures correlates well with whether that crystallographic water is conserved or displaceable. Furthermore, the calculated entropy of the water probe relative to the continuum shows a significant degree of correlation with the B-factors associated with the oxygen atoms of the water molecules. Taken together, these results indicate that SZMAP is capable of quantitatively predicting water positions and their energetics and is potentially a useful tool for determining which waters to attempt to displace, maintain, or build in through water-mediated interactions when evolving a lead series during a drug discovery program.

  7. Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters.

    Directory of Open Access Journals (Sweden)

    Rafael Tapia-Rojo

    2014-10-01

    Full Text Available The identification of protein binding sites in promoter sequences is a key problem to understand and control regulation in biochemistry and biotechnological processes. We use a computational method to analyze promoters from a given genome. Our approach is based on a physical model at the mesoscopic level of protein-DNA interaction based on the influence of DNA local conformation on the dynamics of a general particle along the chain. Following the proposed model, the joined dynamics of the protein particle and the DNA portion of interest, only characterized by its base pair sequence, is simulated. The simulation output is analyzed by generating and analyzing the Free Energy Landscape of the system. In order to prove the capacity of prediction of our computational method we have analyzed nine promoters of Anabaena PCC 7120. We are able to identify the transcription starting site of each of the promoters as the most populated macrostate in the dynamics. The developed procedure allows also to characterize promoter macrostates in terms of thermo-statistical magnitudes (free energy and entropy, with valuable biological implications. Our results agree with independent previous experimental results. Thus, our methods appear as a powerful complementary tool for identifying protein binding sites in promoter sequences.

  8. Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent:  Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase.

    Science.gov (United States)

    Su, Yang; Gallicchio, Emilio; Das, Kalyan; Arnold, Eddy; Levy, Ronald M

    2007-01-01

    Expressions for Linear Interaction Energy (LIE) estimators for the binding of ligands to a protein receptor in implicit solvent are derived based on linear response theory and the cumulant expansion expression for the free energy. Using physical arguments, values of the LIE linear response proportionality coefficients are predicted for the explicit and implicit solvent electrostatic and van der Waals terms. Motivated by the fact that the receptor and solution media may respond differently to the introduction of the ligand, a novel form of the LIE regression equation is proposed to model independently the processes of insertion of the ligand in the receptor and in solution. We apply these models to the problem of estimating the binding free energy of two non-nucleoside classes of inhibitors of HIV-1 RT (HEPT and TIBO analogues). We develop novel regression models with greater predictive ability than more standard LIE formulations. The values of the regression coefficients generally conform to linear response predictions, and we use this fact to develop a LIE regression equation with only one adjustable parameter (excluding the intercept parameter) which is superior to the other models we tested and to previous results in terms of predictive accuracy for the HEPT and TIBO compounds individually. The new models indicate that, due to the different effects of induced steric strain of the receptor, an increase of ligand size alone opposes binding for ligands of the HEPT class, whereas it favors binding for ligands of the TIBO class.

  9. Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies.

    Science.gov (United States)

    Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew

    2011-06-02

    The independent trajectory thermodynamic integration (IT-TI) approach (Lawrenz et. al J. Chem. Theory. Comput. 2009, 5:1106-1116(1)) for free energy calculations with distributed computing is employed to study two distinct cases of protein-ligand binding: first, the influenza surface protein N1 neuraminidase bound to the inhibitor oseltamivir, and second, the M. tuberculosis enzyme RmlC complexed with the molecule CID 77074. For both systems, finite molecular dynamics (MD) sampling and varied molecular flexibility give rise to IT-TI free energy distributions that are remarkably centered on the target experimental values, with a spread directly related to protein, ligand, and solvent dynamics. Using over 2 μs of total MD simulation, alternative protocols for the practical, general implementation of IT-TI are investigated, including the optimal use of distributed computing, the total number of alchemical intermediates, and the procedure to perturb electrostatics and van der Waals interactions. A protocol that maximizes predictive power and computational efficiency is proposed. IT-TI outperforms traditional TI predictions and allows a straightforward evaluation of the reliability of free energy estimates. Our study has broad implications for the use of distributed computing in free energy calculations of macromolecular systems.

  10. 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.

  11. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.

    Science.gov (United States)

    Deng, Nanjie; Flynn, William F; Xia, Junchao; Vijayan, R S K; Zhang, Baofeng; He, Peng; Mentes, Ahmet; Gallicchio, Emilio; Levy, Ronald M

    2016-09-01

    We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein-ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate

  12. 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

    2016-05-04

    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.

  13. Binding Energy and Lifetime of Excitons in InxGa1-xAs/GaAs Quantum Wells

    DEFF Research Database (Denmark)

    Orani, D.; Polimeni, A.; Patane, A.;

    1997-01-01

    We report a systematic study of exciton binding energies and lifetimes in InGaAs/GaAs quantum wells. The experimental binding energies have been deduced from photoluminescence excitation measurements taking into account the contribution of the 2s state of the exciton and the line broadening....... The experimental results have been compared with accurate calculations in a four-band model, where exciton energies take into account the polaron correction. The theory accounts for all the experimental observations and provides a good quantitative agreement with the experimental values....

  14. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.

    Science.gov (United States)

    Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew

    2012-01-01

    The Independent-Trajectory Thermodynamic Integration (IT-TI) approach for free energy calculation with distributed computing is described. IT-TI utilizes diverse conformational sampling obtained from multiple, independent simulations to obtain more reliable free energy estimates compared to single TI predictions. The latter may significantly under- or over-estimate the binding free energy due to finite sampling. We exemplify the advantages of the IT-TI approach using two distinct cases of protein-ligand binding. In both cases, IT-TI yields distributions of absolute binding free energy estimates that are remarkably centered on the target experimental values. Alternative protocols for the practical and general application of IT-TI calculations are investigated. We highlight a protocol that maximizes predictive power and computational efficiency.

  15. On the binding energy and the charge symmetry breaking in A ≤ 16 Λ-hypernuclei

    Science.gov (United States)

    Botta, E.; Bressani, T.; Feliciello, A.

    2017-04-01

    In recent years, several experiments using magnetic spectrometers provided high precision results in the field of Hypernuclear Physics. In particular, the accurate determination of the Λ-binding energy, BΛ, contributed to stimulate considerably the discussion about the Charge Symmetry Breaking effect in Λ-hypernuclei isomultiplets. We have reorganized the results from the FINUDA experiment and we have obtained a series of BΛ values for Λ-hypernuclei with A≤ 16 by taking into account data only from magnetic spectrometers implementing an absolute calibration of the energy scale (FINUDA at DAΦNE and electroproduction experiments at JLab and at MaMi). We have then critically revisited the results obtained at KEK by the SKS Collaboration in order to make possible a direct comparison between data from experiments with and without such an absolute energy scale. A synopsis of recent spectrometric measurements of BΛ is presented, including also emulsion experiment results. Several interesting conclusions are drawn, among which the equality within the errors of BΛ for the A = 7 , 12 , 16 isomultiplets, based only on recent spectrometric data. This observation is in nice agreement with a recent theoretical prediction. Ideas for possible new measurements which should improve the present experimental knowledge are finally put forward.

  16. Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis.

    Science.gov (United States)

    Morozenko, A; Leontyev, I V; Stuchebrukhov, A A

    2014-10-14

    The energetics of water molecules in proteins is studied using the water placement software Dowser. We compared the water position predictions for 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules. From the analysis of the outputs of Dowser with variable parameters and comparison with experimental X-ray data, we derived an estimate of the average dipole moment of water molecules located in the internal cavities of the protein and their binding energies. The water parameters thus obtained from the experimental data are then analyzed within the framework of charge-scaling theory developed recently by this group; the parameters are shown to be in good agreement with the predictions that the theory makes for the dipole moment in a protein environment. The water dipole in the protein environment is found to be much different from that in the bulk and in such models as SPC or TIPnP. The role of charge scaling due to electronic polarizability of the protein is discussed.

  17. Improving the Volume Dependence of Two-Body Binding Energies Calculated with Lattice QCD

    CERN Document Server

    Davoudi, Zohreh

    2011-01-01

    Volume modifications to the binding of two-body systems in large cubic volumes of extent L depend upon the total momentum and exponentially upon the ratio of L to the size of the boosted system. Recent work by Bour et al determined the momentum dependence of the leading volume modifications to nonrelativistic systems with periodic boundary conditions imposed on the single-particle wavefunctions, enabling them to numerically determine the scattering of such bound states using a low-energy effective field theory and Luschers finite-volume method. The calculation of bound nuclear systems directly from QCD using Lattice QCD has begun, and it is important to reduce the systematic uncertainty introduced into such calculations by the finite spatial extent of the gauge-field configurations. We extend the work of Bour et al from nonrelativistic quantum mechanics to quantum field theory by generalizing the work of Luscher and of Gottlieb and Rummukainen to boosted two-body bound states. The volume modifications to bind...

  18. 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...

  19. Potential energy surface and binding energy in the presence of an external electric field: modulation of anion-π interactions for graphene-based receptors.

    Science.gov (United States)

    Foroutan-Nejad, Cina; Marek, Radek

    2014-02-14

    Measuring the binding energy or scanning the potential energy surface (PES) of the charged molecular systems in the presence of an external electric field (EEF) requires a careful evaluation of the origin-dependency of the energy of the system and references. Scanning the PES for charged or purely ionic systems for obtaining the intrinsic energy barriers needs careful analysis of the electric work applied on ions by the EEF. The binding energy in the presence of an EEF is different from that in the absence of an electric field as the binding energy is an anisotropic characteristic which depends on the orientation of molecules with respect to the EEF. In this contribution we discuss various aspects of the PES and the concept of binding energy in the presence of an EEF. In addition, we demonstrate that the anion-π bonding properties can be modulated by applying a uniform EEF, which has a more pronounced effect on the larger, more polarizable π-systems. An analogous behavior is presumed for cation-π systems. We predict that understanding the phenomenon introduced in the present account has enormous potential, for example, for separating charged species on the surface of polarizable two-dimensional materials such as graphene or the surface of carbon nanotubes, in desalination of water.

  20. 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.

  1. Exciton binding energies and absorption in intermixed GaAs-AlGaAs quantum wells

    Science.gov (United States)

    Meney, Alistair T.

    1992-12-01

    The optical properties of excitons in layer-intermixed GaAs-AlGaAs quantum wells are studied theoretically. The electronic dispersion is obtained using the 6×6 Luttinger-Kohn Hamiltonian for the valence bands, and an accurate expression for the conduction band dispersion which includes the effects of nonparabolicity and warping to fourth order in k. The HH1-CB1 (1s) and LH1-CB1(1s) exciton binding energies are calculated as a function of diffusion time. The absorption for both TE and TM polarization is obtained at several wavelengths, and is seen to decrease significantly with increased intermixing. The decrease in absorption is larger for narrow wells, where the effects of intermixing are more pronounced for a given diffusion time.

  2. 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.

  3. Scaling Universality between Band Gap and Exciton Binding Energy of Two-Dimensional Semiconductors

    Science.gov (United States)

    Jiang, Zeyu; Liu, Zhirong; Li, Yuanchang; Duan, Wenhui

    2017-06-01

    Using first-principles G W Bethe-Salpeter equation calculations and the k .p theory, we unambiguously show that for two-dimensional (2D) semiconductors, there exists a robust linear scaling law between the quasiparticle band gap (Eg) and the exciton binding energy (Eb), namely, Eb≈Eg/4 , regardless of their lattice configuration, bonding characteristic, as well as the topological property. Such a parameter-free universality is never observed in their three-dimensional counterparts. By deriving a simple expression for the 2D polarizability merely with respect to Eg, and adopting the screened hydrogen model for Eb, the linear scaling law can be deduced analytically. This work provides an opportunity to better understand the fantastic consequence of the 2D nature for materials, and thus offers valuable guidance for their property modulation and performance control.

  4. Role of Codeposited Impurities in Growth: Dependence of Morphology on Binding and Barrier Energies

    Science.gov (United States)

    Sathiyanarayanan, Rajesh; Hamouda, A. Bh.; Pimpinelli, A.; Einstein, T. L.

    2010-03-01

    The previous talk showed that codeposition of impurity atoms during epitaxial growth could be used for nanostructuring of surfaces. Based on their lateral nearest-neighbor binding energies (ENN) to Cu and their diffusion barriers (Ed) on Cu(001), we classify the candidate impurity atoms into four sets. We find that codeposition of impurities from different sets produce qualitatively different surface morphologies both in the step-flow and the submonolayer (θ<= 0.7 ML) regimes. In the submonolayer regime, we characterize these differences through variations of the number of islands (Ni) and the average island size with coverage (θ). Further, we compute the critical nucleus size (i) for all of these cases from the distribution of capture-zone areas using the generalized Wigner distribution.footnotetextA. Pimpinelli, T. L. Einstein, Phys. Rev. Lett. 99, 226102 (2007).

  5. 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

    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......) and compare this range to predictions from several widely used electronic structure methods, including five density functionals, Møller-Plesset perturbation theory, and five coupled cluster methods up to CCSDT quality, considering also the D3 dispersion correctional scheme. With some exceptions, we find...... that most electronic structure methods overestimate ΔG°295 K. The effects of vibrational anharmonicity is approximated using scaling factors, reducing ΔG°295 K by ca. 1.8 kJ mol(-1), whereby ΔG°295 K predictions well within the experimental range can be obtained....

  6. Comparison between two methods for forward calculation of ambient noise H/V spectral ratios

    Science.gov (United States)

    Garcia-Jerez, A.; Luzón, F.; Sanchez-Sesma, F. J.; Santoyo, M. A.; Albarello, D.; Lunedei, E.; Campillo, M.; Iturrarán-Viveros, U.

    2011-12-01

    The analysis of horizontal-to-vertical spectral ratios of ambient noise (NHVSR) is a valuable tool for seismic prospecting, particularly if both a dense spatial sampling and a low-cost procedure are required. Unfortunately, the computation method still lacks of a unanimously accepted theoretical basis and different approaches are currently being used for inversion of the ground structure from the measured H/V curves. Two major approaches for forward calculation of NHVSRs in a layered medium are compared in this work. The first one was developed by Arai and Tokimatsu (2004) and recently improved by Albarello and Lunedei (2011). It consists of a description of the wavefield as generated by Far Surface point Forces (FSF method). The second one is based on the work of Sánchez-Sesma et al. (2011) who consider ambient noise as a Diffuse WaveField (DWF method), taking advantage of the proportionality between its Fourier-transformed autocorrelation (power spectrum) and the imaginary part of the Green function when source and receiver are the same. In both methods, the NHVSR is written as (PH/PV)1/2, where PH and PV are the horizontal and vertical power spectra. In the FSF method these quantities are given by PV∝⊙m(1+1/2χm2α2)(ARm/kRm)2 PH∝⊙m{(1+1/2χm2α2)(ARm/kRm)2χm2+1/2α2(ALm/kLm)2} where kRm, χm and ARm are wavenumber, ellipticity and medium response of the m-th Rayleigh wave mode; kLm and ALm correspond to the m-th Love wave mode and α is the horizontal-to-vertical load ratio of the ambient noise sources. Some common factors are omitted in the expressions of PV and PH. On the other hand, the DWF method deals with the full wavefield including both surface and body waves. In order to make the comparison easier, and taking into account that surface waves are often the dominant components in wide spectral ranges, body wave contributions are neglected here. In this case, the PH and PV power spectra for the DWF method are reduced to the simple expressions: PV

  7. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.

    Science.gov (United States)

    Reif, Maria M; Oostenbrink, Chris

    2014-01-30

    The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved.

  8. 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

  9. 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

  10. Exciton and donor binding energies in quantum-well wires and quantum dots a fractional-dimensional space approach

    Institute of Scientific and Technical Information of China (English)

    Li Hong; Kong Xiao-Jun

    2004-01-01

    A simple method for calculating the free-exciton binding energies in the fractional-dimensional-space model for single-quantum-well structure has been extended to quantum-well wires and quantum dots, in which the real anisotropic system is modelled through an effective isotropic environment with a fractional dimension. In this scheme, the fractionaldimensional parameter is chosen via an analytical procedure and involves no ansatz. We calculated the ground-state binding energies of excitons and donors in quantum-well wires with rectangular cross sections. Our results are found to be in good agreement with previous variational calculations and available experimental measurements. We also discussed the ground-state exciton binding energy changing with different shapes of quantum-well wires.

  11. Experimentally Determined Binding Energies of Astrophysically Relevant Hydrocarbons in Pure and H2O-Layered Ices

    Science.gov (United States)

    Behmard, Aida; Graninger, Dawn; Fayolle, Edith; Oberg, Karin I.

    2017-01-01

    Small hydrocarbons represent an important organic reservoir in a variety of interstellar environments. Constraints on desorption temperatures and binding energies of hydrocarbons are thus necessary for accurate predictions of where and in which phase these molecules exist. Through a series of temperature programmed desorption experiments, we determined binding energies of 1, 2, and 3-carbon interstellar hydrocarbons (CH4, C2H2, C2H4, C2H6, C3H4, C3H6, and C3H8) in pure ices and in relation to water ice, the dominant ice constituent during star and planet formation. These empirically determined values can be used to inform observations and models of the molecular spatial distribution in protoplanetary disks, thus providing insight into planetesimal composition. In addition, knowledge of hydrocarbon binding energies will refine simulations of grain surface chemistry, allowing for better predictions of the chemical conditions that lead to the production of complex organic molecules vital for life.

  12. Binding energies of trions and biexcitons in two-dimensional semiconductors from diffusion quantum Monte Carlo calculations

    Science.gov (United States)

    Szyniszewski, M.; Mostaani, E.; Drummond, N. D.; Fal'ko, V. I.

    2017-02-01

    Excitonic effects play a particularly important role in the optoelectronic behavior of two-dimensional (2D) semiconductors. To facilitate the interpretation of experimental photoabsorption and photoluminescence spectra we provide statistically exact diffusion quantum Monte Carlo binding-energy data for Mott-Wannier models of excitons, trions, and biexcitons in 2D semiconductors. We also provide contact pair densities to allow a description of contact (exchange) interactions between charge carriers using first-order perturbation theory. Our data indicate that the binding energy of a trion is generally larger than that of a biexciton in 2D semiconductors. We provide interpolation formulas giving the binding energy and contact density of 2D semiconductors as functions of the electron and hole effective masses and the in-plane polarizability.

  13. 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 kJ/mol. Subsequent......Predicting binding affinities for receptor-ligand complexes is still one of the challenging processes in computational structure-based ligand design. Many computational methods have been developed to achieve this goal, such as docking and scoring methods, the linear interaction energy (LIE) method...

  14. Role of codeposited impurities during growth. II. Dependence of morphology on binding and barrier energies

    Science.gov (United States)

    Sathiyanarayanan, Rajesh; Hamouda, Ajmi Bh.; Pimpinelli, A.; Einstein, T. L.

    2011-01-01

    In an accompanying article we showed that surface morphologies obtained through codeposition of a small quantity (2%) of impurities with Cu during growth (step-flow mode, θ = 40 ML) significantly depends on the lateral nearest-neighbor binding energy (ENN) to Cu adatom and the diffusion barrier (Ed) of the impurity atom on Cu(0 0 1). Based on these two energy parameters, ENN and Ed, we classify impurity atoms into four sets. We study island nucleation and growth in the presence of codeposited impurities from different sets in the submonolayer (θ⩽ 0.7 ML) regime. Similar to growth in the step-flow mode, we find different nucleation and growth behavior for impurities from different sets. We characterize these differences through variations of the number of islands (Ni) and the average island size with coverage (θ). Further, we compute the critical nucleus size (i) for all of these cases from the distribution of capture-zone areas using the generalized Wigner distribution.

  15. Binding energies of the lithium isoelectronic sequence approaching the critical charge

    Science.gov (United States)

    Katriel, Jacob; Puchalski, Mariusz; Pachucki, Krzysztof

    2012-10-01

    The Simon-Zhislin-Hunziker theorem implies that Zc, the critical charge below which the three electron atom is not bound, is at most 2. The vanishing electron affinity of He implies that Zc is not less than 2. Hence, Zc=2. To elucidate the approach to the critical charge, we calculated nonrelativistic binding energies for the third electron in the ground state, 1s22s2S, and in the first and second excited states, 1s22p2P and 1s23s2S, for nuclear charges approaching Zc. At this limit the quantum defects for both 2S states are found to approach unity. This implies that the orbital specifying the outer (ns,n=2,3) electron becomes a very diffuse (n-1)s-type orbital, except within the relatively tiny space occupied by the inner two-electron shell. For the 2P state the quantum defect approaches zero both as Z→∞ and as Z→2. An expression for the s-p splitting at Z→2 is suggested, that improves upon earlier results based on energies computed (or measured) at integer values of Z. Rigorous large Z asymptotic expressions for the quantum defects in the 1s2ns2S states are presented, exhibiting the expected mild dependence on the principal quantum number.

  16. 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.

  17. Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.

    Directory of Open Access Journals (Sweden)

    Adrien Nicolaï

    Full Text Available ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD of Hsp70 propagates a signal to its substrate-binding domain (SBD. Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in

  18. Mapping the geophysical bedrock of the Moesian Platform using H/V ratios and borehole data.

    Science.gov (United States)

    Florinela Manea, Elena; Michel, Clotaire; Fäh, Donat; Ortanza Cioflan, Carmen

    2016-04-01

    The strong effects at long periods observed in the extra-Carpathian area of Romania during large Vrancea intermediate-depth earthquakes were explained by the influence of both source mechanism and mechanical properties of the geological structure. Complex basin geometry and the low seismic velocities of the sediments are the primary responsible for the large amplification and long duration of the seismic records from the extra-Carpathian area during intermediate-depth earthquakes. The aim of this study is to map the geophysical bedrock of this area correlating and interpolating the results obtained from local resonance phenomena evaluation with the available surface geological data. The site was investigated through the computation of H/V spectral ratios from three-directional single station measurements of ambient vibration. The first step was to estimate the depth of the geophysical bedrock at all the Romanian seismic stations located in the extra-Carpathian area (velocity sensors) using the fundamental frequency retrieved from the H/V curves. In the second stage of the study all the relevant peaks from the H/V curves were interpreted in consonance with the available information of the geology. The geological data were obtained from the database developed in the national BIGSEES project by National Institute of Earth Physics. In this database are integrated all the geological, geophysical data from all the past projects, contracts, studies (as refraction, reflexion, etc.), geotechnical drillings and other information publicly available. The mapping of the geophysical bedrock was done interpolating the geological database and information gathered/resulted from H/V using a geographical informational system(GIS). The geology of this area displays very complex features as outcrops in small zones/lines/ near the Danube and then is gradually dipping to about 2 km depth in the N-NE. The depth of the bedrock is (nearly) constant around 100 m depth on the right side of

  19. 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.

  20. Effect of Magnetic Field and Shell Thickness on Binding Energies of a ZnSe/ZnS Core Shell Quantum Dot

    Science.gov (United States)

    Bhat, Bashir Mohi ud din; Parvaiz, Muhammad Shunaid; Sen, Pratima

    2017-02-01

    We investigated the effect of external magnetic field and shell thickness on the binding energies of a ZnSe/ZnS core shell quantum dot. The binding energies were calculated using the variational method within the effective mass approximation and confinement potential. The binding energy of the 2 s and 2 p + states was found to increase with magnetic field. However, the 2 p 0 state was found to be independent of the magnetic field at a shell thickness of 0.5 nm. Degeneracy of the lifted 2 p states was found to occur. The results also showed that the electron binding energy increases at the outset with the increasing shell thickness, and at larger shell thicknesses, the binding energy saturates. The binding energy was found to be decreasing with increasing core diameter and becomes appreciably smaller at core radius of 0.42 nm. The observed results were compared with the previously reported results.

  1. Evaluations of the Absolute and Relative Free Energies for Antidepressant Binding to the Amino Acid Membrane Transporter LeuT with Free Energy Simulations.

    Science.gov (United States)

    Zhao, Chunfeng; Caplan, David A; Noskov, Sergei Yu

    2010-06-08

    The binding of ligands to protein receptors with high affinity and specificity is central to many cellular processes. The quest for the development of computational models capable of accurately evaluating binding affinity remains one of the main goals of modern computational biophysics. In this work, free energy perturbation/molecular dynamics simulations were used to evaluate absolute and relative binding affinity for three different antidepressants to a sodium-dependent membrane transporter, LeuT, a bacterial homologue of human serotonin and dopamine transporters. Dysfunction of these membrane transporters in mammals has been implicated in multiple diseases of the nervous system, including bipolar disorder and depression. Furthermore, these proteins are key targets for antidepressants including fluoxetine (aka Prozac) and tricyclic antidepressants known to block transport activity. In addition to being clinically relevant, this system, where multiple crystal structures are readily available, represents an ideal testing ground for methods used to study the molecular mechanisms of ligand binding to membrane proteins. We discuss possible pitfalls and different levels of approximation required to evaluate binding affinity, such as the dependence of the computed affinities on the strength of constraints and the sensitivity of the computed affinities to the particular partial charges derived from restrained electrostatic potential fitting of quantum mechanics electrostatic potential. Finally, we compare the effects of different constraint schemes on the absolute and relative binding affinities obtained from free energy simulations.

  2. Changes in the zero-point energy of the protons as the source of the binding energy of water to A-phase DNA.

    Science.gov (United States)

    Reiter, G F; Senesi, R; Mayers, J

    2010-10-01

    The measured changes in the zero-point kinetic energy of the protons are entirely responsible for the binding energy of water molecules to A phase DNA at the concentration of 6  water molecules/base pair. The changes in kinetic energy can be expected to be a significant contribution to the energy balance in intracellular biological processes and the properties of nano-confined water. The shape of the momentum distribution in the dehydrated A phase is consistent with coherent delocalization of some of the protons in a double well potential, with a separation of the wells of 0.2 Å.

  3. 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.

  4. Temperature dependence of the nuclear binding energy: effects on the EOS for hot nuclear matter using different models

    Energy Technology Data Exchange (ETDEWEB)

    Benvenuto, O.G. [La Plata Univ. (Argentina). Fac. of Astron. and Geophys.; Civitarese, O. [Dept. of Physics, Univ. of La Plata (Argentina); Reboiro, M. [Dept. of Physics, Univ. of La Plata (Argentina)

    1997-05-01

    Effects due to the temperature dependence of the nuclear binding energy upon the equation of state (EOS) for hot nuclear matter are studied. Nuclear contributions to the free energy are represented by temperature dependent liquid drop model terms. Phase coexistence is assumed for temperatures of the order of 1 MeV {<=} T {<=} 6 MeV, baryon number densities {rho} of the order of 10{sup -4}fm{sup -3} {<=} {rho} {<=} 10{sup -1}fm{sup -3} and lepton fractions of the order of 0.2 {<=} y{sub 1} {<=} 0.4. It is found that the total pressure of the system is not affected by the temperature dependence of the nuclear free energy, in spite of changes observed in the nuclear pressure due to the different parametrizations used to represent the nuclear binding energy. (orig.).

  5. Ambient noise H/V spectral ratio in site effects estimation in Fateh jang area, Pakistan

    Institute of Scientific and Technical Information of China (English)

    S.M.Talha Qadri; Bushra Nawaz; S.H.Sajjad; Riaz Ahmad Sheikh

    2015-01-01

    Local geology or local site effect is a crucial component while conducting seismic risk assessment studies.Investigations made by utilization of ambient noise are an effective tool for local site estimation.The present study is conducted to perform site response analysis at 13 different sites within urban settlements of Fateh jang area (Pakistan).The aim of this study was achieved by utilizing Nakamura method or H/V spectral ratio method.Some important local site parameters,e.g.,the fundamental frequencies f0 of soft sediments,amplitudes A0 of corresponding H/V spectral ratios,and alluvium thicknesses over 13 sites within the study area,were measured and analyzed.The results show that the study area reflects low fundamental frequency f0.The fundamental frequencies of the sediments are highly variable and lie in a range of 0.6-13.0 Hz.Similarly,amplification factors at these sites are in the range of 2.0-4.0.

  6. Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.

    Directory of Open Access Journals (Sweden)

    M Olivia Kim

    2015-10-01

    Full Text Available BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer's disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems.

  7. 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

    2015-01-01

    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. PMID:26220470

  8. Effects due to temperature-dependent nuclear binding energies on the equation of state for hot nuclear matter

    Energy Technology Data Exchange (ETDEWEB)

    Benvenuto, O.G. (Facultad de Ciencias Astronomica y Geofisicas, Universidad Nacional de La Plata, La Plata, Buenos Aires (Argentina)); Civitarese, O.; Reboiro, M. (Departamento de Fisica, Universidad Nacional de La Plata, La Plata, Buenos Aires (Argentina))

    1993-05-01

    The influence of finite temperature nuclear effects upon the adiabatic index, for a system of nuclei, nucleons, and leptons, is discussed. It is found that the inclusion of temperature-dependent nuclear binding energies affects the behavior of the adiabats and of the adiabatic index, particularly, at low entropies.

  9. Investigating the relative influences of molecular dimensions and binding energies on diffusivities of guest species inside nanoporous crystalline materials

    NARCIS (Netherlands)

    Krishna, R.; van Baten, J.M.

    2012-01-01

    The primary objective of this article is to investigate the relative influences of molecular dimensions and adsorption binding energies on unary diffusivities of guest species inside nanoporous crystalline materials such as zeolites and metal-organic frameworks (MOFs). The investigations are based o

  10. Development of molecular docking-based binding energy to predict the joint effect of BPA and its analogs.

    Science.gov (United States)

    Zhang, Hong-Chang; Hu, Xia-Lin; Yin, Da-Qiang; Lin, Zhi-Fen

    2011-04-01

    A general proposal for predicting the joint effect of endocrine disrupting chemicals by examining binding energy models was developed in this study. 2,2-bis(4-hydroxyphenyl)propane (BPA) and 11 of its analogs were chosen, and the estrogenic activity of each compound was measured by determining its EC50 value using a recombinant gene yeast assay. Binding energies (BEs) were calculated using Surflex-Docking software. The analysis of the relationship between EC50 values and BEs showed that there is a linear correlation between the BEs and EC50 values. Furthermore, the analysis of the given binary and quaternary mixtures of BPA and three of its analogs showed that the joint effects of the mixtures were affected by the proportions of the chemicals in each mixture and their relative binding energy. The correlation between the joint effects of mixtures and the binding energy of the individual compounds has been described using one formula, which can be used to predict the joint effects of other mixtures.

  11. Development of homogeneous binding assays based on fluorescence resonance energy transfer between quantum dots and Alexa Fluor fluorophores.

    Science.gov (United States)

    Nikiforov, Theo T; Beechem, Joseph M

    2006-10-01

    We studied the fluorescence resonance energy transfer (FRET) between quantum dots emitting at 565, 605, and 655 nm as energy donors and Alexa Fluor fluorophores with absorbance maxima at 594, 633, 647, and 680 nm as energy acceptors. As a first step, we prepared covalent conjugates between all three types of quantum dots and each of the Alexa Fluor fluorophores that could act as an energy acceptor. All of these conjugates displayed efficient resonance energy transfer. Then we prepared covalent conjugates of these quantum dots with biotin, fluorescein, and cortisol and established that the binding of these conjugates to suitable Alexa Fluor-labeled antibodies and streptavidin (in the case of biotin) can be efficiently detected by measuring the resonance energy transfer in homogeneous solutions. Finally, based on these observations, competitive binding assays for these three small analytes were developed. The performance of these assays as a function of the degree of labeling of the quantum dots was evaluated. It was found that decreasing the degree of loading of the quantum dots leads to decreases of the limits of detection. The results show the great potential of this FRET system for the development of new homogeneous binding assays.

  12. 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.

  13. Measurement of the binding energy of ultracold 87Rb133Cs molecules using an offset-free optical frequency comb

    Science.gov (United States)

    Molony, Peter K.; Kumar, Avinash; Gregory, Philip D.; Kliese, Russell; Puppe, Thomas; Le Sueur, C. Ruth; Aldegunde, Jesus; Hutson, Jeremy M.; Cornish, Simon L.

    2016-08-01

    We report the binding energy of 87Rb133Cs 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 T Hz ; 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 ×114 268 135.24 (4 )(3 )M Hz . To our knowledge, this is the most accurate determination to date of the dissociation energy of a molecule.

  14. Theoretical study of the binding energy of a methane molecule in a (H2O)20 dodecahedral cage.

    Science.gov (United States)

    Deible, Michael J; Tuguldur, Odbadrakh; Jordan, Kenneth D

    2014-07-17

    The interaction energy of a methane molecule encapsulated in a dodecahedral water cage is calculated using the MP2, MP2C, various dispersion-corrected DFT, and diffusion Monte Carlo (DMC) methods. The MP2, MP2C, and DMC methods give binding energies of -5.04, -4.60, and -5.3 ± 0.5 kcal/mol, respectively. In addition, the two- and three-body contributions are evaluated using the DFT, MP2, and CCSD(T) methods. All of the DFT methods considered appreciably overestimate the magnitude of the three-body contribution to the interaction energy. The two- and three-body energies are further analyzed by use of symmetry-adapted perturbation theory (SAPT) which allows decomposition into electrostatics, exchange, induction, and dispersion contributions. The SAPT calculations reveal that the induction, dispersion, and exchange three-body contributions to the methane-cage binding energy are all sizable, with the net three-body contribution to the binding energy being about 1 kcal/mol.

  15. Simulation of symmetric nuclei and the role of Pauli potential in binding energies

    Energy Technology Data Exchange (ETDEWEB)

    M. Angeles Perez-Garcia, K. Tsushima, A. Valcarce

    2009-05-01

    It is shown that the use of a density dependent effective Pauli potential together with a nucleon-nucleon interaction potential plays a crucial role to reproduce not only the binding energies but also the matter root mean square radii of medium mass range spin-isospin saturated nuclei. This study is performed with a semiclassical Monte Carlo many-body simulation within the context of a simplified nucleon-nucleon interaction to focus on the effect of the genuine correlations due to the fermionic nature of nucleons. The procedure obtained is rather robust and it does not depend on the detailed features of the nucleon-nucleon interaction. For nuclei below saturation the density dependence may be represented in terms either of the nucleon number, $A$, or the associated Fermi momenta. When testing the simulation procedure for idealized "infinite" symmetric nuclear matter within the corresponding range of densities, it turns out that finite size effects affect the Pauli potential strength parametrization in systems up to about 120 particles while remaining approximately stable for larger systems.

  16. Spectroscopy of mesons and proton binding energy in the statistical model with three-quarkonium potentials

    Energy Technology Data Exchange (ETDEWEB)

    Ikhdair, S.M.; Sever, R.; Magdy, M.A. [Middle East Technical Univ., Ankara (Turkey)

    1994-04-01

    The mass spectra of the lowest S, P and D levels of the self-conjugate (Q{bar Q}) and the non-self-conjugate (Q{bar q}) mesons are studied with the three flavour-dependent static quark-antiquark potentials, belong to the class U(r)=a{sub 1}r{sup {gamma}}{minus}a{sub 2}r{sup {minus}{gamma}}+a{sub 3}, for {gamma}=1, 1/2, 3/4 cases. The non-relativistic form of statistical model is used in the calculations. The leptonic decay widths and decay constants of the vector Q{bar Q} and the psuedoscalar Q{bar q} mesons are estimated by considering the improved version of the Van Royen-Weisskopf formula. Moreover, the binding energy, the form factor and the charge radius of the proton have also been calculated. These results are in reasonably good agreement with experimental and theoretical findings. 21 refs., 6 tabs.

  17. Binding energy and mechanical stability of single- and multi-walled carbon nanotube serpentines

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Junhua, E-mail: junhua.zhao@163.com, E-mail: timon.rabczuk@uni-weimar.de [Jiangsu Key Laboratory of Advanced Food Manufacturing Equipment and Technology, Jiangnan University, 214122 Wuxi (China); Institute of Structural Mechanics, Bauhaus University, 99423 Weimar (Germany); Lu, Lixin [Jiangsu Key Laboratory of Advanced Food Manufacturing Equipment and Technology, Jiangnan University, 214122 Wuxi (China); Rabczuk, Timon, E-mail: junhua.zhao@163.com, E-mail: timon.rabczuk@uni-weimar.de [Institute of Structural Mechanics, Bauhaus University, 99423 Weimar (Germany)

    2014-05-28

    Recently, Geblinger et al. [Nat. Nanotechnol. 3, 195 (2008)] and Machado et al. [Phys. Rev. Lett. 110, 105502 (2013)] reported the experimental and molecular dynamics realization of S-like shaped single-walled carbon nanotubes (CNTs), the so-called CNT serpentines. We reported here results from continuum modeling of the binding energy γ between different single- and multi-walled CNT serpentines and substrates as well as the mechanical stability of the CNT serpentine formation. The critical length for the mechanical stability and adhesion of different CNT serpentines are determined in dependence of E{sub i}I{sub i}, d, and γ, where E{sub i}I{sub i} and d are the CNT bending stiffness and distance of the CNT translation period. Our continuum model is validated by comparing its solution to full-atom molecular dynamics calculations. The derived analytical solutions are of great importance for understanding the interaction mechanism between different single- and multi-walled CNT serpentines and substrates.

  18. High level theoretical study of binding and of the potential energy surface in benzene-hydride system

    Energy Technology Data Exchange (ETDEWEB)

    Coletti, Cecilia, E-mail: ccoletti@unich.it [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy); Re, Nazzareno [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy)

    2012-04-04

    Graphical abstract: In-plane minimum geometries for benzene-H{sup -} 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: Black-Right-Pointing-Pointer Theoretical study on covalent and non-covalent binding in benzene-hydride. Black-Right-Pointing-Pointer Two non-covalent stable adducts were characterized in the in-plane geometry. Black-Right-Pointing-Pointer Significant sections of the potential energy surface were determined. Black-Right-Pointing-Pointer Formation of a very stable C{sub 6}H{sub 7}{sup -} 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{sup -} can easily covalently bind to one of the carbon atoms of benzene to form a stable C{sub 6}H{sub 7}{sup -} 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 C{sub 6}H{sub 7}{sup -} structure was also identified, corresponding to the transition state for the flipping motion of the puckered species.

  19. 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.

  20. Conformational selection through electrostatics: Free energy simulations of GTP and GDP binding to archaeal initiation factor 2.

    Science.gov (United States)

    Satpati, Priyadarshi; Simonson, Thomas

    2012-05-01

    Archaeal Initiation Factor 2 is a GTPase involved in protein biosynthesis. In its GTP-bound, "ON" conformation, it 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 their dependence on the conformational state, molecular dynamics free energy simulations were performed. The ON state specificity was predicted to be weak, with a GTP/GDP binding free energy difference of -1 kcal/mol, favoring GTP. The OFF state specificity is larger, 4 kcal/mol, favoring GDP. The overall effects result from a competition among many interactions in several complexes. To interpret them, we use a simpler, dielectric continuum model. Several effects are robust with respect to the model details. Both nucleotides have a net negative charge, so that removing them from solvent into the binding pocket carries a desolvation penalty, which is large for the ON state, and strongly disfavors GTP binding compared to GDP. Short-range interactions between the additional GTP phosphate group and ionized sidechains in the binding pocket offset most, but not all of the desolvation penalty; more distant groups also contribute significantly, and the switch 1 loop only slightly. The desolvation penalty is lower for the more open, wetter OFF state, and the GTP/GDP difference much smaller. Short-range interactions in the binding pocket and with more distant groups again make a significant contribution. Overall, the simulations help explain how conformational selection is achieved with a single phosphate group. Copyright © 2012 Wiley Periodicals, Inc.

  1. Modelling Sediment Thickness for Site-Effect Characterisation using H/V Spectral Ratio Analysis and Electrical Resistivity Tomography

    Science.gov (United States)

    Van Noten, Koen; Lecocq, Thomas; Watlet, Arnaud; Camelbeeck, Thierry

    2014-05-01

    The H/V Spectral Ratio (HVSR) analysis of ambient seismic noise has been widely used to estimate the fundamental site resonance frequency in the context of site-effect characterisation. In regions of unknown subsurface structure, in which there is a significant acoustic impedance contrast between sediments and the underlying bedrock, HVSR can be a very powerful tool to map bedrock morphology and sediment thickness. Calibrating the power-law relationship between the variation in fundamental frequency and sediment thickness around these unknown sites is crucial for sediment thickness mapping. This empirical relationship can be easily calculated by conducting HVSR analysis of ambient noise measurements above boreholes with known bedrock depth. Additional local H/V measurements above near-surface geophysical profiles, for instance created by Electrical Resistivity Tomography (ERT), allow training and improving the power-law relationship for sites with a shallow bedrock depth. As the compaction of sediments influences the Vs, one has however to take into account that this empirical relationship can only be applied in relative small areas with a similar local geology. Between 2008 and 2010, a seismic swarm (MLmax = 3.2) occurred in a hilly area, 20 km SE of Brussels (Belgium). 60 of the 300 recorded events were felt/heard by the local residents and were reported in the corresponding 'Did You Feel It' internet inquiries held by Royal Observatory of Belgium. Several low-magnitude events show a distinct macroseismic intensity variation that can be explained by the geological site effect, i.e. the local sediment thickness, affecting the human perception of these earthquake-induced ground motions. In this presentation, we apply the above described methodology and discuss the results of a geophysical survey including ERT-profiling, ambient noise recording, HVSR analysis in Geopsy and DEM-modelling to characterise the local site effects. The resulting sediment thickness model

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

    Science.gov (United States)

    Lemke, Kono H.

    2017-06-01

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

  3. 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.

  4. 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...

  5. Molecular dynamics simulation of tryptophan hydroxylase-1: binding modes and free energy analysis to phenylalanine derivative inhibitors.

    Science.gov (United States)

    Zhong, Hao; Huang, Wei; He, Gu; Peng, Cheng; Wu, Fengbo; Ouyang, Liang

    2013-05-10

    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.

  6. 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.

  7. 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

    2014-03-25

    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.

  8. Donor Binding Energy in GaAs/Ga1-x AlxAs Quantum Well: the Laser Field and Temperature Effects

    Institute of Scientific and Technical Information of China (English)

    WEI Shu-Yi; HOU Wen-Xiu; CHEN Xiao-Yang; XIA Cong-Xin

    2013-01-01

    Based on the effective-mass approximation theory and variational method,the laser field and temperature effects on the ground-state donor binding energy in the GaAs/Ga1-xAlxAs quantum well (QW) are investigated.Numerical results show that the donor binding energy depends on the impurity position,laser parameter,temperature,Al composition,and well width.The donor binding energy is decreased when the laser field and temperature are increased in the QW for any impurity position and QW parameter case.Moreover,the laser field has an obvious influence on the donor binding energy of impurity located at the vicinity of the QW center.In addition,our results also show that the donor binding energy decreases (or increases) as the well width (or Al composition x) increases in the QW.

  9. 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)

  10. CBS domains form energy-sensing modules whose binding of adenosine ligands is disrupted by disease mutations

    Science.gov (United States)

    Scott, John W.; Hawley, Simon A.; Green, Kevin A.; Anis, Miliea; Stewart, Greg; Scullion, Gillian A.; Norman, David G.; Hardie, D. Grahame

    2004-01-01

    CBS domains are defined as sequence motifs that occur in several different proteins in all kingdoms of life. Although thought to be regulatory, their exact functions have been unknown. However, their importance was underlined by findings that mutations in conserved residues within them cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): Wolff-Parkinson-White syndrome (γ2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members); and homocystinuria (cystathionine β-synthase). AMP-activated protein kinase is a sensor of cellular energy status that is activated by AMP and inhibited by ATP, but the location of the regulatory nucleotide-binding sites (which are prime targets for drugs to treat obesity and diabetes) was not characterized. We now show that tandem pairs of CBS domains from AMP-activated protein kinase, IMP dehydrogenase-2, the chloride channel CLC2, and cystathionine β-synthase bind AMP, ATP, or S-adenosyl methionine,while mutations that cause hereditary diseases impair this binding. This shows that tandem pairs of CBS domains act, in most cases, as sensors of cellular energy status and, as such, represent a newly identified class of binding domain for adenosine derivatives. PMID:14722619

  11. 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.

  12. Simultaneous effects of pressure and temperature on the binding energy and diamagnetic susceptibility of a laser dressed donor in a spherical quantum dot

    Science.gov (United States)

    Vaseghi, B.; Sajadi, T.

    2012-07-01

    Binding energies and diamagnetic susceptibility of an impurity in a spherical GaAs quantum dot under the simultaneous influence of static pressure, temperature and laser radiation are investigated. Pressure- and temperature-dependent dressed potential which is produced by the combined effects of laser radiation and impurity considerably change the energy spectrum and diamagnetic susceptibility of the system. It is shown that binding energies and diamagnetic susceptibility increase with increasing pressure. Moreover, laser radiation effects on the diamagnetic susceptibility are not significant in comparison with its effects on the binding energy.

  13. Simultaneous effects of pressure and temperature on the binding energy and diamagnetic susceptibility of a laser dressed donor in a spherical quantum dot

    Energy Technology Data Exchange (ETDEWEB)

    Vaseghi, B., E-mail: behroozv1@yahoo.com [Department of Physics, College of Sciences, Yasouj University, Yasouj 75914-353 (Iran, Islamic Republic of); Sajadi, T. [Department of Physics, College of Sciences, Yasouj University, Yasouj 75914-353 (Iran, Islamic Republic of)

    2012-07-15

    Binding energies and diamagnetic susceptibility of an impurity in a spherical GaAs quantum dot under the simultaneous influence of static pressure, temperature and laser radiation are investigated. Pressure- and temperature-dependent dressed potential which is produced by the combined effects of laser radiation and impurity considerably change the energy spectrum and diamagnetic susceptibility of the system. It is shown that binding energies and diamagnetic susceptibility increase with increasing pressure. Moreover, laser radiation effects on the diamagnetic susceptibility are not significant in comparison with its effects on the binding energy.

  14. Fluorescence Resonance Energy Transfer Imaging Reveals that Chemokine-Binding Modulates Heterodimers of CXCR4 and CCR5 Receptors

    OpenAIRE

    2008-01-01

    BACKGROUND: Dimerization has emerged as an important feature of chemokine G-protein-coupled receptors. CXCR4 and CCR5 regulate leukocyte chemotaxis and also serve as a co-receptor for HIV entry. Both receptors are recruited to the immunological synapse during T-cell activation. However, it is not clear whether they form heterodimers and whether ligand binding modulates the dimer formation. METHODOLOGY/PRINCIPAL FINDINGS: Using a sensitive Fluorescence Resonance Energy Transfer (FRET) imaging ...

  15. 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.

  16. Energy coupling to periplasmic binding protein-dependent transport systems: stoichiometry of ATP hydrolysis during transport in vivo.

    OpenAIRE

    Mimmack, M L; Gallagher, M P; Pearce, S R; Hyde, S C; Booth, I R; Higgins, C F

    1989-01-01

    Periplasmic binding protein-dependent transport systems mediate the accumulation of many diverse substrates in prokaryotic cells. Similar transport systems, including the P-glycoprotein responsible for multidrug resistance in human tumors, are also found in eukaryotes. The mechanism by which energy is coupled to the accumulation of substrate by these transport systems has been controversial. In this paper we demonstrate that ATP hydrolysis occurs in vivo concomitantly with transport. These da...

  17. Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context.

    Science.gov (United States)

    Homeyer, Nadine; Stoll, Friederike; Hillisch, Alexander; Gohlke, Holger

    2014-08-12

    Correctly ranking compounds according to their computed relative binding affinities will be of great value for decision making in the lead optimization phase of industrial drug discovery. However, the performance of existing computationally demanding binding free energy calculation methods in this context is largely unknown. We analyzed the performance of the molecular mechanics continuum solvent, the linear interaction energy (LIE), and the thermodynamic integration (TI) approach for three sets of compounds from industrial lead optimization projects. The data sets pose challenges typical for this early stage of drug discovery. None of the methods was sufficiently predictive when applied out of the box without considering these challenges. Detailed investigations of failures revealed critical points that are essential for good binding free energy predictions. When data set-specific features were considered accordingly, predictions valuable for lead optimization could be obtained for all approaches but LIE. Our findings lead to clear recommendations for when to use which of the above approaches. Our findings also stress the important role of expert knowledge in this process, not least for estimating the accuracy of prediction results by TI, using indicators such as the size and chemical structure of exchanged groups and the statistical error in the predictions. Such knowledge will be invaluable when it comes to the question which of the TI results can be trusted for decision making.

  18. Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor

    Directory of Open Access Journals (Sweden)

    Sentot Joko Raharjo

    2014-01-01

    Full Text Available To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2 synthase (PGHS/COX, the three-dimensional (3D structure of COX-1/COX-2 was assessed by means of binding energy calculation of virtual molecular dynamic with using ligand alpha-Patchouli alcohol isomers. Molecular interaction studies with COX-1 and COX-2 were done using the molecular docking tools by Hex 8.0. Interactions were further visualized by using Discovery Studio Client 3.5 software tool. The binding energy of molecular interaction was calculated by AMBER12 and Virtual Molecular Dynamic 1.9.1 software. The analysis of the alpha-Patchouli alcohol isomer compounds showed that all alpha-Patchouli alcohol isomers were suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent of alpha-Patchouli alcohol isomer compounds (CID442384, CID6432585, CID3080622, CID10955174, and CID56928117 was suggested as candidate for a selective COX-1 inhibitor and CID521903 as nonselective COX-1/COX-2.

  19. Global analysis of steady-state energy transfer measurements in membranes: resolution of structural and binding parameters.

    Science.gov (United States)

    Domanov, Yegor A; Gorbenko, Galina P; Molotkovsky, Julian G

    2004-01-01

    A method has been developed allowing structural and binding parameters to be recovered by global analysis of two-dimensional array of steady-state RET data in the special case where energy acceptors distribute between aqueous and lipid phases while donors are embedded in the membrane at a known depth. To test the validity of this approach, correlation and error analyses have been performed using simulated data. To exemplify the method application to the membrane studies, energy transfer from anthrylvinyl-labeled phosphatidylcholine incorporated into mixed phosphatidylcholine/cardiolipin unilamellar vesicles to heme group of cytochrome c is analyzed.

  20. Effects of low-energy excitations on spectral properties at higher binding energy: the metal-insulator transition of VO(2).

    Science.gov (United States)

    Gatti, Matteo; Panaccione, Giancarlo; Reining, Lucia

    2015-03-20

    The effects of electron interaction on spectral properties can be understood in terms of coupling between excitations. In transition-metal oxides, the spectral function close to the Fermi level and low-energy excitations between d states have attracted particular attention. In this work we focus on photoemission spectra of vanadium dioxide over a wide (10 eV) range of binding energies. We show that there are clear signatures of the metal-insulator transition over the whole range due to a cross coupling of the delocalized s and p states with low-energy excitations between the localized d states. This coupling can be understood by advanced calculations based on many-body perturbation theory in the GW approximation. We also advocate the fact that tuning the photon energy up to the hard-x-ray range can help to distinguish fingerprints of correlation from pure band-structure effects.

  1. A structure-based design of new C2- and C13-substituted taxanes: tubulin binding affinities and extended quantitative structure-activity relationships using comparative binding energy (COMBINE) analysis.

    Science.gov (United States)

    Coderch, Claire; Tang, Yong; Klett, Javier; Zhang, Shu-En; Ma, Yun-Tao; Shaorong, Wang; Matesanz, Ruth; Pera, Benet; Canales, Angeles; Jiménez-Barbero, Jesús; Morreale, Antonio; Díaz, J Fernando; Fang, Wei-Shuo; Gago, Federico

    2013-05-14

    Ten novel taxanes bearing modifications at the C2 and C13 positions of the baccatin core have been synthesized and their binding affinities for mammalian tubulin have been experimentally measured. The design strategy was guided by (i) calculation of interaction energy maps with carbon, nitrogen and oxygen probes within the taxane-binding site of β-tubulin, and (ii) the prospective use of a structure-based QSAR (COMBINE) model derived from an earlier series comprising 47 congeneric taxanes. The tubulin-binding affinity displayed by one of the new compounds (CTX63) proved to be higher than that of docetaxel, and an updated COMBINE model provided a good correlation between the experimental binding free energies and a set of weighted residue-based ligand-receptor interaction energies for 54 out of the 57 compounds studied. The remaining three outliers from the original training series have in common a large unfavourable entropic contribution to the binding free energy that we attribute to taxane preorganization in aqueous solution in a conformation different from that compatible with tubulin binding. Support for this proposal was obtained from solution NMR experiments and molecular dynamics simulations in explicit water. Our results shed additional light on the determinants of tubulin-binding affinity for this important class of antitumour agents and pave the way for further rational structural modifications.

  2. Modeling and inversion of the microtremor H/ V spectral ratio: physical basis behind the diffuse field approach

    Science.gov (United States)

    Sánchez-Sesma, Francisco J.

    2017-07-01

    Microtremor H/ V spectral ratio (MHVSR) has gained popularity to assess the dominant frequency of soil sites. It requires measurement of ground motion due to seismic ambient noise at a site and a relatively simple processing. Theory asserts that the ensemble average of the autocorrelation of motion components belonging to a diffuse field at a given receiver gives the directional energy densities (DEDs) which are proportional to the imaginary parts of the Green's function components when both source and receiver are the same point and the directions of force and response coincide. Therefore, the MHVSR can be modeled as the square root of 2 × Im G 11/Im G 33, where Im G 11 and Im G 33 are the imaginary parts of Green's functions at the load point for the horizontal (sub-index 1) and vertical (sub-index 3) components, respectively. This connection has physical implications that emerge from the duality DED force and allows understanding the behavior of the MHVSR. For a given model, the imaginary parts of the Green's functions are integrals along a radial wavenumber. To deal with these integrals, we have used either the popular discrete wavenumber method or the Cauchy's residue theorem at the poles that account for surface waves normal modes giving the contributions due to Rayleigh and Love waves. For the retrieval of the velocity structure, one can minimize the weighted differences between observations and calculated values using the strategy of an inversion scheme. In this research, we used simulated annealing but other optimization techniques can be used as well. This last approach allows computing separately the contributions of different wave types. An example is presented for the mouth of Andarax River at Almería, Spain. [Figure not available: see fulltext.

  3. The inversion of spectral ratio H/V in a layered system using the diffuse field assumption (DFA)

    Science.gov (United States)

    Piña-Flores, José; Perton, Mathieu; García-Jerez, Antonio; Carmona, Enrique; Luzón, Francisco; Molina-Villegas, Juan C.; Sánchez-Sesma, Francisco J.

    2017-01-01

    In order to evaluate the site effects on seismic ground motion and establish preventive measures to mitigate these effects, the dynamic characterization of sites is mandatory. Among the various geophysical tools aimed to this end, the horizontal to vertical spectral ratio (H/V) is a simple way to assess the dominant frequency of a site from seismic ambient noise. The aim of this communication is contributing to enhance the potential of this measurement with a novel method that allows extracting from the H/V the elastic properties of the subsoil, assumed here as a multilayer medium. For that purpose, we adopt the diffuse field assumption from both the experimental and the modelling perspectives. At the experimental end, the idea is to define general criteria that make the data processing closely supported by theory. On the modelling front, the challenge is to compute efficiently the imaginary part of Green's function. The Cauchy's residue theory in the horizontal wavenumber complex plane is the selected approach. This method allows both identifying the contributions of body and surface waves and computing them separately. This permits exploring the theoretical properties of the H/V under different compositions of the seismic ambient noise. This answers some questions that historically aroused and gives new insights into the H/V method. The efficient forward calculation is the prime ingredient of an inversion scheme based on both gradient and heuristic searches. The availability of efficient forward calculation of H/V allows exploring some relevant relationships between the H/V curves and the parameters. This allows generating useful criteria to speed up inversion. As in many inverse problems, the non-uniqueness issues also emerge here. A joint inversion method that considers also the dispersion curves of surface waves extracted from seismic ambient noise is presented and applied to experimental data. This joint scheme mitigates effectively the non-uniqueness.

  4. The inversion of spectral ratio H/V in a layered system using the Diffuse Field Assumption (DFA)

    Science.gov (United States)

    Piña-Flores, José; Perton, Mathieu; García-Jerez, Antonio; Carmona, Enrique; Luzón, Francisco; Molina-Villegas, Juan C.; Sánchez-Sesma, Francisco J.

    2016-11-01

    In order to evaluate the site effects on seismic ground motion and establish preventive measures to mitigate these effects, the dynamic characterization of sites is mandatory. Among the various geophysical tools aimed to this end, the horizontal to vertical spectral ratio (H/V) is a simple way to assess the dominant frequency of a site from seismic ambient noise. The aim of this communication is contributing to enhance the potential of this measurement with a novel method that allows extracting from the H/V the elastic properties of the subsoil, assumed here as a multilayer medium. For that purpose, we adopt the Diffuse Field Assumption from both the experimental and the modeling perspectives. At the experimental end, the idea is to define general criteria that make the data processing closely supported by theory. On the modeling front, the challenge is to compute efficiently the imaginary part of Green's function. The Cauchy's residue theory in the horizontal wavenumber complex plane is the selected approach. This method allows both identifying the contributions of body and surface waves and computing them separately. This permits exploring the theoretical properties of the H/V under different compositions of the seismic ambient noise. This answers some questions that historically aroused and gives new insights into the H/V method. The efficient forward calculation is the prime ingredient of an inversion scheme based on both gradient and heuristic searches. The availability of efficient forward calculation of H/V allows exploring some relevant relationships between the H/V curves and the parameters. This allows generating useful criteria to speed up inversion. As in many inverse problems, the non-uniqueness issues also emerge here. A joint inversion method that considers also the dispersion curves of surface waves extracted from seismic ambient noise is presented and applied to experimental data. This joint scheme mitigates effectively the non-uniqueness.

  5. Inversion of H/V in layered media from seismic ambient noise based on the diffuse field theory and on improved calculation of Green functions

    Science.gov (United States)

    Sánchez-Sesma, Francisco J.; Piña, José; García-Jerez, Antonio; Luzón, Francisco; Perton, Mathieu

    2014-05-01

    The microtremor H/V spectral ratio (MHVSR) is widely used to assess the dominant frequency of soil sites. Measurements are relatively simple as only one station is needed. It has been recently proposed a theoretical basis linking ambient noise vibrations with diffuse field theory. In this theory the directional energy density computed as the average spectral density of motion at a point, is proportional to the imaginary part of Green function at the observation point. Appropriate normalization is crucial to make the experimental spectral ratios closer to the theoretical counterpart. According to this theory the square of H/V is twice the ratio ImG11 / ImG33, where ImG11 and ImG33 are the imaginary part of Green functions at the load point for horizontal and vertical components, respectively. In order to efficiently compute the imaginary part of Green's functions in a layered medium we start from an integral on the complex k plane and, using Harkrider's nomenclature, separate formulae for body-, Rayleigh-, and Love-wave components to the spectral densities are obtained. Then the poles allow for integration using the Cauchy residue theorem plus some contributions from branch integrals. It is possible to isolate pseudo reflections from ImG11 and thus constrain the inversion of soil profile. We assess ImG11 removing the influence of illumination spectrum using the H/V spectral ratio and an estimate of ImG33 (from an a priori model) by means of ImG11=0.5(H/V )2*ImG33. It has been found that ImG33 is less sensitive to details of stratigraphy. In fact, the Poisson ratio of the uppermost layer controls the slope in high frequency. With the obtained model ImG33 can be updated and the estimate of ImG11 will be improved. ACKNOWLEDGEMENTS. This research has been partially supported by DGAPA-UNAM under Project IN104712, by the MINECO research project CGL2010-16250, Spain, by the EU with FEDER, and the AXA Research Fund.

  6. Insight into the modified Ibalizumab-human CD4 receptor interactions: using a computational binding free energy approach

    Science.gov (United States)

    Wang, Yeng-Tseng; Chuang, Lea-Yea

    2015-01-01

    Antibody drugs are very useful tools for the treatment of many chronic diseases. Recently, however, patients and doctors have encountered the problem of drug resistance. How to improve the affinity of antibody drugs has therefore become a pressing issue. Ibalizumab is a humanized monoclonal antibody that binds human CD4, the primary receptor for human immunodeficiency virus type 1. This study investigates the mutation residues of the complementarity determining regions of Ibalizumab. We propose using the wild and mutations of Ibalizumab-human CD4 receptor complex structures, molecular dynamics techniques, alanine-scanning mutagenesis calculations and solvated interaction energies methods to predict the binding free energy of the Ibalizumab-human CD4 receptor complex structures. This work found that revealed three key positions (31th, 32th and 33th in HCDR-1) of the residues may play an important role in Ibalizumab-human CD4 receptor complex interactions. Therefore, bioengineering substitutions of the three key positions and increasing number of intermolecular interactions (HCDR-1 of Ibalizumab/human CD4 receptor) might improve the binding affinities of this complex structure.

  7. BEESEM: estimation of binding energy models using HT-SELEX data.

    Science.gov (United States)

    Ruan, Shuxiang; Swamidass, S Joshua; Stormo, Gary D

    2017-08-01

    Characterizing the binding specificities of transcription factors (TFs) is crucial to the study of gene expression regulation. Recently developed high-throughput experimental methods, including protein binding microarrays (PBM) and high-throughput SELEX (HT-SELEX), have enabled rapid measurements of the specificities for hundreds of TFs. However, few studies have developed efficient algorithms for estimating binding motifs based on HT-SELEX data. Also the simple method of constructing a position weight matrix (PWM) by comparing the frequency of the preferred sequence with single-nucleotide variants has the risk of generating motifs with higher information content than the true binding specificity. We developed an algorithm called BEESEM that builds on a comprehensive biophysical model of protein-DNA interactions, which is trained using the expectation maximization method. BEESEM is capable of selecting the optimal motif length and calculating the confidence intervals of estimated parameters. By comparing BEESEM with the published motifs estimated using the same HT-SELEX data, we demonstrate that BEESEM provides significant improvements. We also evaluate several motif discovery algorithms on independent PBM and ChIP-seq data. BEESEM provides significantly better fits to in vitro data, but its performance is similar to some other methods on in vivo data under the criterion of the area under the receiver operating characteristic curve (AUROC). This highlights the limitations of the purely rank-based AUROC criterion. Using quantitative binding data to assess models, however, demonstrates that BEESEM improves on prior models. Freely available on the web at http://stormo.wustl.edu/resources.html . stormo@wustl.edu. Supplementary data are available at Bioinformatics online.

  8. Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors.

    Science.gov (United States)

    Saladino, G; Gauthier, L; Bianciotto, M; Gervasio, F L

    2012-04-10

    The accurate yet efficient evaluation of the free energy profiles of ligand-target association is a long sought goal in rational drug design. Methods that calculate the free energy along realistic association pathways, such as metadynamics, have been shown to provide reliable profiles, while accounting properly for solvation and target flexibility. However, these approaches usually require prohibitive computational resources and expert human intervention. Here, we show how multiple walkers metadynamics, when performed with optimal path collective variables (PCV), provides in a predetermined amount of computer time an accurate set of free energy profiles for a series of p38 inhibitors. The chosen test set, spanning a wide range of activity, is a challenging benchmark, both for computational methods and for human intuition, as the correct order for the binding affinity cannot be easily guessed. An excellent ranking of the ligands was obtained with minimal human assistance, an important step toward a fully automated pharmaceutical work-flow.

  9. Internal field induced exciton binding energy and the optical transition in a strained Mg based II–VI quantum well

    Energy Technology Data Exchange (ETDEWEB)

    Elangovan, P. [Department of Physics, Maamallan Institute of Technology, Chennai 602105 (India); John Peter, A., E-mail: a.john.peter@gmail.com [Department of Physics, Government Arts College, Melur 625 106. Madurai (India); Kyoo Yoo, Chang [Center for Environmental Studies/Green Energy Center, Deptartment of Environmental Science and Engineering, College of Engineering, Kyung Hee University, Seocheon-dong 1, Giheung-gu, Yongin-Si, Gyeonggi-Do, 446-701 (Korea, Republic of)

    2013-11-15

    Binding energy of an exciton in a wurtzite ZnO/Zn{sub 1−x}Mg{sub x}O strained quantum well is investigated theoretically in which the strong built-in electric field due to the spontaneous and piezoelectric polarizations is included. Numerical calculations are performed using variational procedure within the single band effective mass approximation by varying the Mg composition in the barrier. The exciton oscillator strength and the exciton lifetime for radiative recombination as functions of well width and Mg content have been computed. The internal field induced interband emission energy of strained ZnO/Zn{sub 1−x}Mg{sub x}O well is investigated with the various structural parameters. The total optical absorption coefficients and the changes of refractive index as a function of normalized photon energy in the presence of built-in internal field are analyzed. The result shows that the strong built-in electric field has influence on the oscillator strength and the recombination life time of the exciton. The optical absorption coefficients and the refractive index changes strongly depend on Mg composition. The occurred blue shift of the resonant peak due to the incorporation of Mg ions will give the information about the variation of two energy levels in the quantum well. -- Highlights: • Binding energy of an exciton in a wurtzite ZnO/Zn{sub 1−x}Mg{sub x}O strained quantum well is investigated. • The built-in internal fields due to the spontaneous and piezoelectric polarizations are included. • The oscillator strength and the exciton lifetime for radiative recombination are computed. • The internal field induced transition energy of strained ZnO/Zn{sub 1−x}Mg{sub x}O well is investigated. • The results show that the nonlinear optical properties strongly depend on Mg composition.

  10. Exploring the free-energy landscape of carbohydrate-protein complexes: development and validation of scoring functions considering the binding-site topology

    Science.gov (United States)

    Eid, Sameh; Saleh, Noureldin; Zalewski, Adam; Vedani, Angelo

    2014-12-01

    Carbohydrates play a key role in a variety of physiological and pathological processes and, hence, represent a rich source for the development of novel therapeutic agents. Being able to predict binding mode and binding affinity is an essential, yet lacking, aspect of the structure-based design of carbohydrate-based ligands. We assembled a diverse data set comprising 273 carbohydrate-protein crystal structures with known binding affinity and evaluated the prediction accuracy of a large collection of well-established scoring and free-energy functions, as well as combinations thereof. Unfortunately, the tested functions were not capable of reproducing binding affinities in the studied complexes. To simplify the complex free-energy surface of carbohydrate-protein systems, we classified the studied proteins according to the topology and solvent exposure of the carbohydrate-binding site into five distinct categories. A free-energy model based on the proposed classification scheme reproduced binding affinities in the carbohydrate data set with an r 2 of 0.71 and root-mean-squared-error of 1.25 kcal/mol ( N = 236). The improvement in model performance underlines the significance of the differences in the local micro-environments of carbohydrate-binding sites and demonstrates the usefulness of calibrating free-energy functions individually according to binding-site topology and solvent exposure.

  11. Probing inter- and intrachain Zhang-Rice excitons in Li2CuO2 and determining their binding energy

    Science.gov (United States)

    Monney, Claude; Bisogni, Valentina; Zhou, Ke-Jin; Kraus, Roberto; Strocov, Vladimir N.; Behr, Günter; Drechsler, Stefan-Ludwig; Rosner, Helge; Johnston, Steve; Geck, Jochen; Schmitt, Thorsten

    2016-10-01

    Cuprate materials, such as those hosting high-temperature superconductivity, represent a famous class of materials where the correlations between the strongly entangled charges and spins produce complex phase diagrams. Several years ago, the Zhang-Rice singlet was proposed as a natural quasiparticle in hole-doped cuprates. The occurrence and binding energy of this quasiparticle, consisting of a pair of bound holes with antiparallel spins on the same CuO4 plaquette, depends on the local electronic interactions, which are fundamental quantities for understanding the physics of the cuprates. Here, we employ state-of-the-art resonant inelastic x-ray scattering (RIXS) to probe the correlated physics of the CuO4 plaquettes in the quasi-one-dimensional chain cuprate Li2CuO2 . By tuning the incoming photon energy to the O K edge, we populate bound states related to the Zhang-Rice quasiparticles in the RIXS process. Both intra- and interchain Zhang-Rice singlets are observed and their occurrence is shown to depend on the nearest-neighbor spin-spin correlations, which are readily probed in this experiment. We also extract the binding energy of the Zhang-Rice singlet and identify the Zhang-Rice triplet excitation in the RIXS spectra.

  12. 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.)

  13. Collaborative interactions to enhance gas binding energy in porous metal-organic frameworks.

    Science.gov (United States)

    Lin, Rui-Biao; Chen, Banglin

    2017-03-01

    Metal-organic frameworks (MOFs) are potentially useful materials for hydrogen and methane storage. However, the weak interactions between the MOF host and gas guest molecules have limited their storage capacities at elevated temperatures. In this issue, Alkordi et al. [IUCrJ (2017), 4, 131-135] illustrate an example of a porous MOF with a suitable pore size and unique pore surface for enhanced interaction with hydrogen molecules, providing the promise of further increasing the gas binding affinity through collaborative interactions.

  14. Mapping a part of Neuquen Basin in Argentina by global-phase H/V spectral ratio

    NARCIS (Netherlands)

    Nishitsuji, Y.; Ruigrok, E.; Gomez, M.; Draganov, D.S.

    2015-01-01

    We investigated the applicability of global phases (epicentral distances of ≥ 120° and ≥ 150°) for the H/V spectral ratio to identify the fundamental resonance frequency. We applied the method to delineate a part of Neuquén basin in Argentina without the need for active seismic sources. We obtained

  15. Alkali metal cation-hexacyclen complexes: effects of alkali metal cation size on the structure and binding energy.

    Science.gov (United States)

    Austin, C A; Rodgers, M T

    2014-07-24

    Threshold collision-induced dissociation (CID) of alkali metal cation-hexacyclen (ha18C6) complexes, M(+)(ha18C6), with xenon is studied using guided ion beam tandem mass spectrometry techniques. The alkali metal cations examined here include: Na(+), K(+), Rb(+), and Cs(+). In all cases, M(+) is the only product observed, corresponding to endothermic loss of the intact ha18C6 ligand. The cross-section thresholds are analyzed to extract zero and 298 K M(+)-ha18C6 bond dissociation energies (BDEs) after properly accounting for the effects of multiple M(+)(ha18C6)-Xe collisions, the kinetic and internal energy distributions of the M(+)(ha18C6) and Xe reactants, and the lifetimes for dissociation of the activated M(+)(ha18C6) complexes. Ab initio and density functional theory calculations are used to determine the structures of ha18C6 and the M(+)(ha18C6) complexes, provide molecular constants necessary for the thermodynamic analysis of the energy-resolved CID data, and theoretical estimates for the M(+)-ha18C6 BDEs. Calculations using a polarizable continuum model are also performed to examine solvent effects on the binding. In the absence of solvent, the M(+)-ha18C6 BDEs decrease as the size of the alkali metal cation increases, consistent with the noncovalent nature of the binding in these complexes. However, in the presence of solvent, the ha18C6 ligand exhibits selectivity for K(+) over the other alkali metal cations. The M(+)(ha18C6) structures and BDEs are compared to those previously reported for the analogous M(+)(18-crown-6) and M(+)(cyclen) complexes to examine the effects of the nature of the donor atom (N versus O) and the number donor atoms (six vs four) on the nature and strength of binding.

  16. Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis.

    Science.gov (United States)

    Wang, Qiantao; Edupuganti, Ramakrishna; Tavares, Clint D J; Dalby, Kevin N; Ren, Pengyu

    2015-01-01

    A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r (2) coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r (2) of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.

  17. 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....

  18. 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....

  19. A search for lowest energy structures of ZnS quantum dots: Genetic algorithm tight-binding study.

    Science.gov (United States)

    Pal, Sougata; Sharma, Rahul; Goswami, Biplab; Sarkar, Pranab; Bhattacharyya, S P

    2009-06-07

    The lowest energy structures of ZnS quantum dots of different sizes have been determined by an unbiased search using genetic algorithm (GA) coupled with the density-functional tight-binding method. The GA search converges to a rather new ringlike configurations of ZnS quantum dots. We have studied the structural, electronic, and optical properties of these ringlike clusters and compared these properties with those of other reported structures of ZnS quantum dots, namely, hollow, zinc-blende, wurtzite, and rocksalt structures.

  20. THE ΛΛ - ΞN Coupling and the Binding Energy of 6Λ Λ He

    Science.gov (United States)

    Afnan, I. R.

    2000-09-01

    To understand the difference between the value of the nn and ΛΛ two-body matrix elements, we examine the role of the coupling between the ΛΛ and ΞN channels, first within the framework of SU(3), and second in the numerical results for the binding energy of 6Λ Λ He. We find that it is essential to include the coupled channel nature of the BB interaction as we proceed from strangeness zero to the strangeness -1 and -2 channels if we are to understand the relative magnitude of the two-body matrix elements in the different strangeness channels.

  1. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

    Science.gov (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given.

  2. Binding energy and dephasing of biexcitons in In0.18Ga0.82As/GaAs single quantum wells

    DEFF Research Database (Denmark)

    Borri, Paola; Langbein, Wolfgang Werner; Hvam, Jørn Märcher

    1999-01-01

    Biexciton binding energies and biexciton dephasing in In0.18Ga0.82As/GaAs single quantum wells have been measured by time-integrated and spectrally resolved four-wave mixing. The biexciton binding energy increases from 1.5 to 2.6 meV for well widths increasing from 1 to 4 nm. The ratio between ex...

  3. Binding site characterization of G protein-coupled receptor by alanine-scanning mutagenesis using molecular dynamics and binding free energy approach: application to C-C chemokine receptor-2 (CCR2).

    Science.gov (United States)

    Chavan, Swapnil; Pawar, Shirishkumar; Singh, Rajesh; Sobhia, M Elizabeth

    2012-05-01

    The C-C chemokine receptor 2 (CCR2) was proved as a multidrug target in many diseases like diabetes, inflammation and AIDS, but rational drug design on this target is still lagging behind as the information on the exact binding site and the crystal structure is not yet available. Therefore, for a successful structure-based drug design, an accurate receptor model in ligand-bound state is necessary. In this study, binding-site residues of CCR2 was determined using in silico alanine scanning mutagenesis and the interactions between TAK-779 and the developed homology model of CCR2. Molecular dynamic simulation and Molecular Mechanics-Generalized Born Solvent Area method was applied to calculate binding free energy difference between the template and mutated protein. Upon mutating 29 amino acids of template protein and comparison of binding free energy with wild type, six residues were identified as putative hot spots of CCR2.

  4. Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

    Science.gov (United States)

    Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

    2014-11-20

    Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

  5. Fluorescence resonance energy transfer imaging reveals that chemokine-binding modulates heterodimers of CXCR4 and CCR5 receptors.

    Directory of Open Access Journals (Sweden)

    Nilgun Isik

    Full Text Available BACKGROUND: Dimerization has emerged as an important feature of chemokine G-protein-coupled receptors. CXCR4 and CCR5 regulate leukocyte chemotaxis and also serve as a co-receptor for HIV entry. Both receptors are recruited to the immunological synapse during T-cell activation. However, it is not clear whether they form heterodimers and whether ligand binding modulates the dimer formation. METHODOLOGY/PRINCIPAL FINDINGS: Using a sensitive Fluorescence Resonance Energy Transfer (FRET imaging method, we investigated the formation of CCR5 and CXCR4 heterodimers on the plasma membrane of live cells. We found that CCR5 and CXCR4 exist as constitutive heterodimers and ligands of CCR5 and CXCR4 promote different conformational changes within these preexisting heterodimers. Ligands of CCR5, in contrast to a ligand of CXCR4, induced a clear increase in FRET efficiency, indicating that selective ligands promote and stabilize a distinct conformation of the heterodimers. We also found that mutations at C-terminus of CCR5 reduced its ability to form heterodimers with CXCR4. In addition, ligands induce different conformational transitions of heterodimers of CXCR4 and CCR5 or CCR5(STA and CCR5(Delta4. CONCLUSIONS/SIGNIFICANCE: Taken together, our data suggest a model in which CXCR4 and CCR5 spontaneously form heterodimers and ligand-binding to CXCR4 or CCR5 causes different conformational changes affecting heterodimerization, indicating the complexity of regulation of dimerization/function of these chemokine receptors by ligand binding.

  6. The {Lambda}{Lambda} - {Xi}N coupling and the binding energy of {sub {Lambda}{Lambda}}{sup 6}He

    Energy Technology Data Exchange (ETDEWEB)

    Carr, S.B.; Afnan, I.R.; Gibson, B.F.

    1995-04-01

    {Lambda}{Lambda} hypernuclei can be used to gain insight into the {Lambda}{Lambda} interaction and the limitation of the SU(3) relation between the N N, the YN and {Lambda}{Lambda} potentials. The presence of the coupling between the {Lambda}{Lambda} and {Xi}N channels can have considerable influence on the strength of the {Lambda}{Lambda} potential. To examine the role of this coupling, the authors have constructed the S = {minus}2 baryon-baryon interaction by SU(3) rotation of the OBE potential of Nijmegen Model D. The short range behavior of the potential was adjusted to give a bound, almost bound, or unbound {Lambda}{Lambda} system. The phase shift for these potentials were used as data to construct separable potentials with and without the {Lambda}{Lambda} - {Xi}N coupling. The binding energy of {sup 6}{sub {Lambda}{Lambda}}He was calculated as an {Lambda}{Lambda}{alpha} system with these different {Lambda}{Lambda} potentials. They find that the coupling between the {Lambda}{Lambda} and {Xi}N channels plays an important role in the binding energy of {sup 6}{sub {Lambda}{Lambda}}He.

  7. Binding energy and work function of organic electrode materials phenanthraquinone, pyromellitic dianhydride and their derivatives adsorbed on graphene.

    Science.gov (United States)

    Yu, Yang-Xin

    2014-09-24

    Electroactive organic compounds are a novel group of green cathode materials for rechargeable metal-ion batteries. However, the organic battery life is short because the organic compounds can be dissolved by nonaqueous electrolytes. Here a comparative investigation of phenanthraquinone (PQ), pyromellitic dianhydride (PMDA) and their derivatives, i.e., benzo[1,2-b:4,3-b']difuran-4,5-dione (BDFD), benzo[1,2-b:4,3-b']dithiophene-4,5-quinone (BDTQ), 3,8-phenanthroline-5,6-dione (PAD), pyromellitic dithioanhydride (PMDT), pyromellitic diimide (PMDI) and 1,4,5,8-anthracenetetrone (ATO), adsorbed on graphene is performed using a density functional theory (DFT) with a van der Waals (vdW) dispersion-correction. The computed results show a strong physisorption with the binding energies between 1.10 and 1.56 eV. A sequence of the calculated binding energies from weak to strong is found to be BDFD work functions for the nanocomposites are found to be strongly affected by the work function of each organic compound. To understand the DFT results, a novel simple expression is proposed to predict the work function of the nanocomposites from the interfacial dipole and the work functions of the isolated graphene nanosheet and organic molecules. The predicted work functions for the nanocomposites from the new equation agree quite well with the values calculated from the vdW dispersion-corrected DFT.

  8. Magnetic field-dependent of binding energy in GaN/InGaN/GaN spherical QDQW nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    El Ghazi, Haddou, E-mail: hadghazi@gmail.com [Solid State Laboratory, Faculty of science, Dhar EL Mehrez, BP 1796 Fes-Atlas (Morocco); Special mathematics, CPGE Kénitra, Chakib Arsalane Street (Morocco); Jorio, Anouar; Zorkani, Izeddine [Solid State Laboratory, Faculty of science, Dhar EL Mehrez, BP 1796 Fes-Atlas (Morocco)

    2013-10-15

    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.

  9. 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.

  10. Binding of oxygen with titanium dioxide on singlet potential energy surface: An ab initio investigation

    Science.gov (United States)

    Bogdanchikov, Georgii A.; Baklanov, Alexey V.

    2017-01-01

    Ab initio calculations have been carried out to investigate interaction of titanium dioxide TiO2 with oxygen O2 in ground triplet and excited singlet states. On a singlet potential energy surface (PES) formation of a stable compound of titanium peroxide TiO4 is revealed which should appear in reaction of TiO2 with singlet oxygen without activation barrier. This peroxide is lower in energy than the ground state of two individual molecules TiO2 + 3O2 by 34.6 kcal/mol. Location of conical intersection between triplet and singlet PESs of TiO2sbnd O2 is also investigated.

  11. What can be learned from binding energy differences about nuclear structure: the example of delta V_{pn}

    CERN Document Server

    Bender, Michael

    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 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 are that (i) the structures seen in the systematics of delta V_{pn} 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 delta V_{pn} around a doubly-magic nucleus is a trivial consequence of the asymmetric definition o...

  12. S-Wave Velocity Structure of Taipei Basin by Using the Simulation of Microtremor H/V Ratios

    Science.gov (United States)

    Cheng-Yi, Lin; Kuo-Liang, Wen; Che-Min, Lin

    2014-05-01

    In this report here the investigation of the S-wave velocity structures of the Taipei basin which is located in the northern Taiwan. Previous study, the dense microtremor measurement analysis have been confirmed in Taipei Basin. However, within the basin around the layer effects on seismic site characterization and contribution have still needed to clarify more details, as the strata in Taipei basin with reference to estimate ground motion prediction. The detail site response all over the Taipei basin has been studied by using the H/V ratios of dense microtremor surveys. In this study, a method, GA-Haskell, combining Genetic Algorithm and Thomson-Haskell propagator matrix was used to simulate the microtremor H/V ratios according to the previous results of dense microtremor surveys. The near-surface S-wave velocity structures of over 400 sites in the Taipei basin were evaluated by the simulations of the H/V ratios. Through the numerous microtremor data are helpful to figure the S-wave velocity and thickness of the Sungshan Formation and the other deeper formations which control the seismic site-effect in the basin. While many strong motion stations have also been performed microtremor measurement and single station spectrum to understand the earthquake site characteristics analysis. Compared with other research results, confirmed the applicability of the method for estimating the velocity structure in Taipei Basin. Finally, accord with the actual site earthquake and microtremor response, established a complete and detailed S-wave velocity model of the Taipei basin. It will benefit the strong motion prediction and simulation in the future. Key Words: Taipei Basin, Microtremor, H/V Ratio, S-wave Velocity, Site Effect

  13. Applications of a tight-binding total energy method for transition and noble metals Elastic Constants, Vacancies, and Surfaces of Monatomic Metals

    CERN Document Server

    Mehl, M J; Mehl, Michael J.; Papaconstantopoulos, Dimitrios A.

    1996-01-01

    A recent tight-binding scheme provides a method for extending the results of first principles calculations to regimes involving $10^2 - 10^3$ atoms in a unit cell. The method uses an analytic set of two-center, non-orthogonal tight-binding parameters, on-site terms which change with the local environment, and no pair potential. The free parameters in this method are chosen to simultaneously fit band structures and total energies from a set of first-principles calculations for monatomic fcc and bcc crystals. To check the accuracy of this method we evaluate structural energy differences, elastic constants, vacancy formation energies, and surface energies, comparing to first-principles calculations and experiment. In most cases there is good agreement between this theory and experiment. We present a detailed account of the method, a complete set of tight-binding parameters, and results for twenty-nine of the alkaline earth, transition and noble metals.

  14. 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.

  15. 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.

  16. Binding Energy of D- and D0 Centers Confined by Spherical Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    BAO Yuan-Peng; XIE Wen-Fang

    2008-01-01

    We study a negative donor center, a neutral donor in a spherical Gaussian potential quantum dot by using the matrix diagonalization of Hamiltonian within the effective-mass approximation. We calculate the energy E(D-) as functions of Gaussian potential size and depth, the same calculations as performed with the parabolic approximation. The dependence of the ground state of the neutral shallow donor and the negatively charged donor on the dot size and the potential depth is investigated.

  17. Study of quark mass dependence of binding energy for light nuclei in 2+1 flavor lattice QCD

    CERN Document Server

    Yamazaki, Takeshi; Kuramashi, Yoshinobu; Ukawa, Akira

    2015-01-01

    We investigate the formation of light nuclei with the nuclear mass number less than or equal to four in 2+1 flavor QCD using a non-perturbative improved Wilson quark and Iwasaki gauge actions. The quark mass is decreased from our previous work to the one corresponding to the pion mass of 0.30 GeV. In each multi-nucleon channel, the energy shift of the ground state relative to the assembly of free nucleons is calculated on two volumes, whose spatial extents are 4.3 fm and 5.8 fm. From the volume dependence of the energy shift, we distinguish a bound state of multi nucleons from an attractive scattering state. We find that all the ground states measured in this calculation are bound states. As in the previous studies at larger $m_\\pi$, our result indicates that at $m_\\pi = 0.30$ GeV the effective interaction between nucleons in the light nuclei is relatively stronger than the one in nature, since the results for the binding energies are larger than the experimental values and a bound state appears in the dineut...

  18. 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 ...

  19. Pulsed-field ionization electron spectroscopy and binding energies of alkali metal-dimethyl ether and -dimethoxyethane complexes.

    Science.gov (United States)

    Sohnlein, Bradford R; Li, Shenggang; Fuller, Jason F; Yang, Dong-Sheng

    2005-07-01

    Lithium and sodium complexes of dimethyl ether (DME) and dimethoxyethane (DXE) were produced by reactions of laser-vaporized metal atoms with organic vapors in a pulsed nozzle cluster source. The mono-ligand complexes were studied by photoionization and pulsed field ionization zero electron kinetic energy (ZEKE) spectroscopy. Vibrationally resolved ZEKE spectra were obtained for Li(DME), Na(DME) and Li(DXE) and a photoionization efficiency spectrum for Na(DXE). The ZEKE spectra were analyzed by comparing with the spectra of other metal-ether complexes and with electronic structure calculations and spectral simulations. Major vibrations measured for the M(DME) (M=Li,Na) ions were M-O and C-O stretches and M-O-C and C-O-C bends. These vibrations and additional O-Li-O and O-C-C-O bends were observed for the Li(DXE) ion. The M(DME) complexes were in C2v symmetry with the metal atom binding to oxygen, whereas Li(DXE) was in a C2 ring configuration with the Li atom attaching to both oxygen atoms. Moreover, the ionization energies of these complexes were measured from the ZEKE or photoionization spectra and bond dissociation energies were derived from a thermodynamic cycle.

  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. Amine basicity (pKb) controls the analyte binding energy on single walled carbon nanotube electronic sensor arrays.

    Science.gov (United States)

    Lee, Chang Young; Strano, Michael S

    2008-02-06

    A wide range of analytes adsorb irreversibly to the surfaces of single walled carbon nanotube electronic networks typically used as sensors or thin-film transistors, although to date, the mechanism is not understood. Using thionyl chloride as a model electron-withdrawing adsorbate, we show that reversible adsorption sites can be created on the nanotube array via noncovalent functionalization with amine-terminated molecules of pKa nanotube network comprising single, largely unbundled nanotubes, near the electronic percolation threshold is required for the effective conversion to a reversibly binding array. By examining 11 types of amine-containing molecules, we show that analyte adsorption is largely affected by the basicity (pKb) of surface groups. The binding energy of the analyte is apparently reduced by its adsorption on the surface chemical groups instead of directly on the SWNT array itself. This mediated adsorption mechanism is supported by X-ray photoelectron spectroscopy (XPS) and molecular potential calculations. Reversible detection with no active regeneration at the parts-per-trillion level is demonstrated for the first time by creating a higher adsorption site density with a polymer amine, such as polyethyleneimine (PEI). Last, we demonstrate that this transition to reversibility upon surface functionalization is a general phenomenon.

  2. Binding energies of shallow impurities in asymmetric strained wurtzite AlxGa1-xN/ GaN/Aly Ga1-yN quantum wells*

    Institute of Scientific and Technical Information of China (English)

    Ha Sihua; Ban Shiliang; Zhu Jun

    2011-01-01

    The ground state binding energies of hydrogenic impurities in strained wurtzite AlxGa1-xN/GaN/AlyGa1-yN quantum wells are calculated numerically by a variational method. The dependence of the binding energy on well width, impurity location and Al concentrations of the left and right barriers is discussed, including the effect of the built-in electric field induced by spontaneous and piezoelectric polarizations. The results show that the change in binding energy with well width is more sensitive to the impurity position and barrier heights than the barrier widths, especially in asymmetric well structures where the barrier widths and/or barrier heights differ. The binding energy as a function of the impurity position in symmetric and asymmetric structures behaves like a map of the spatial distribution of the ground state wave function of the electron. It is also found that the influence on the binding energy from the Al concentration of the left barrier is more obvious than that of the right barrier.

  3. 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.

  4. Adsorption and desorption of propane on Pd (111): A van der Waals density functional study. Energy binding sites and geometries

    Science.gov (United States)

    e Silva, Tadeu Leonardo Soares; Schmal, Martin

    2017-10-01

    Palladium supported catalysts used for the partial oxidation of propane reaction aiming the H2 production deserves specific characterizations and theoretical modeling for the explanation of the transition phase and energy needed for the adsorption and desorption of propane on top of the palladium atoms. On the other hand, the product distribution will depend on the adsorption and desorption capacity of the different compounds present during the reaction. In this work, the adsorption of propane on a Pd (111) surface was studied by using different approximations. A periodic method based on the Density Functional Theory (DFT) formalism employing vdW-DF functional was investigated for determining preferred binding sites of propane on palladium. The results show that the adsorption on hcp site is more stable than on top site and predictions fit well the experimental results.

  5. Effective nucleon mass, incompressibility, and third derivative of nuclear binding energy in the nonlinear relativistic mean field theory

    Energy Technology Data Exchange (ETDEWEB)

    Kouno, H.; Kakuta, N.; Noda, N.; Koide, K.; Mitsumori, T.; Hasegawa, A.; Nakano, M. (Department of Physics, Saga University, Saga 840 (Japan))

    1995-04-01

    We have studied the equations of state of nuclear matter using the nonlinear [sigma]-[omega] model. At the normal density, there is a strong correlation among the effective nucleon mass [ital M][sub 0][sup *], the incompressibility, [ital K] and the third derivative [ital K][prime] of binding energy. The results are compared with the empirical analysis of the giant isoscalar monopole resonances data. It is difficult to fit the data when [ital K][approx lt]200 MeV, using the model. It is also found that [ital K]=300[plus minus]50 MeV is favorable to account for the volume-symmetry properties of nuclear matter.

  6. Metastable innershell molecular state (MIMS) III: The universal binding energy and bond length of the homonucleus K-shell MIMS

    Science.gov (United States)

    Bae, Young K.

    2016-03-01

    This paper reports the discovery of a universal Z2-dependency of the binding energy of the homonucleus K-shell MIMS (K-MIMS: Metastable Innershell Molecular State bound by K-shell electrons), which has been established by analyzing extensive existing experimental data over several decades. An intuitive analytical theory on the K-MIMS has been developed for the homologous molecules to the He*2 excimer, which elucidates the universal Z-dependent behavior of the K-MIMS. The theory predicts a 1 / Z-dependency of the K-MIMS bond length, which is in agreement with the quasimolecule sizes estimated from the x-ray generation cross-sections in H-like Bi82+ and U91+ impact on Au solids.

  7. MMPBSA decomposition of the binding energy throughout a molecular dynamics simulation of amyloid-beta (Abeta(10-35)) aggregation.

    Science.gov (United States)

    Campanera, Josep M; Pouplana, Ramon

    2010-04-15

    Recent experiments with amyloid-beta (Abeta) peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta 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 Abeta(10-35) 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.

  8. 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.

  9. 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.

  10. Virtual screening of mandelate racemase mutants with enhanced activity based on binding energy in the transition state.

    Science.gov (United States)

    Gu, Jiali; Liu, Min; Guo, Fei; Xie, Wenping; Lu, Wenqiang; Ye, Lidan; Chen, Zhirong; Yuan, Shenfeng; Yu, Hongwei

    2014-02-05

    Mandelate racemase (MR) is a promising candidate for the dynamic kinetic resolution of racemates. However, the poor activity of MR towards most of its non-natural substrates limits its widespread application. In this work, a virtual screening method based on the binding energy in the transition state was established to assist in the screening of MR mutants with enhanced catalytic efficiency. Using R-3-chloromandelic acid as a model substrate, a total of 53 mutants were constructed based on rational design in the two rounds of screening. The number of mutants for experimental validation was brought down to 17 by the virtual screening method, among which 14 variants turned out to possess improved catalytic efficiency. The variant V26I/Y54V showed 5.2-fold higher catalytic efficiency (k(cat)/K(m)) towards R-3-chloromandelic acid than that observed for the wild-type enzyme. Using this strategy, mutants were successfully obtained for two other substrates, R-mandelamide and R-2-naphthylglycolate (V26I and V29L, respectively), both with a 2-fold improvement in catalytic efficiency. These results demonstrated that this method could effectively predict the trend of mutational effects on catalysis. Analysis from the energetic and structural assays indicated that the enhanced interactions between the active sites and the substrate in the transition state led to improved catalytic efficiency. It was concluded that this virtual screening method based on the binding energy in the transition state was beneficial in enzyme rational redesign and helped to better understand the catalytic properties of the enzyme.

  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. Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level.

    Science.gov (United States)

    Jayaram, B; McConnell, K; Dixit, S B; Das, A; Beveridge, D L

    2002-01-15

    Noncovalent association of proteins to specific target sites on DNA--a process central to gene expression and regulation--has thus far proven to be idiosyncratic and elusive to generalizations on the nature of the driving forces. The spate of structural information on protein--DNA complexes sets the stage for theoretical investigations on the molecular thermodynamics of binding aimed at identifying forces responsible for specific macromolecular recognition. Computation of absolute binding free energies for systems of this complexity transiting from structural information is a stupendous task. Adopting some recent progresses in treating atomic level interactions in proteins and nucleic acids including solvent and salt effects, we have put together an energy component methodology cast in a phenomenological mode and amenable to systematic improvements and developed a computational first atlas of the free energy contributors to binding in approximately 40 protein-DNA complexes representing a variety of structural motifs and functions. Illustrating vividly the compensatory nature of the free energy components contributing to the energetics of recognition for attaining optimal binding, our results highlight unambiguously the roles played by packing, electrostatics including hydrogen bonds, ion and water release (cavitation) in protein-DNA binding. Cavitation and van der Waals contributions without exception favor complexation. The electrostatics is marginally unfavorable in a consensus view. Basic residues on the protein contribute favorably to binding despite the desolvation expense. The electrostatics arising from the acidic and neutral residues proves unfavorable to binding. An enveloping mode of binding to short stretches of DNA makes for a strong unfavorable net electrostatics but a highly favorable van der Waals and cavitation contribution. Thus, noncovalent protein-DNA association is a system-specific fine balancing act of these diverse competing forces. With the

  13. 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.

  14. 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.

  15. Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations

    Science.gov (United States)

    Selwa, Edithe; Elisée, Eddy; Zavala, Agustin; Iorga, Bogdan I.

    2017-09-01

    Our participation to the D3R Grand Challenge 2 involved a protocol in two steps, with an initial analysis of the available structural data from the PDB allowing the selection of the most appropriate combination of docking software and scoring function. Subsequent docking calculations showed that the pose prediction can be carried out with a certain precision, but this is dependent on the specific nature of the ligands. The correct ranking of docking poses is still a problem and cannot be successful in the absence of good pose predictions. Our free energy calculations on two different subsets provided contrasted results, which might have the origin in non-optimal force field parameters associated with the sulfonamide chemical moiety.

  16. Core-level binding-energy shifts due to end effects in polymers: A Hartree-Fock Green's-function study

    Science.gov (United States)

    Seel, M.; Ladik, J.

    1985-10-01

    Hartree-Fock Green's-function studies of end effects on the core-level structure of metallic and insulating quasi-one-dimensional model polymers reveal additional core peaks outside the bulk bands. In the metallic case, shifts to both lower (~-150 meV) and higher (~+50 meV) binding energies are observed, whereas in the insulating case, split-off peaks occur only at the lower-binding-energy side (~-150 meV). It is shown that a positive or negative net valence population alone does not determine the direction of the shift. The binding-energy changes are determined by a detailed balance between the energy loss due to a decrease in the electron-nuclear attraction and the energy gain due to a decrease in the electron-electron repulsion experienced by the core electrons of the end atoms. This can probably also explain why for some metal surfaces, shifts towards lower, and for others, shifts towards higher, binding energies are found. In the valence region of the investigated lithium chains, the ends do not produce localized end states.

  17. Effect of magnetic field and soft potential barrier on off-axis donor binding energy in a nanotube with two quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, Jesus D. [Grupo en Teoria de la Materia Condensada, Universidad del Magdalena, Santa Marta (Colombia); Grupo de Fisica Mesoscopica, Departamento de Fisica, Universidad Nacional de Colombia, Bogota (Colombia); Rondano, F.J. [Grupo en Teoria de la Materia Condensada, Universidad del Magdalena, Santa Marta (Colombia); Barba-Ortega, J., E-mail: jjbarbao@unal.edu.co [Grupo de Fisica Mesoscopica, Departamento de Fisica, Universidad Nacional de Colombia, Bogota (Colombia)

    2012-12-15

    We analyze the effect of the magnetic field parallel to the axis and different potential shape on the ground-state binding energy of the off-axis donors in cylindrical nanotubes containing two GaAs/GaAlAs quantum wells (QWs) in a section of the tube layer. We express the wave function as a product of combinations of s and p subband wave functions and an envelope function that depends only on the electron-ion separation. By using the variational principle we derive a differential equation for the envelope function, which we solve numerically. Two peaks in the curves for the dependence of the ground-state binding energies on the donor distance from the axis are presented and it is shown that the increasing the magnetic field increasing the binding energy while the impurity is located in the QW1, whereas the opposite occurs when the impurity is located in the QW2.

  18. 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...

  19. Photoexcited triplet state provides a quantitative measure of intercalating drug-DNA binding energies

    Science.gov (United States)

    Maki, August H.; Alfredson, T. V.; Waring, M. J.

    1992-04-01

    A linear correlation between spectroscopic and thermodynamic properties of systems is rarely encountered. In triplet state ODMR studies of various DNA complexes of echinomycin, a quinoxaline-containing cyclic depsipeptide bis-intercalating antibiotic, and its biosynthesized quinoline analogs, such correlations are observed. The zero field splitting D-parameter of the intercalated quinoxaline or quinoline residue varies linearly with the free energy of drug-DNA complexing. From previous work, the DNA sequence specificity of echinomycin analogs is known to be influenced by the identity of the intercalating residue (e.g., quinoxaline vs. quinoline). The present results strongly suggest that the DNA sequence-specificity of these drugs is controlled largely by the intercalated residue, and that the energetics of the peptide- DNA interaction, although considerable, are relatively sequence independent. These conclusions run counter to the generally accepted idea that DNA recognition by sequence- seeking proteins is controlled by specific hydrogen bonding interactions. The high degree of N-methylation of the echinomycin peptide portion severely restricts these interactions, however. A simple theoretical model is presented to support the experimentally observed linear correlation between (Delta) D and (Delta) G.

  20. Continuous H/V spectral ratio analysis of ambient noise: a necessity to understand microzonation results obtained by mobile stations

    Science.gov (United States)

    Van Noten, Koen; Lecocq, Thomas

    2016-04-01

    Estimating the resonance frequency (f0) and amplification factor of unconsolidated sediments by H/V spectral ratio (HVSR) analysis of seismic ambient noise has been widely used since Nakamura's proposal in 1989. To measure f0 properly, Nakamura suggested to perform microzonation surveys at night when the artificial microtremor is small and does not fully disrupt the ambient seismic noise. As nightly fieldwork is not always a reasonable demand, we propose an alternative workflow of Nakamura's technique to improve the quality of HVSR results obtained by ambient noise measurements of mobile stations during the day. This new workflow includes the automated H/V calculation of continuous seismic data of a stationary or permanent station installed near the microzonation site for as long as the survey lasts in order to control the error in the HVSR analysis obtained by the mobile stations. In this presentation, we apply this workflow on one year of seismic data at two different case studies; i.e. a rural site with a shallow bedrock depth of 30 m and an urban site (Brussels, capital of Belgium, bedrock depth of 110 m) where human activity is continuous 24h/day. By means of an automated python script, the fundamental peak frequency and the H/V amplitude are automatically picked from H/V spectra that are calculated from 50% overlapping, 30 minute windows during the whole year. Afterwards, the f0 and amplitude picks are averaged per hour/per day for the whole year. In both case studies, the H/V amplitude and the fundamental frequencies range considerable, up to ˜15% difference between the daily and nightly measurements. As bedrock depth is known from boreholes at both sites, we concluded that the nightly picked f0 is the true one. Our results thus suggest that changes in the determined f0 and H/V amplitude are dominantly caused by the human behaviour which is stored in the ambient seismic noise (e.g. later onset of traffic in a weekend, quiet Sundays, differences between

  1. Energy-dependent reduced drug binding as a mechanism of Vinca alkaloid resistance in human leukemic lymphoblasts.

    Science.gov (United States)

    Beck, W T; Cirtain, M C; Lefko, J L

    1983-11-01

    ) was required only for subsequent release of what appeared to be a more tightly bound cell-associated fraction of VLB. Results of zero-time binding studies tended to confirm that VLB binding by resistant cells has two components, one requiring and the other not requiring metabolic energy. Differences in the proportions of these two components between the sensitive and resistant cells suggest a mechanism for resistance to VLB and similar compounds.

  2. Study on binding and fluorescence energy transfer efficiency of Rhodamine B with Pluronic F127-gold nanohybrid using optical spectroscopy methods

    Science.gov (United States)

    Antonisamy, Jenif Dsouza; Swain, Jitendriya; Dash, Sasmita

    2017-02-01

    This work focuses on the binding efficiency and fluorescence resonance energy transfer (FRET) of fluorescent dye Rhodamine B (Rh B) to Pluronic F127-gold nanohybrid. The formation of gold nanoparticles inside Rh B doped Pluronic F127 copolymer have been characterized using dynamic light scattering study, HR-TEM images, UV-visible spectra and fluorescence studies. Fluorescence quenching and the constant fluorescence lifetime of the Rhodamine B present in the cavity of Pluronic F127-gold nanohybrid suggested a strong binding ability (3.5 × 103 L mol- 1), static nature of quenching and better energy transfer efficiency of fluorescent dye towards Pluronic F127-gold (Au) nanohybrids.

  3. Binding energy and preferred adsorption sites of CO on gold and silver-gold cluster cations: adsorption kinetics and quantum chemical calculations.

    Science.gov (United States)

    Neumaier, Marco; Weigend, Florian; Hampe, Oliver; Kappes, Manfred M

    2008-01-01

    We revisit the reactivity of trapped pure gold (Au(n)+, n cluster cations (Ag(m)Au(n)+, m + n metal as a function of cluster size and composition. Starting from results for pure gold cluster cations for which an overall decrease of CO binding energy with increasing cluster size was experimentally observed--from about 1.09 +/- 0.1 eV (for n = 6) to below 0.65 +/- 0.1 eV (for n > 26) we demonstrate that metal--CO bond energies correlate with the total electron density and with the energy of the lowest unoccupied molecular orbital (LUMO) on the bare metal cluster cation as obtained by density functional theory (DFT) computations. This is a consequence of the predominantly sigma-donating character of the CO-M bond. Further support for this concept is found by contrasting the predictions of binding energies to the experimental results for small alloy cluster cations (Ag(m)Au(n)+, 4 < m + n < 7) as a function of composition. Here, binding energy drops with increasing silver content, while CO still binds always in a head-on fashion to a gold atom. Finally we show how the CO stretch frequency of Ag(m)Au(n)CO+ may be used to identify possible adsorption sites and pre-screen favorable isomers.

  4. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

    Science.gov (United States)

    Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

    2016-09-01

    We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

  5. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

    Science.gov (United States)

    Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

    2016-09-01

    We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

  6. Seasonal changes in H/V spectral ratio at high-latitude seismic stations

    Science.gov (United States)

    Lee, R. F.; Abbott, R. E.; Knox, H. A.; Pancha, A.

    2014-12-01

    We present results demonstrating seasonal variations in the Horizontal-to-Vertical Spectral Ratio (HVSR) at high-latitude seismic stations. We analyze data from two sites at Poker Flat Research Range, near Fairbanks, Alaska. From the first site, we analyze 3 stations installed by Sandia National Labs (SNL) in a valley with marshy summer conditions. We also analyze the PASSCAL Instrument Center station PIC2, which is installed on rock approximately 3.2 km from the SNL stations. These stations continuously record data at 125 (SNL) and 200 (PIC2) samples per second. Seasonal changes in HVSR at high frequencies (> 20 Hz) appear to be caused by impedance contrasts between frozen and thawed ground. Thawed active layers are known to have slower shear-wave velocities than frozen layers or bedrock. An estimate of active layer thickness at each station is obtained from the quarter-wavelength approximation. We verify the accuracy of this technique by obtaining ground-truth measurements at the sites for both thickness and shear-wave velocity. We use physical probing for the thickness measurements and active-source Refraction-Microtremor (ReMi) surveys for the shear-wave velocities. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000

  7. Application Of The Wavelet Packet Transform For Selecting Transient Seismic Noise And Study Of Its Effect On Estimates Of The H/V Spectral Ratio

    Science.gov (United States)

    Galiana-Merino, J.; Parolai, S.

    2005-12-01

    The Horizontal-to-Vertical (H/V) spectral ratio of seismic noise has become a widely used tool in microzonation, although it has not yet been clearly established whether or not only the stationary part of the recorded signal may be used. In fact, while some studies have suggested the use of only stationary signals others have shown that including transients may improve the results. In this study, we have employed a filtering method based on the wavelet packet transform for removing the stationary part of the noise recordings in the frequency band of interest for the H/V spectral ratio. In this way, we have obtained filtered seismograms with only transients, which have been used for performing the H/V spectral ratio calculation. Moreover, we have also calculated the H/V spectral ratio selecting only stationary noise windows from the seismograms and without making any a priori selection on them. Finally, we have compared the results and analysed the influence of transient noise on the shape of the H/V spectral ratio. The analysis has been carried out on noise recordings collected at 7 stations installed in the Cologne-Bonn region (Germany). Results show that the H/V spectral ratios calculated using only stationary noise do not significantly differ from those obtained without performing any data selection, independent of the site resonance frequency and of the frequency content of the transient. On the contrary, H/V spectral ratios obtained using only transients show a large variability that may be attributed to the kind of source and the source to receiver distance. These results indicate that the effect of transient noise is negligible when the H/V spectral ratios are calculated without performing any data selection, making the H/V spectral ratio technique more attractive for urban area measurements.

  8. The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method

    Science.gov (United States)

    Yin, Jian; Henriksen, Niel M.; Slochower, David R.; Gilson, Michael K.

    2017-01-01

    The absolute binding free energies and binding enthalpies of twelve host-guest systems in the SAMPL5 blind challenge were computed using our attach-pull-release (APR) approach. This method has previously shown good correlations between experimental and calculated binding data in retrospective studies of cucurbit[7]uril (CB7) and β-cyclodextrin (βCD) systems. In the present work, the computed binding free energies for host octa acid (OA or OAH) and tetra-endo-methyl octa-acid (TEMOA or OAMe) with guests are in good agreement with prospective experimental data, with a coefficient of determination (R2) of 0.8 and root-mean-squared error of 1.7 kcal/mol using the TIP3P water model. The binding enthalpy calculations achieve moderate correlations, with R2 of 0.5 and RMSE of 2.5 kcal/mol, for TIP3P water. Calculations using the newly developed OPC water model also show good performance. Furthermore, the present calculations semi-quantitatively capture the experimental trend of enthalpy-entropy compensation observed, and successfully predict guests with the strongest and weakest binding affinity. The most populated binding poses of all twelve systems, based on clustering analysis of 750 ns molecular dynamics (MD) trajectories, were extracted and analyzed. Computational methods using MD simulations and explicit solvent models in a rigorous statistical thermodynamic framework, like APR, can generate reasonable predictions of binding thermodynamics. Especially with continuing improvement in simulation force fields, such methods hold the promise of making substantial contributions to hit identification and lead optimization in the drug discovery process.

  9. Tuning the Exciton Binding Energies in Single Self-Assembled InGaAs/GaAs Quantum Dots by Piezoelectric-Induced Biaxial Stress

    NARCIS (Netherlands)

    Ding, F.; Singh, R.; Plumhof, J.D.; Zander, T.; Křápek, V.; Chen, Y.H.; Benyoucef, M.; Zwiller, V.; Dörr, K.; Bester, G.; Rastelli, A.; Schmidt, O.G.

    2010-01-01

    We study the effect of an external biaxial stress on the light emission of single InGaAs/GaAs(001) quantum dots placed onto piezoelectric actuators. With increasing compression, the emission blueshifts and the binding energies of the positive trion (X+) and biexciton (XX) relative to the neutral exc

  10. 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.

  11. 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.

  12. Spectral ratios of ambient noise based on the diffuse field theory: Improved inversion of H/V in layered media using analytical properties of Green functions

    Science.gov (United States)

    Sanchez-Sesma, F. J.; Perton, M.; Piña, J.; Luzón, F.; Garcia-Jerez, A.; Rodriguez-Castellanos, A.

    2013-12-01

    It is well know the popularity of H/V spectral ratio to extract the dominant frequency of soil sites for microzonation studies (Nakamura, 1989). It is relatively easy to make measurements as only one station is needed. Despite its success, this approach had not solid theoretical basis until a proposal to link ambient noise vibrations with diffuse field theory was made (Sánchez-Sesma et al, 2011a). Based on this theory the average spectral density of a given motion of a point, also called directional energy density (Perton et al, 2009), is proportional to the imaginary part of Green function precisely at the observation point. The proportionality implies that vector components are all multiplied by the current spectral level of the diffuse illumination. Appropriate normalization is crucial to make the experimental spectral ratios closer to the theoretical counterpart. According to this theory the square of H/V is twice the ratio of ImG11 and ImG33, where ImG11 and ImG33 are the imaginary part of Green functions at the load point for horizontal and vertical components, respectively. From ImG11 it could be possible through Fourier analysis to extract pseudo reflections and thus constrain the inversion of soil profile. We propose to assess ImG11 removing the influence of illumination spectrum using the H/V spectral ratio and an estimate of ImG33 (obtained from a priori model) by means of ImG11=0.5(H/V)2*ImG33. It has been found that ImG33 is less sensitive to details of stratigraphy. In fact, the most relevant property is the Poisson ratio of the uppermost layer which controls the slope in high frequency (Sánchez-Sesma et al, 2011b). Pseudo-reflection seismograms are thus obtained from Fourier transform, back to time domain, of i{ImG11-ImG11HSS}, where ImG11HSS is the imaginary part of Green functions at the load point for horizontal load at the surface of a half-space with the properties of the uppermost layer. With the obtained model ImG33 can be updated and the

  13. Febrifugine analogues as Leishmania donovani trypanothione reductase inhibitors: binding energy analysis assisted by molecular docking, ADMET and molecular dynamics simulation.

    Science.gov (United States)

    Pandey, Rajan Kumar; Kumbhar, Bajarang Vasant; Srivastava, Shubham; Malik, Ruchi; Sundar, Shyam; Kunwar, Ambarish; Prajapati, Vijay Kumar

    2017-01-01

    Visceral leishmaniasis affects people from 70 countries worldwide, mostly from Indian, African and south American continent. The increasing resistance to antimonial, miltefosine and frequent toxicity of amphotericin B drives an urgent need to develop an antileishmanial drug with excellent efficacy and safety profile. In this study we have docked series of febrifugine analogues (n = 8813) against trypanothione reductase in three sequential docking modes. Extra precision docking resulted into 108 ligands showing better docking score as compared to two reference ligand. Furthermore, 108 febrifugine analogues and reference inhibitor clomipramine were subjected to ADMET, QikProp and molecular mechanics, the generalized born model and solvent accessibility study to ensure the toxicity caused by compounds and binding-free energy, respectively. Two best ligands (FFG7 and FFG2) qualifying above screening parameters were further subjected to molecular dynamics simulation. Conducting these studies, here we confirmed that 6-chloro-3-[3-(3-hydroxy-2-piperidyl)-2-oxo-propyl]-7-(4-pyridyl) quinazolin-4-one can be potential drug candidate to fight against Leishmania donovani parasites.

  14. Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants.

    Science.gov (United States)

    Feenstra, K Anton; Starikov, Eugene B; Urlacher, Vlada B; Commandeur, Jan N M; Vermeulen, Nico P E

    2007-03-01

    Hydroxylations of octane and lauric acid by Cytochrome P450-BM3 (CYP102A1) wild-type and three active site mutants--F87A, L188Q/A74G, and F87V/L188Q/A74G--were rationalized using a combination of substrate orientation from docking, substrate binding statistics from molecular dynamics simulations, and barrier energies for hydrogen atom abstraction from quantum mechanical calculations. Wild-type BM3 typically hydroxylates medium- to long-chain fatty acids on subterminal (omega-1, omega-2, omega-3) but not the terminal (omega) positions. The known carboxylic anchoring site Y51/R47 for lauric acid, and hydrophobic interactions and steric exclusion, mainly by F87, for octane as well as lauric acid, play a role in the binding modes of the substrates. Electrostatic interactions between the protein and the substrate strongly modulate the substrate's regiodependent activation barriers. A combination of the binding statistics and the activation barriers of hydrogen-atom abstraction in the substrates is proposed to determine the product formation. Trends observed in experimental product formation for octane and lauric acid by wild-type BM3 and the three active site mutants were qualitatively explained. It is concluded that the combination of substrate binding statistics and hydrogen-atom abstraction barrier energies is a valuable tool to rationalize substrate binding and product formation and constitutes an important step toward prediction of product ratios.

  15. Effects of an Intense Laser Field and Hydrostatic Pressure on the Intersubband Transitions and Binding Energy of Shallow Donor Impurities in a Quantum Well

    Institute of Scientific and Technical Information of China (English)

    U. Yesilgul; F. Ungan; E. Kasapoglu; H. Sari; I. S(o)kmen

    2011-01-01

    We have calculated the intersubband transitions and the ground-state binding energies of a hydrogenic donor impurity in a quantum well in the presence of a high-frequency laser field and hydrostatic pressure.The calculations are performed within the effective mass approximation,using a variational method. We conclude that the laser field amplitude and the hydrostatic pressure provide an important effect on the electronic and optical properties of the quantum wells.According to the results obtained from the present work,it is deduced that (i) the binding energies of donor impurity decrease as the laser field increase,(ii) the binding energies of donor impurity increase as the hydrostatic pressure increase,(iii) the intersubband absorption coefficients shift toward lower energies as the hydrostatic pressure increases,(iv) the magnitude of absorption coefficients decrease and also shift toward higher energies as the laser field increase.It is hopeful that the obtained results will provide important improvements in device applications.

  16. Electron binding energies and the fundamental gap of a push-pull dye in a polar environment: p-nitroaniline in liquid water

    Science.gov (United States)

    Cabral, Benedito J. C.

    2017-01-01

    The outer valence electron binding energies and the fundamental gap of p-nitroaniline (PNA) in water were determined by electron propagator theory. The adopted methodology relies on the calculation of electron binding energies by using configurations generated by Born-Oppenheimer molecular dynamics of PNA in water. The fundamental gap (Eg) of PNA in water was estimated from the first ionisation energy (IE) and the first vertical electron affinity VEA (Eg = IE-VEA). In liquid water Eg is predicted to be 6.5 ± 0.5 eV (OVGF), which is ∼3.3 eV greater than the experimental optical gap (3.25 eV).

  17. Control of the binding energy by tuning the single dopant position, magnetic field strength and shell thickness in ZnS/CdSe core/shell quantum dot

    Science.gov (United States)

    Talbi, A.; Feddi, E.; Zouitine, A.; Haouari, M. El; Zazoui, M.; Oukerroum, A.; Dujardin, F.; Assaid, E.; Addou, M.

    2016-10-01

    Recently, the new tunable optoelectronic devices associated to the inclusion of the single dopant are in continuous emergence. Combined to other effects such as magnetic field, geometrical confinement and dielectric discontinuity, it can constitute an approach to adjusting new transitions. In this paper, we present a theoretical investigation of magnetic field, donor position and quantum confinement effects on the ground state binding energy of single dopant confined in ZnS/CdSe core/shell quantum dot. Within the framework of the effective mass approximation, the Schrödinger equation was numerically been solved by using the Ritz variational method under the finite potential barrier. The results show that the binding energy is very affected by the core/shell sizes and by the external magnetic field. It has been shown that the single dopant energy transitions can be controlled by tuning the dopant position and/or the field strength.

  18. Using H/V Spectral Ratio Analysis to Map Sediment Thickness and to Explain Macroseismic Intensity Variation of a Low-Magnitude Seismic Swarm in Central Belgium

    Science.gov (United States)

    Van Noten, K.; Lecocq, T.; Camelbeeck, T.

    2013-12-01

    Between 2008 and 2010, the Royal Observatory of Belgium received numerous ';Did You Feel It'-reports related to a 2-year lasting earthquake swarm at Court-Saint-Etienne, a small town in a hilly area 20 km SE of Brussels, Belgium. These small-magnitude events (-0.7 ≤ ML ≤ 3.2, n = c. 300 events) were recorded both by the permanent seismometer network in Belgium and by a locally installed temporary seismic network deployed in the epicentral area. Relocation of the hypocenters revealed that the seismic swarm can be related to the reactivation of a NW-SE strike-slip fault at 3 to 6 km depth in the basement rocks of the Lower Palaeozoic London-Brabant Massif. This sequence caused a lot of emotion in the region because more than 60 events were felt by the local population. Given the small magnitudes of the seismic swarm, most events were more often heard than felt by the respondents, which is indicative of a local high-frequency earthquake source. At places where the bedrock is at the surface or where it is covered by thin alluvial sediments ( 30 m). In those river valleys that have a considerable alluvial sedimentary cover, macroseismic intensities are again lower. To explain this variation in macroseismic intensity we present a macroseismic analysis of all DYFI-reports related to the 2008-2010 seismic swarm and a pervasive H/V spectral ratio (HVSR) analysis of ambient noise measurements to model the thickness of sediments covering the London-Brabant Massif. The HVSR method is a very powerful tool to map the basement morphology, particularly in regions of unknown subsurface structure. By calculating the soil's fundamental frequency above boreholes, we calibrated the power-law relationship between the fundamental frequency, shear wave velocity and the thickness of sediments. This relationship is useful for places where the sediment thickness is unknown and where the fundamental frequency can be calculated by H/V spectral ratio analysis of ambient noise. In a

  19. Integration of V2H/V2G Hybrid System for Demand Response in Distribution Network

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yubo; Sheikh, Omar; Hu, Boyang; Chu, Chi-Cheng; Gadh, Rajit

    2014-11-03

    Integration of Electrical Vehicles (EVs) with power grid not only brings new challenges for load management, but also opportunities for distributed storage and generation in distribution network. With the introduction of Vehicle-to-Home (V2H) and Vehicle-to-Grid (V2G), EVs can help stabilize the operation of power grid. This paper proposed and implemented a hybrid V2H/V2G system with commercialized EVs, which is able to support both islanded AC/DC load and the power grid with one single platform. Standard industrial communication protocols are implemented for a seamless respond to remote Demand Respond (DR) signals. Simulation and implementation are carried out to validate the proposed design. Simulation and implementation results showed that the hybrid system is capable of support critical islanded DC/AC load and quickly respond to the remote DR signal for V2G within 1.5kW of power range.

  20. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

    Science.gov (United States)

    Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

    2015-01-22

    The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

  1. Characteristics of DNA-binding proteins determine the biological sensitivity to high-linear energy transfer radiation

    NARCIS (Netherlands)

    H. Wang (Hong); X. Zhang (Xiangming); P. Wang (Ping); X. Yu (Xiaoyan); J. Essers (Jeroen); D.J. Chen (David); R. Kanaar (Roland); S. Takeda (Shiunichi); Y. Wang (Ya)

    2010-01-01

    textabstractNon-homologous end-joining (NHEJ) and homologous recombination repair (HRR), contribute to repair ionizing radiation (IR)-induced DNA double-strand breaks (DSBs). Mre11 binding to DNA is the first step for activating HRR and Ku binding to DNA is the first step for initiating NHEJ. High-l

  2. Absolute Free Energy of Binding and Entropy of the FKBP12-FK506 Complex: Effects of the Force Field.

    Science.gov (United States)

    General, Ignacio J; Meirovitch, Hagai

    2013-10-08

    The hypothetical scanning molecular dynamics (HSMD) method combined with thermodynamic integration (HSMD-TI) has been extended recently for calculating ΔA(0)-the absolute free energy of binding of a ligand to a protein. With HSMD-TI, ΔA(0) is obtained in a new way as a sum of several components, among them is ΔSligand-the change in the conformational entropy as the ligand is transferred from the bulk solvent to the active site-this entropy is obtained by a specific reconstruction procedure. This unique aspect of HSMD (which is useful in rational drug design) is in particular important for treating large ligands, where ΔSligand might be significant. Technically, one should verify that the results for ΔSligand converge-a property that might become more difficult for large ligands; therefore, studying ligands of increasing size would define the range of applicability of HSMD-TI for binding. In this paper, we check the performance of HSMD-TI by applying it to the relatively large ligand FK506 (126 atoms) complexed with the protein FKBP12, where ΔA(0) = -12.8 kcal/mol is known experimentally as well as the crystal structure of the complex. This structure was initially equilibrated by carrying out a 100 ns molecular dynamics trajectory, where the system is modeled by the AMBER force field, TIP3P water, and Particle Mesh Ewald. HSMD-TI calculations were carried out in three conformational regions defined by the intervals [0.2,2], [2,5], and [5,100] ns along the trajectory, where local equilibration of the total energy has been observed; we obtained ΔA(0) = -13.6 ± 1.1, -16.6 ± 1.4, and -16.7 ± 1.4 kcal/mol, respectively indicating the following: (1) The second and third regions belong to the same conformational subspace of the complex, which is different from the [0.2,2] ns subspace. (2) The unsatisfactory result for ΔA(0) obtained in the well equilibrated (hence theoretically preferred) latter regions reflects the nonperfect modeling used, which however (3

  3. Linear free energy relationships for metal-ligand complexation: Bidentate binding to negatively-charged oxygen donor atoms

    Science.gov (United States)

    Carbonaro, Richard F.; Atalay, Yasemin B.; Di Toro, Dominic M.

    2011-05-01

    Stability constants for metal complexation to bidentate ligands containing negatively-charged oxygen donor atoms can be estimated from the following linear free energy relationship (LFER): log KML = χOO( αO log KHL,1 + αO log KHL,2) where KML is the metal-ligand stability constant for a 1:1 complex, KHL,1 and KHL,2 are the proton-ligand stability constants (the ligand p Ka values), and αO is the Irving-Rossotti slope. The parameter χOO is metal specific and has slightly different values for five and six membered chelate rings. LFERs are presented for 21 different metal ions and are accurate to within approximately 0.30 log units in predictions of log KML values. Ligands selected for use in LFER development include dicarboxylic acids, carboxyphenols, and ortho-diphenols. For ortho-hydroxybenzaldehydes, α-hydroxycarboxylic acids, and α-ketocarboxylic acids, a modification of the LFER where log KHL,2 is set equal to zero is required. The chemical interpretation of χOO is that it accounts for the extra stability afforded to metal complexes by the chelate effect. Cu-NOM binding constants calculated from the bidentate LFERs are similar in magnitude to those used in WHAM 6. This LFER can be used to make log KML predictions for small organic molecules. Since natural organic matter (NOM) contains many of the same functional groups (i.e. carboxylic acids, phenols, alcohols), the LFER log KML predictions shed light on the range of appropriate values for use in modeling metal partitioning in natural systems.

  4. 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.

  5. Photoelectron spectrum of valence anions of uracil and first-principles calculations of excess electron binding energies

    Science.gov (United States)

    Bachorz, Rafał A.; Klopper, Wim; Gutowski, Maciej; Li, Xiang; Bowen, Kit H.

    2008-08-01

    The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree-Fock and second-order Møller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within +/-1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of ~-0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.

  6. Binding energy of the complex (D+-X) with Γ-X mixing in GaAs/AlAs quantum wells

    Science.gov (United States)

    Cunha Lima, I. C.; Ghazali, A.; Emmel, P. D.

    1996-11-01

    The binding energy of excitons to ionized shallow donors in a GaAs/AlAs quantum well in the vicinity of the type-I to type-II transition is obtained for impurities lying anywhere in the structure. We include the Γ-X hybridization in the Brillouin zone, which comes into play when the energies of the conduction subband minima in the two materials become closer. The calculation is performed variationally using a three parameters trial function similar to the one describing a singly ionized molecule. The same model allows the calculation of the binding energies of the neutral impurity and of the free exciton. We obtain that a ratio between the binding energy of the exciton to an ionized donor and that of the neutral donor equals 0.95+/-0.005, for all values of well widths explored, and independent of the impurity position inside the well. The joint density of states for the transition from free to bound exciton is obtained, and a discussion is presented on the role played by the doping and the compensation on the exciton dynamics.

  7. 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.

  8. Piezoelectric and spontaneous polarization effects on exciton binding energy and light emission properties of wurtzite ZnO/MgO quantum dots

    Science.gov (United States)

    Park, Seoung-Hwan; Hong, Woo-Pyo; Kim, Jong-Jae

    2017-08-01

    Exciton binding energies and light emission characteristics for wurtzite (WZ) cubic ZnO/MgO quantum dots (QDs) are investigated by considering piezoelectric (PZ) and spontaneous (SP) polarizations. These results are compared with those for the flat-band without PZ and SP polarizations. The exciton binding energies for the case with PZ and SP polarizations appears to be smaller than those for the flat-band model. In particular, the spontaneous emission coefficients are shown to be reduced significantly by the built-in field because the existence of the built-in field results in the decrease in the overlap between the electron and hole wave functions. These results show that the consideration of PZ and SP polarizations is very important in predicting optical properties of ZnO-based QD devices.

  9. Seismic microzonation and velocity models of El Ejido area (SE Spain) from the diffuse-field H/V method

    Science.gov (United States)

    García-Jerez, Antonio; Seivane, Helena; Navarro, Manuel; Piña-Flores, José; Luzón, Francisco; Vidal, Francisco; Posadas, Antonio M.; Aranda, Carolina

    2016-04-01

    El Ejido town is located in the Campo de Dalías coastal plain (Almería province, SE Spain), emplaced in one of the most seismically active regions of Spain. The municipality has 84000 inhabitants and presented a high growth rate during the last twenty years. The most recent intense seismic activity occurred close to this town was in 1993 and 1994, with events of Mb = 4.9 and Mb = 5.0, respectively. To provide a basis for site-specific hazard analysis, we first carried out a seismic microzonation of this town in terms of predominant periods and geotechnical properties. The predominant periods map was obtained from ambient noise observations on a grid of 250 x 250 m in the main urban area, and sparser measurements on the outskirts. These broad-band records, of about 20 minutes long each, were analyzed by using the horizontal-to-vertical spectral ratio technique (H/V). Dispersion curves obtained from two array measurements of ambient noise and borehole data provided additional geophysical information. All the surveyed points in the town were found to have relatively long predominant periods ranging from 0.8 to 2.3 s and growing towards the SE. Secondary high-frequency (> 2Hz) peaks were found at about the 10% of the points only. On the other hand, Vs30 values of 550 - 650 m/s were estimated from the array records, corresponding to cemented sediments and medium-hard rocks. The local S-wave velocity structure has been inverted from the H/V curves for a subset of the measurement sites. We used an innovative full-wavefield method based on the diffuse-wavefield approximation (Sánchez-Sesma et al., 2011) combined with the simulated annealing algorithm. Shallow seismic velocities and deep boreholes data were used as constraints. The results show that the low-frequency resonances are related with the impedance contrast between several hundred meters of medium-hard sedimentary rocks (marls and calcarenites) with the stiffer basement of the basin, which dips to the SE. These

  10. The electronic structure and grain boundary segregation by boron addition——A binding energy shifting criterion for the brittle-ductile fracture transition in Ni3Al

    Institute of Scientific and Technical Information of China (English)

    张云; 林栋梁

    1997-01-01

    The electronic structure and grain boundary segregation caused by boron addition to Ni3Al have been studied by X-ray photoelectron spectroscopy and Auger electron spectroscopy, respectively. The obtained results show that the Ni2p3/2 electron binding energy rises gradually in the sequence of pure Ni< Ni76Al24< Ni74Al26 < Ni25Al25, while it reduces monotonously with an increase in boron addition to Ni3Al. Besides, it is found that the gram boundary segregation of boron occurring in Ni3Al is a combined equilibrium and non-equilibrium type in nature. Based on the concept of the bonding environmental inhomogeneity, measured by the shift in Ni2p3/2 electron binding energy from the nickel atoms in the simple substance nickel to those in the intermetallic compound Ni3Al (ΔEB), being responsible for the brittle behavior of the alloy, a binding energy shifting criterion for the brittle-ductile fracture transition in Ni3Al is presented: when ΔEB>0, the brittle failure occurs in Ni3Al; when ΔEB<0, the ductile o

  11. Reducing exciton binding energy by increasing thin film permittivity: an effective approach to enhance exciton separation efficiency in organic solar cells.

    Science.gov (United States)

    Leblebici, Sibel Y; Chen, Teresa L; Olalde-Velasco, Paul; Yang, Wanli; Ma, Biwu

    2013-10-23

    Photocurrent generation in organic solar cells requires that excitons, which are formed upon light absorption, dissociate into free carriers at the interface of electron acceptor and donor materials. The high exciton binding energy, arising from the low permittivity of organic semiconductor films, generally causes low exciton separation efficiency and subsequently low power conversion efficiency. We demonstrate here, for the first time, that the exciton binding energy in B,O-chelated azadipyrromethene (BO-ADPM) donor films is reduced by increasing the film permittivity by blending the BO-ADPM donor with a high dielectric constant small molecule, camphoric anhydride (CA). Various spectroscopic techniques, including impedance spectroscopy, photon absorption and emission spectroscopies, as well as X-ray spectroscopies, are applied to characterize the thin film electronic and photophysical properties. Planar heterojunction solar cells are fabricated with a BO-ADPM:CA film as the electron donor and C60 as the acceptor. With an increase in the dielectric constant of the donor film from ∼4.5 to ∼11, the exciton binding energy is reduced and the internal quantum efficiency of the photovoltaic cells improves across the entire spectrum, with an ∼30% improvement in the BO-ADPM photoactive region.

  12. A computer code for forward calculation and inversion of the H/V spectral ratio under the diffuse field assumption

    Science.gov (United States)

    García-Jerez, Antonio; Piña-Flores, José; Sánchez-Sesma, Francisco J.; Luzón, Francisco; Perton, Mathieu

    2016-12-01

    During a quarter of a century, the main characteristics of the horizontal-to-vertical spectral ratio of ambient noise HVSRN have been extensively used for site effect assessment. In spite of the uncertainties about the optimum theoretical model to describe these observations, over the last decade several schemes for inversion of the full HVSRN curve for near surface surveying have been developed. In this work, a computer code for forward calculation of H/V spectra based on the diffuse field assumption (DFA) is presented and tested. It takes advantage of the recently stated connection between the HVSRN and the elastodynamic Green's function which arises from the ambient noise interferometry theory. The algorithm allows for (1) a natural calculation of the Green's functions imaginary parts by using suitable contour integrals in the complex wavenumber plane, and (2) separate calculation of the contributions of Rayleigh, Love, P-SV and SH waves as well. The stability of the algorithm at high frequencies is preserved by means of an adaptation of the Wang's orthonormalization method to the calculation of dispersion curves, surface-waves medium responses and contributions of body waves. This code has been combined with a variety of inversion methods to make up a powerful tool for passive seismic surveying.

  13. A computer code for forward calculation and inversion of the H/V spectral ratio under the diffuse field assumption

    CERN Document Server

    García-Jerez, Antonio; Sánchez-Sesma, Francisco J; Luzón, Francisco; Perton, Mathieu

    2016-01-01

    During a quarter of a century, the main characteristics of the horizontal-to-vertical spectral ratio of ambient noise HVSRN have been extensively used for site effect assessment. In spite of the uncertainties about the optimum theoretical model to describe these observations, several schemes for inversion of the full HVSRN curve for near surface surveying have been developed over the last decade. In this work, a computer code for forward calculation of H/V spectra based on the diffuse field assumption (DFA) is presented and tested.It takes advantage of the recently stated connection between the HVSRN and the elastodynamic Green's function which arises from the ambient noise interferometry theory. The algorithm allows for (1) a natural calculation of the Green's functions imaginary parts by using suitable contour integrals in the complex wavenumber plane, and (2) separate calculation of the contributions of Rayleigh, Love, P-SV and SH waves as well. The stability of the algorithm at high frequencies is preserv...

  14. Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design.

    Science.gov (United States)

    You, Wanli; Huang, Yu-Ming M; Kizhake, Smitha; Natarajan, Amarnath; Chang, Chia-En A

    2016-08-01

    Inhibition of the protein-protein interaction (PPI) mediated by breast-cancer-gene 1 C-terminal (BRCT) is an attractive strategy to sensitize breast and ovarian cancers to chemotherapeutic agents that induce DNA damage. Such inhibitors could also be used for studies to understand the role of this PPI in DNA damage response. However, design of BRCT inhibitors is challenging because of the inherent flexibility associated with this domain. Several studies identified short phosphopeptides as tight BRCT binders. Here we investigated the thermodynamic properties of 18 phosphopeptides or peptide with phosphate mimic and three compounds with phosphate groups binding to BRCT to understand promiscuous molecular recognition and guide inhibitor design. We performed molecular dynamics (MD) simulations to investigate the interactions between inhibitors and BRCT and their dynamic behavior in the free and bound states. MD simulations revealed the key role of loops in altering the shape and size of the binding site to fit various ligands. The mining minima (M2) method was used for calculating binding free energy to explore the driving forces and the fine balance between configuration entropy loss and enthalpy gain. We designed a rigidified ligand, which showed unfavorable experimental binding affinity due to weakened enthalpy. This was because it lacked the ability to rearrange itself upon binding. Investigation of another phosphate group containing compound, C1, suggested that the entropy loss can be reduced by preventing significant narrowing of the energy well and introducing multiple new compound conformations in the bound states. From our computations, we designed an analog of C1 that introduced new intermolecular interactions to strengthen attractions while maintaining small entropic penalty. This study shows that flexible compounds do not always encounter larger entropy penalty, compared with other more rigid binders, and highlights a new strategy for inhibitor design.

  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. Investigations on Binding Pattern of Kinase Inhibitors with PPARγ: Molecular Docking, Molecular Dynamic Simulations, and Free Energy Calculation Studies

    Science.gov (United States)

    Mazumder, Mohit; Das, Umashankar; Gourinath, Samudrala

    2017-01-01

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential target for the treatment of several disorders. In view of several FDA approved kinase inhibitors, in the current study, we have investigated the interaction of selected kinase inhibitors with PPARγ using computational modeling, docking, and molecular dynamics simulations (MDS). The docked conformations and MDS studies suggest that the selected KIs interact with PPARγ in the ligand binding domain (LBD) with high positive predictive values. Hence, we have for the first time shown the plausible binding of KIs in the PPARγ ligand binding site. The results obtained from these in silico investigations warrant further evaluation of kinase inhibitors as PPARγ ligands in vitro and in vivo.

  17. 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

  18. On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge

    Science.gov (United States)

    Bansal, Nupur; Zheng, Zheng; Cerutti, David S.; Merz, Kenneth M.

    2017-01-01

    We review our performance in the SAMPL5 challenge for predicting host-guest binding affinities using the movable type (MT) method. The challenge included three hosts, acyclic Cucurbit[2]uril and two octa-acids with and without methylation at the entrance to their binding cavities. Each host was associated with 6-10 guest molecules. The MT method extrapolates local energy landscapes around particular molecular states and estimates the free energy by Monte Carlo integration over these landscapes. Two blind submissions pairing MT with variants of the KECSA potential function yielded mean unsigned errors of 1.26 and 1.53 kcal/mol for the non-methylated octa-acid, 2.83 and 3.06 kcal/mol for the methylated octa-acid, and 2.77 and 3.36 kcal/mol for Cucurbit[2]uril host. While our results are in reasonable agreement with experiment, we focused on particular cases in which our estimates gave incorrect results, particularly with regard to association between the octa-acids and an adamantane derivative. Working on the hypothesis that differential solvation effects play a role in effecting computed binding affinities for the parent octa-acid and the methylated octa-acid and that the ligands bind inside the pockets (rather than on the surface) we devised a new solvent accessible surface area term to better quantify solvation energy contributions in MT based studies. To further explore this issue a, molecular dynamics potential of mean force (PMF) study indicates that, as found by our docking calculations, the stable binding mode for this ligand is inside (rather than surface bound) the octa-acid cavity whether the entrance is methylated or not. The PMF studies also obtained the correct order for the methylation-induced change in binding affinities and associated the difference, to a large extent to differential solvation effects. Overall, the SAMPL5 challenge yielded in improvements our solvation modeling and also demonstrated the need for thorough validation of input data

  19. Structures, stabilization energies, and binding energies of quinoxaline···(H2O)(n), quinoxaline dimer, and quinoxaline···Cu complexes: a theoretical study.

    Science.gov (United States)

    Kabanda, Mwadham M; Ebenso, Eno E

    2013-02-21

    Quinoxaline is a parent structure for a broad class of N-heteroaromatic compounds, many of which exhibit various biological activities. The interaction of quinoxaline with explicit water molecules or metal ions and the formation of quinoxaline dimer play an important role in many of the biological activities of quinoxaline. This study investigates the structures, stabilization, and binding energies of quinoxaline complexes with water, transition metal ions, and quinoxaline dimer to provide information on the preferred geometries, interaction energies, and type of noncovalent interactions accounting for the stability of the complexes. The investigations are performed in vacuo and in water solution using MP2 and DFT methods. The results of the study on the quinoxaline···(H(2)O)(n) show that the preferred adducts in vacuo involve one, two, or three water molecules hydrogen bonded to the N atom and the neighboring H atom of the C(sp2)-H group. The results in water solution show a preference for water-water clustering. The dimers of quinoxaline are stabilized by either π-π stacking or weak C-H···N intermolecular hydrogen bonds. The relative stability of the quinoxaline···Cu complexes depends on the site on which the Cu ion binds and the binding strength depends on both the nature of the cation and the binding site.

  20. Dispersion-correcting potentials can significantly improve the bond dissociation enthalpies and noncovalent binding energies predicted by density-functional theory

    Energy Technology Data Exchange (ETDEWEB)

    DiLabio, Gino A., E-mail: Gino.DiLabio@nrc.ca [National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9 (Canada); Department of Chemistry, University of British Columbia, Okanagan, 3333 University Way, Kelowna, British Columbia V1V 1V7 (Canada); Koleini, Mohammad [National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9 (Canada); Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4 (Canada)

    2014-05-14

    Dispersion-correcting potentials (DCPs) are atom-centered Gaussian functions that are applied in a manner that is similar to effective core potentials. Previous work on DCPs has focussed on their use as a simple means of improving the ability of conventional density-functional theory methods to predict the binding energies of noncovalently bonded molecular dimers. We show in this work that DCPs developed for use with the LC-ωPBE functional along with 6-31+G(2d,2p) basis sets are capable of simultaneously improving predicted noncovalent binding energies of van der Waals dimer complexes and covalent bond dissociation enthalpies in molecules. Specifically, the DCPs developed herein for the C, H, N, and O atoms provide binding energies for a set of 66 noncovalently bonded molecular dimers (the “S66” set) with a mean absolute error (MAE) of 0.21 kcal/mol, which represents an improvement of more than a factor of 10 over unadorned LC-ωPBE/6-31+G(2d,2p) and almost a factor of two improvement over LC-ωPBE/6-31+G(2d,2p) used in conjunction with the “D3” pairwise dispersion energy corrections. In addition, the DCPs reduce the MAE of calculated X-H and X-Y (X,Y = C, H, N, O) bond dissociation enthalpies for a set of 40 species from 3.2 kcal/mol obtained with unadorned LC-ωPBE/6-31+G(2d,2p) to 1.6 kcal/mol. Our findings demonstrate that broad improvements to the performance of DFT methods may be achievable through the use of DCPs.

  1. Dielectric confinement on exciton binding energy and nonlinear optical properties in a strained Zn1-xinMgxinSe/Zn1-xoutMgxoutSe quantum well

    Institute of Scientific and Technical Information of China (English)

    J. Abraham Hudson Mark; A. John Peter

    2012-01-01

    The band offsets for a Zn1-xinMgxin Se/Zn1-xoutMgxout Se quantum well heterostructure are determined using the model solid theory.The heavy hole exciton binding energies are investigated with various Mg alloy contents.The effect of mismatch between the dielectric constants between the well and the barrier is taken into account.The dependence of the excitonic transition energies on the geometrical confinement and the Mg alloy is discussed.Non-linear optical properties are determined using the compact density matrix approach.The linear,third order non-linear optical absorption coefficient values and the refractive index changes of the exciton are calculated for different concentrations of magnesium.The results show that the occurred blue shifts of the resonant peak due to the Mg incorporation give the information about the variation of two energy levels in the quantum well width.

  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. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T)

    Science.gov (United States)

    Caldararu, Octav; Olsson, Martin A.; Riplinger, Christoph; Neese, Frank; Ryde, Ulf

    2017-01-01

    We have tried to calculate the free energy for the binding of six small ligands to two variants of the octa-acid deep cavitand host in the SAMPL5 blind challenge. We employed structures minimised with dispersion-corrected density-functional theory with small basis sets and energies were calculated using large basis sets. Solvation energies were calculated with continuum methods and thermostatistical corrections were obtained from frequencies calculated at the HF-3c level. Care was taken to minimise the effects of the flexibility of the host by keeping the complexes as symmetric and similar as possible. In some calculations, the large net charge of the host was reduced by removing the propionate and benzoate groups. In addition, the effect of a restricted molecular dynamics sampling of structures was tested. Finally, we tried to improve the energies by using the DLPNO-CCSD(T) approach. Unfortunately, results of quite poor quality were obtained, with no correlation to the experimental data, systematically too positive affinities (by 50 kJ/mol) and a mean absolute error (after removal of the systematic error) of 11-16 kJ/mol. DLPNO-CCSD(T) did not improve the results, so the accuracy is not limited by the energy function. Instead, four likely sources of errors were identified: first, the minimised structures were often incorrect, owing to the omission of explicit solvent. They could be partly improved by performing the minimisations in a continuum solvent with four water molecules around the charged groups of the ligands. Second, some ligands could bind in several different conformations, requiring sampling of reasonable structures. Third, there is an indication the continuum-solvation model has problems to accurately describe the binding of both the negatively and positively charged guest molecules. Fourth, different methods to calculate the thermostatistical corrections gave results that differed by up to 30 kJ/mol and there is an indication that HF-3c overestimates

  4. Energy-resolved collision-induced dissociation studies of 1,10-phenanthroline complexes of the late first-row divalent transition metal cations: determination of the third sequential binding energies.

    Science.gov (United States)

    Nose, Holliness; Chen, Yu; Rodgers, M T

    2013-05-23

    The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M(2+)(Phen)3 complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion-neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M(2+)(Phen)x complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+), previously investigated.

  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. Experimental measurements of water molecule binding energies for the second and third solvation shells of [Ca(H2O)n]2+ complexes

    Science.gov (United States)

    Bruzzi, E.; Stace, A. J.

    2017-01-01

    Further understanding of the biological role of the Ca2+ ion in an aqueous environment requires quantitative measurements of both the short- and long-range interactions experienced by the ion in an aqueous medium. Here, we present experimental measurements of binding energies for water molecules occupying the second and, quite possibly, the third solvation shell surrounding a central Ca2+ ion in [Ca(H2O)n]2+ complexes. Results for these large, previously inaccessible, complexes have come from the application of finite heat bath theory to kinetic energy measurements following unimolecular decay. Even at n = 20, the results show water molecules to be more strongly bound to Ca2+ than would be expected just from the presence of an extended network of hydrogen bonds. For n > 10, there is very good agreement between the experimental binding energies and recently published density functional theory calculations. Comparisons are made with similar data recorded for [Ca(NH3)n]2+ and [Ca(CH3OH)n]2+ complexes.

  7. 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...

  8. 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.

  9. Four-body calculation of 4He binding energy and tensor analysing powers for dd → dd and dd → p 3H reactions

    Science.gov (United States)

    Fonseca, A. C.

    1990-02-01

    Four-body integral equations are used to calculate the binding energy of 4He as well as dd → dd and dd → p 3H amplitudes using a single term separable nucleon-nucleon potential in channels 1S 0 and 3S 1- 3D 1, together with the energy dependent pole expansion to set up an N term representation of all (3)+1 subamplitudes of interest. The (2)+(2) subamplitudes are treated exactly by convolution. The 4He binding energy is obtained from the exact solution of the equations. In the scattering region first order perturbation theory is used to separate the contribution of the s-wave components of the N-N t-matrix and s- and p-wave three-nucleon channels to the tour-nucleon Kernel, from the contribution of d-wave two- and three-nucleon channel components that result from the tensor-force. Cross sections and analysing powers are calculated using all positive and negative parity four-body amplitudes with total angular momentum J⩽4. Comparison with data is presented.

  10. Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking

    Science.gov (United States)

    Olsson, Martin A.; García-Sosa, Alfonso T.; Ryde, Ulf

    2017-09-01

    We have studied the binding of 102 ligands to the farnesoid X receptor within the D3R Grand Challenge 2016 blind-prediction competition. First, we employed docking with five different docking software and scoring functions. The selected docked poses gave an average root-mean-squared deviation of 4.2 Å. Consensus scoring gave decent results with a Kendall's τ of 0.26 ± 0.06 and a Spearman's ρ of 0.41 ± 0.08. For a subset of 33 ligands, we calculated relative binding free energies with free-energy perturbation. Five transformations between the ligands involved a change of the net charge and we implemented and benchmarked a semi-analytic correction (Rocklin et al., J Chem Phys 139:184103, 2013) for artifacts caused by the periodic boundary conditions and Ewald summation. The results gave a mean absolute deviation of 7.5 kJ/mol compared to the experimental estimates and a correlation coefficient of R 2 = 0.1. These results were among the four best in this competition out of 22 submissions. The charge corrections were significant (7-8 kJ/mol) and always improved the results. By employing 23 intermediate states in the free-energy perturbation, there was a proper overlap between all states and the precision was 0.1-0.7 kJ/mol. However, thermodynamic cycles indicate that the sampling was insufficient in some of the perturbations.

  11. Characterization of H/V Spectral Ratios for the Assessment of Slope Stability in the Gas Hydrate-rich Area: an Example from Offshore SW Taiwan

    Science.gov (United States)

    Lin, J. Y.; Tsia, C. H.; Cheng, W. B.; Chin, S. J.; Lin, S. S.; Liang, C. W.

    2015-12-01

    The Nakamura's method, which calculates the ratios between horizontal and vertical component spectra of seismic signals (H/V), is widely used in the inland area. However, few related estimations were performed for the offshore area and little knowledge for the marine sediments were obtained. From 2013 to 2015, three passive ocean bottom seismometer (OBS) experiments were conducted in gas hydrate-rich area offshore SW Taiwan in the aim of acquiring information related to the physical properties of seafloor sediments. The H/V of the seafloor sediments in the three areas were estimated by using the ambient noise and seismic signal recorded by OBSs. The resonance frequency of each site was estimated from the main peak of H/V distribution and a range between 5 and 10 Hz were obtained. Based on the empirical law, this resonance frequency range should correspond to a sediment thickness of approximately several to ten of meters. This estimation is consistent with the thickness of the sedimentary cover imaged by chirp sonar survey, suggesting that the site response of seafloor is dominantly controlled by the unconsolidated sedimentary layer on the top of the sea bed. Remarkably, the H/V ratios obtained in our study area are much larger than that calculated for the inland areas. The magnification can reach as high as 50 to more than 100. This observation infers that the sea water movement might emphasize the horizontal motion of the marine sediments, which is crucial for the slope stability assessment. Moreover, for most stations located in the active margin, no distinct peak is observed for the H/V pattern calculated during earthquakes. However, in the passive margin, the H/V peak calculated from ambient noise and earthquakes is mostly identical. This phenomenon may suggest that relatively unclear sedimentary boundary exist in the active margin environment. Estimating H/V spectral ratios of data recorded by the OBSs deployed in the southwest Taiwan offshore area offers a

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

    Science.gov (United States)

    Miliordos, Evangelos; Xantheas, Sotiris S.

    2015-03-01

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

  13. Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study.

    Directory of Open Access Journals (Sweden)

    Dimitrios Spiliotopoulos

    Full Text Available PHD fingers represent one of the largest families of epigenetic readers capable of decoding post-translationally modified or unmodified histone H3 tails. Because of their direct involvement in human pathologies they are increasingly considered as a potential therapeutic target. Several PHD/histone-peptide structures have been determined, however relatively little information is available on their dynamics. Studies aiming to characterize the dynamic and energetic determinants driving histone peptide recognition by epigenetic readers would strongly benefit from computational studies. Herein we focus on the dynamic and energetic characterization of the PHD finger subclass specialized in the recognition of histone H3 peptides unmodified in position K4 (H3K4me0. As a case study we focused on the first PHD finger of autoimmune regulator protein (AIRE-PHD1 in complex with H3K4me0. PCA analysis of the covariance matrix of free AIRE-PHD1 highlights the presence of a "flapping" movement, which is blocked in an open conformation upon binding to H3K4me0. Moreover, binding free energy calculations obtained through Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA methodology are in good qualitative agreement with experiments and allow dissection of the energetic terms associated with native and alanine mutants of AIRE-PHD1/H3K4me0 complexes. MM/PBSA calculations have also been applied to the energetic analysis of other PHD fingers recognizing H3K4me0. In this case we observe excellent correlation between computed and experimental binding free energies. Overall calculations show that H3K4me0 recognition by PHD fingers relies on compensation of the electrostatic and polar solvation energy terms and is stabilized by non-polar interactions.

  14. Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors.

    Science.gov (United States)

    Peddi, Saikiran Reddy; Sivan, Sree Kanth; Manga, Vijjulatha

    2017-02-01

    The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔGbind and experimental pIC50 values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC50 values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC50 values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.

  15. Shining light on radiation detection and energy transfer : Triazole ligands used for detection of radiation and lanthanide binding

    NARCIS (Netherlands)

    Dijkstra, Peter

    2016-01-01

    Some substances, fluorophores, absorb light and then emit that light again as fluorescence. Apart from absorption of light, some of these substances can also emit light after having absorbed energy from radiation. A substance which can absorb radiation and emit the energy as light is called a scinti

  16. Extended x-ray--absorption fine structure of small Cu and Ni clusters: Binding-energy and bond-length changes with cluster size

    Energy Technology Data Exchange (ETDEWEB)

    Apai, G.; Hamilton, J.F.; Stohr, J.; Thompson, A.

    1979-07-09

    Extended x-ray--absorption fine-structure measurements have been made on metal clusters of Cu and Ni which were formed by vapor deposition on amorphous carbon substrates. Small clusters of both elements show a substantial contraction of the nearest-neighbor metal-metal distance and an increase in binding energy for the onset of the K absorption edge. The results are explained by the increasing surface-to-volume ratio as the cluster size decreases resulting in a more free-atom--like configuration of the metal atoms.

  17. 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.

  18. Bimodal intramolecular excitation energy transfer in a multichromophore photosynthetic model system: hybrid fusion proteins comprising natural phycobilin- and artificial chlorophyll-binding domains.

    Science.gov (United States)

    Zeng, Xiao-Li; Tang, Kun; Zhou, Nan; Zhou, Ming; Hou, Harvey J M; Scheer, Hugo; Zhao, Kai-Hong; Noy, Dror

    2013-09-11

    The phycobilisomes of cyanobacteria and red-algae are highly efficient peripheral light-harvesting complexes that capture and transfer light energy in a cascade of excitation energy transfer steps through multiple phycobilin chromophores to the chlorophylls of core photosystems. In this work, we focus on the last step of this process by constructing simple functional analogs of natural phycobilisome-photosystem complexes that are based on bichromophoric protein complexes comprising a phycobilin- and a chlorophyll- or porphyrin-binding domain. The former is based on ApcE(1-240), the N-terminal chromophore-binding domain of the phycobilisome's L(CM) core-membrane linker, and the latter on HP7, a de novo designed four-helix bundle protein that was originally planned as a high-affinity heme-binding protein, analogous to b-type cytochromes. We fused a modified HP7 protein sequence to ApcEΔ, a water-soluble fragment of ApcE(1-240) obtained by excising a putative hydrophobic loop sequence of residues 77-153. HP7 was fused either to the N- or the C-terminus of ApcEΔ or inserted between residues 76 and 78, thereby replacing the native hydrophobic loop domain. We describe the assembly, spectral characteristics, and intramolecular excitation energy transfer of two unique systems: in the first, the short-wavelength absorbing zinc-mesoporphyrin is bound to the HP7 domain and serves as an excitation-energy donor to the long-wavelength absorbing phycocyanobilin bound to the ApcE domain; in the second, the short-wavelength absorbing phycoerythrobilin is bound to the ApcE domain and serves as an excitation energy donor to the long-wavelength absorbing zinc-bacteriochlorophyllide bound to the HP7 domain. All the systems that were constructed and tested exhibited significant intramolecular fluorescence resonance energy transfer with yields ranging from 21% to 50%. This confirms that our modular, covalent approach for studying EET between the cyclic and open chain tetrapyrroles is

  19. Nanoscale characteristics of triacylglycerol oils: phase separation and binding energies of two-component oils to crystalline nanoplatelets.

    Science.gov (United States)

    MacDougall, Colin J; Razul, M Shajahan; Papp-Szabo, Erzsebet; Peyronel, Fernanda; Hanna, Charles B; Marangoni, Alejandro G; Pink, David A

    2012-01-01

    Fats are elastoplastic materials with a defined yield stress and flow behavior and the plasticity of a fat is central to its functionality. This plasticity is given by a complex tribological interplay between a crystalline phase structured as crystalline nanoplatelets (CNPs) and nanoplatelet aggregates and the liquid oil phase. Oil can be trapped within microscopic pores within the fat crystal network by capillary action, but it is believed that a significant amount of oil can be trapped by adsorption onto crystalline surfaces. This, however, remains to be proven. Further, the structural basis for the solid-liquid interaction remains a mystery. In this work, we demonstrate that the triglyceride liquid structure plays a key role in oil binding and that this binding could potentially be modulated by judicious engineering of liquid triglyceride structure. The enhancement of oil binding is central to many current developments in this area since an improvement in the health characteristics of fat and fat-structured food products entails a reduction in the amount of crystalline triacylglycerols (TAGs) and a relative increase in the amount of liquid TAGs. Excessive amounts of unbound, free oil, will lead to losses in functionality of this important food component. Engineering fats for enhanced oil binding capacity is thus central to the design of more healthy food products. To begin to address this, we modelled the interaction of triacylglycerol oils, triolein (OOO), 1,2-olein elaidin (OOE) and 1,2-elaidin olein (EEO) with a model crystalline nanoplatelet composed of tristearin in an undefined polymorphic form. The surface of the CNP in contact with the oil was assumed to be planar. We considered pure OOO and mixtures of OOO + OOE and OOO + EEO with 80% OOO. The last two cases were taken as approximations to high oleic sunflower oil (HOSO). The intent was to investigate whether phase separation on a nanoscale took place. We defined an "oil binding capacity" parameter, B

  20. 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. DOI: http://dx.doi.org/10.7554/eLife.11742.001 PMID:26880548

  1. 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...

  2. Benzene on Cu(111): I. Application of van der Waals-Density Functional Formalism to Determine Binding Sites and Energy Contour Map

    Science.gov (United States)

    Berland, Kristian; Einstein, T. L.; Hyldgaard, Per

    2010-03-01

    With a recently developed van der Waals density functional (vdW-DF)footnotetextM. Dion et al., Phys. Rev. Lett. 92 (2004) 246401 we study the adsorption of benzene on Cu(111).footnotetextKB, TLE, and PH, Phys. Rev. B 80 (2009) 155431 The vdW-DF inclusion of nonlocal correlations changes the relative stability of 8 high-symmetry binding-position options and increases the adsorption energy by over an order of magnitude, achieving good agreement with experiment. The metallic surface state survives benzene adsorption. From a contour plot of the potential energy, we find that benzene can move almost freely along a honeycomb web of ``corridors" linking fcc and hcp sites via bridge sites, consistent with the low diffusion barrier in experiment.

  3. Tight-binding branch-point energies and band offsets for cubic InN, GaN, AlN, and AlGaN alloys

    Science.gov (United States)

    Mourad, Daniel

    2013-03-01

    Starting with empirical tight-binding band structures, the branch-point (BP) energies and resulting valence band offsets for the zincblende phase of InN, GaN, and AlN are calculated from their k-averaged midgap energy. Furthermore, the directional dependence of the BPs of GaN and AlN is discussed using the Green's function method of Tersoff. We then show how to obtain the BPs for binary semiconductor alloys within a band-diagonal representation of the coherent potential approximation and apply this method to cubic AlGaN alloys. The resulting band offsets show good agreement to available experimental and theoretical data from the literature. Our results can be used to determine the band alignment in isovalent heterostructures involving pure cubic III-nitrides or AlGaN alloys for arbitrary concentrations.

  4. Photoelectron spectroscopy of aqueous solutions: streaming potentials of NaX (X = Cl, Br, and I) solutions and electron binding energies of liquid water and X-.

    Science.gov (United States)

    Kurahashi, Naoya; Karashima, Shutaro; Tang, Ying; Horio, Takuya; Abulimiti, Bumaliya; Suzuki, Yoshi-Ichi; Ogi, Yoshihiro; Oura, Masaki; Suzuki, Toshinori

    2014-05-07

    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.

  5. Identification of a better Homo sapiens Class II HDAC inhibitor through binding energy calculations and descriptor analysis.

    Science.gov (United States)

    Tambunan, Usman Sumo Friend; Wulandari, Evi Kristin

    2010-10-15

    Human papillomaviruses (HPVs) are the most common on sexually transmitted viruses in the world. HPVs are responsible for a large spectrum of deseases, both benign and malignant. The certain types of HPV are involved in the development of cervical cancer. In attemps to find additional drugs in the treatment of cervical cancer, inhibitors of the histone deacetylases (HDAC) have received much attention due to their low cytotoxic profiles and the E6/E7 oncogene function of human papilomavirus can be completely by passed by HDAC inhibition. The histone deacetylase inhibitors can induce growth arrest, differentiation and apoptosis of cancer cells. HDAC class I and class II are considered the main targets for cancer. Therefore, the six HDACs class II was modeled and about two inhibitors (SAHA and TSA) were docked using AutoDock4.2, to each of the inhibitor in order to identify the pharmacological properties. Based on the results of docking, SAHA and TSA were able to bind with zinc ion in HDACs models as a drug target. SAHA was satisfied almost all the properties i.e., binding affinity, the Drug-Likeness value and Drug Score with 70% oral bioavailability and the carbonyl group of these compound fits well into the active site of the target where the zinc is present. Hence, SAHA could be developed as potential inhibitors of class II HDACs and valuable cervical cancer drug candidate.

  6. Semiphenomenological approximation of the sums of experimental radiative strength functions for dipole gamma transitions of energy E γ below the neutron binding energy B n for mass numbers in the range 40 ≤ A ≤ 200

    Science.gov (United States)

    Sukhovoj, A. M.; Furman, W. I.; Khitrov, V. A.

    2008-06-01

    The sums of radiative strength functions for primary dipole gamma transitions, k( E1) + k( M1), are approximated to a high precision by a superposition of two functional dependences in the energy range 0.5 125Te, 128I, 137,138,139Ba, 140La, 150Sm, 156,158Gd, 160Tb, 163,164,165Dy, 166Ho, 168Er, 170Tm, 174Yb, 176,177Lu, 181Hf, 182Ta, 183,184,185,187W, 188,190,191,193Os, 192Ir, 196Pt, 198Au, and 200Hg nuclei. It is shown that, in any nuclei, radiative strength functions are a dynamical quantity and that the values of k( E1) + k( M1) for specific energies of gamma transitions and specific nuclei are determined by the structure of decaying and excited levels, at least up to the neutron binding energy B n .

  7. Daily energy balance in growth hormone receptor/binding protein (GHR−/−) gene-disrupted mice is achieved through an increase in dark-phase energy efficiency

    Science.gov (United States)

    Longo, Kenneth A.; Berryman, Darlene E.; Kelder, Bruce; Charoenthongtrakul, Soratree; DiStefano, Peter S.; Geddes, Brad J.; Kopchick, John

    2009-01-01

    The goal of this study was to examine factors that contribute to energy balance in female GHR −/− mice. We measured energy intake, energy expenditure (EE), fuel utilization, body mass (Mb) changes and physical activity in 17 month-old female GHR −/− mice and their age-matched wild type littermates. The GHR −/− mice were smaller, consumed more food per unit Mb, had greater EE per unit Mb and had an increase in 24-h EE/Mb that was similar to the increase in their surface-area-to-volume ratio. Locomotor activity (LMA) was reduced in the GHR −/− mice, but the energetic cost associated with their LMA was greater than in wild type controls. Furthermore, Mb and LMA were independent explanatory covariates of most of the variance in EE, and when adjusted for Mb and LMA, the GHR −/− mice had higher EE during both the light and dark phases of the daily cycle. Respiratory quotient was lower in GHR −/− mice during the light phase, which indicated a greater utilization of lipid relative to carbohydrate in these mice. Additionally, GHR −/− mice had higher ratios of caloric intake to EE at several intervals during the dark phase, and this effect was greater and more sustained in the final three hours of the dark phase. Therefore, we conclude that GHR −/− mice are able to overcome the substantial energetic challenges of dwarfism through several mechanisms that promote stable Mb. Relative to wild type mice, the GHR −/− mice consumed more calories per unit Mb, which offset the disproportionate increase in their daily energy expenditure. While GHR −/− mice oxidized a greater proportion of lipid during the light phase in order to meet their energy requirements, they achieved greater energy efficiency and storage during the dark phase through a combination of higher energy consumption and lower LMA. PMID:19747867

  8. Daily energy balance in growth hormone receptor/binding protein (GHR -/-) gene-disrupted mice is achieved through an increase in dark-phase energy efficiency.

    Science.gov (United States)

    Longo, Kenneth A; Berryman, Darlene E; Kelder, Bruce; Charoenthongtrakul, Soratree; Distefano, Peter S; Geddes, Brad J; Kopchick, John J

    2010-02-01

    The goal of this study was to examine factors that contribute to energy balance in female GHR -/- mice. We measured energy intake, energy expenditure (EE), fuel utilization, body mass (M(b)) changes and physical activity in 17month-old female GHR -/- mice and their age-matched wild type littermates. The GHR -/- mice were smaller, consumed more food per unit M(b), had greater EE per unit M(b) and had an increase in 24-h EE/M(b) that was similar to the increase in their surface-area-to-volume ratio. Locomotor activity (LMA) was reduced in the GHR -/- mice, but the energetic cost associated with their LMA was greater than in wild type controls. Furthermore, M(b) and LMA were independent explanatory covariates of most of the variance in EE, and when adjusted for M(b) and LMA, the GHR -/- mice had higher EE during both the light and dark phases of the daily cycle. Respiratory quotient was lower in GHR -/- mice during the light phase, which indicated a greater utilization of lipid relative to carbohydrate in these mice. Additionally, GHR -/- mice had higher ratios of caloric intake to EE at several intervals during the dark phase, and this effect was greater and more sustained in the final 3h of the dark phase. Therefore, we conclude that GHR -/- mice are able to overcome the substantial energetic challenges of dwarfism through several mechanisms that promote stable M(b). Relative to wild type mice, the GHR -/- mice consumed more calories per unit M(b), which offset the disproportionate increase in their daily energy expenditure. While GHR -/- mice oxidized a greater proportion of lipid during the light phase in order to meet their energy requirements, they achieved greater energy efficiency and storage during the dark phase through a combination of higher energy consumption and lower LMA. Copyright 2009 Elsevier Ltd. All rights reserved.

  9. Anderson localization in the multi-particle tight-binding model at low energies or with weak interaction

    CERN Document Server

    Ekanga, Trésor

    2012-01-01

    We consider the multi-particle lattice Anderson model with an i.i.d. random external potential and a short-range interaction. Using the multi-particle multiscale analysis (MPMSA) developed by Chulaevsky and Suhov (2009), we prove spectral localization for such Hamiltonians at low energies under the assumption of log-H\\"{o}lder continuity of the marginal probability distribution of the random potential. Under a stronger assumption of H\\"older continuity, Anderson localization for such systems at low energies was established earlier by Aizenman and Warzel (2009) with the help of the multi-particle Fractional-Moment Method.

  10. Changes in the zero point energy of the protons as the source of the binding energy of water to A phase DNA

    CERN Document Server

    Reiter, G F; Mayers, J

    2010-01-01

    The zero point kinetic energy of protons in water is large on the scale of chemical interaction energies(29 Kj/mol in bulk room temperature water). Its value depends upon the structure of the hydrogen bond network, and can change as the network is confined or as water interacts with surfaces. These changes have been observed to be large on a chemical scale for water confined in carbon nanotubes and in the pores of xerogel, and may play a fundamental, and neglected, role in biological processes involving confined water. We measure the average momentum distribution of the protons in salmon Na-DNA using Deep Inelastic Neutron Scattering, for a weakly hydrated (6w/bp) and a dehydrated fiber sample. This permits the determination of the change in total kinetic energy of the system per water molecule removed from the DNA and placed in the bulk liquid. This energy is equal, within errors, to the measured enthalpy for the same process, demonstrating that changes in the zero point motion of the protons, arising from c...

  11. Calcium Binding Restores Gel Formation of Succinylated Gelatin and Reduces Brittleness with Preservation of the Elastically Stored Energy.

    Science.gov (United States)

    Baigts Allende, Diana; de Jongh, Harmen H J

    2015-08-12

    To better tailor gelatins for textural characteristics in (food) gels, their interactions are destabilized by introduction of electrostatic repulsions and creation of affinity sites for calcium to "lock" intermolecular interactions. For that purpose gelatins with various degrees of succinylation are obtained. Extensive succinylation hampers helix formation and gel strength is slightly reduced. At high degrees of succinylation the helix propensity, gelling/melting temperatures, concomitant transition enthalpy, and gel strength become calcium-sensitive, and relatively low calcium concentrations largely restore these properties. Although succinylation has a major impact on the brittleness of the gels formed and the addition of calcium makes the material less brittle compared to nonmodified gelatin, the modification has no impact on the energy balance in the gel, where all energy applied is elastically stored in the material. This is explained by the unaffected stress relaxation by the network and high water-holding capacity related to the small mesh sizes in the gels.

  12. Nuclear recoil and vacuum-polarization effects on the binding energies of supercritical H-like ions

    CERN Document Server

    Aleksandrov, Ivan A; Shabaev, Vladimir M

    2015-01-01

    The Dirac Hamiltonian including nuclear recoil and vacuum-polarization operators is considered in a supercritical regime Z > 137. It is found that the nuclear recoil operator derived within the Breit approximation regularizes the Hamiltonian for the point-nucleus model and allows the ground state level to go continuously down and reach the negative energy continuum at a critical value Zcr = 145. If the Hamiltonian contains both the recoil operator and the Uehling potential, the 1s level reaches the negative energy continuum at Zcr = 144. The corresponding calculations for the excited states have been also performed. This study shows that, in contrast to previous investigations, a point-like nucleus can have effectively the charge Z > 137.

  13. Optimizing Binding Energies of Key Intermediates for CO2 Hydrogenation to Methanol over Oxide-Supported Copper.

    Science.gov (United States)

    Kattel, Shyam; Yan, Binhang; Yang, Yixiong; Chen, Jingguang G; Liu, Ping

    2016-09-28

    Rational optimization of catalytic performance has been one of the major challenges in catalysis. Here we report a bottom-up study on the ability of TiO2 and ZrO2 to optimize the CO2 conversion to methanol on Cu, using combined density functional theory (DFT) calculations, kinetic Monte Carlo (KMC) simulations, in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) measurements, and steady-state flow reactor tests. The theoretical results from DFT and KMC agree with in situ DRIFTS measurements, showing that both TiO2 and ZrO2 help to promote methanol synthesis on Cu via carboxyl intermediates and the reverse water-gas-shift (RWGS) pathway; the formate intermediates, on the other hand, likely act as a spectator eventually. The origin of the superior promoting effect of ZrO2 is associated with the fine-tuning capability of reduced Zr(3+) at the interface, being able to bind the key reaction intermediates, e.g. *CO2, *CO, *HCO, and *H2CO, moderately to facilitate methanol formation. This study demonstrates the importance of synergy between theory and experiments to elucidate the complex reaction mechanisms of CO2 hydrogenation for the realization of a better catalyst by design.

  14. Ammonium Additives to Dissolve Lithium Sulfide through Hydrogen Binding for High-Energy Lithium–Sulfur Batteries

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Huilin; Han, Kee Sung; Vijayakumar, M.; Xiao, Jie; Cao, Ruiguo; Chen, Junzheng; Zhang, Jiguang; Mueller, Karl T.; Shao, Yuyan; Liu, Jun

    2016-07-01

    In rechargeable Li-S batteries, the uncontrollable passivation of electrodes by highly insulating Li2S limits sulfur utilization, increases polarization and decreases cycling stability. Dissolving Li2S in organic electrolyte is a facile solution to maintain the active reaction interface between electrolyte and sulfur cathode, and thus address the above issues. Herein, ammonium salts are demonstrated as effective additives to promote the dissolution of Li2S to 1.25 M in DMSO solvent at room temperature. NMR measurements show that the strong hydrogen binding effect of N-H groups plays a critical role in dissolving Li2S by forming complex ligands with S2- anions coupled with the solvent’s solvating surrounding. Ammonium additives in electrolyte can also significantly improve the oxidation kinetics of Li2S, therefore enables the direct use of Li2S as cathode material in Li-S battery system in the future. This provides a new approach to manage the solubility of lithium sulfides through cation coordination with sulfide anion.

  15. Evaluation of energy spectral information in nuclear imaging and investigation of protein binding of cationic radionuclides by lactoferrin. Comprehensive progress report, October 1, 1977-September 30, 1980

    Energy Technology Data Exchange (ETDEWEB)

    Hoffer, P. B.

    1980-06-10

    Construction of an Anger camera-computer system which allows collection of both the position and energy signals from events detected by the scintillation camera has been completed. The system allows correction of energy response non-uniformity of the detector and facilitates research related to effects of energy discrimination in radionuclide scintigraphy. The system consists of electronic hardware to transmit and digitize the energy signal, software to record and process that signal in conjunction with spatial positioning signals, and additional hardware for recording the processed images so that they can be evaluated by observers. Preliminary results indicate that the system is useful in evaluating clinical images. Assymetric (eccentric) energy windows do improve image quality and are of value in improving detection of lesions on liver scintigraphs. The mechanisms by which Ga-67 is taken up in infection and tumor has been elucidated, and the uptake of radiogallium in microorganisms as a function of its interaction with siderophores was also studied. The primary function of these low molecular weight compounds is to trap ferric ion. However, gallium may be substituted for ferric ion and becomes trapped within the microorganism. The uptake of radiogallium by neutrophils and the role that lactoferrin plays in both intracellular localization of radiogallium and subsequent deposition of the radionuclide at sites of infection were also studied. Investigation of ferric ion analogs reveals definate differences in the affinity of these metals for binding molecules which helps explain their biologic activity. While ferric ion has the strongest affinity for such molecules, gallium has very high affinity for siderophores, moderate affinity for lactoferrin, and lower affinity for transferrin. The relative affinity of indium for these molecules is in approximately the reverse order.

  16. Application of fluorescence resonance energy transfer techniques to the study of lectin-binding site distribution on Paramecium primaurelia (Protista, Ciliophora) cell surface.

    Science.gov (United States)

    Locatelli, D; Delmonte Corrado, M U; Politi, H; Bottiroli, G

    1998-01-01

    Fluorescence resonance energy transfer (FRET) is a photophysical phenomenon occurring between the molecules of two fluorochromes with suitable spectral characteristics (donor-acceptor dye pair), and consisting in an excitation energy migration through a non-radiative process. Since the efficiency of the process is strictly dependent on the distance and reciprocal orientation of the donor and acceptor molecules, FRET-based techniques can be successfully applied to the study of biomolecules and cell component organisation and distribution. These techniques have been employed in studying Paramecium primaurelia surface membrane for the reciprocal distribution of N-acetylneuraminic acid (NeuAc) and N-acetylglucosamine (GlcNAc) glycosidic residues, which were found to be involved in mating cell pairing. NeuAc and GlcNAc were detected by their specific binding lectins, Limulus polyphemus agglutinin (LPA) and wheat germ agglutinin (WGA), respectively. Microspectrofluorometric analysis afforded the choice of fluorescein isothiocyanate and Texas red conjugated with LPA and WGA, respectively, as a suitable donor-acceptor couple efficiently activating FRET processes. Studies performed both in solution and in cells allowed to define the experimental conditions favourable for a FRET analysis. The comparative study carried out both on the conjugating-region and the non conjugating region of the surface membrane, indicates that FRET distribution appears quite homogeneous in mating-competent mating type (mt) I, whereas, in mating-competent mt II cells, FRET distribution seems to be preferentially localised on the conjugating-region functionally involved in mating cell pairing. This difference in the distribution of lectin-binding sites is suggested to be related to mating-competence acquisition.

  17. Computation of masses and binding energies of some hadrons and bosons according to the rotating lepton model and the relativistic Newton equation

    Science.gov (United States)

    Vayenas, C. G.; Fokas, A. S.; Grigoriou, D.

    2016-08-01

    We compute analytically the masses, binding energies and hamiltonians of gravitationally bound Bohr-type states via the rotating relativistic lepton model which utilizes the de Broglie wavelength equation in conjunction with special relativity and Newton's relativistic gravitational law. The latter uses the inertial-gravitational masses, rather than the rest masses, of the rotating particles. The model also accounts for the electrostatic charge- induced dipole interactions between a central charged lepton, which is usually a positron, with the rotating relativistic lepton ring. We use three rotating relativistic neutrinos to model baryons, two rotating relativistic neutrinos to model mesons, and a rotating relativistic electron neutrino - positron (or electron) pair to model the W± bosons. It is found that gravitationally bound ground states comprising three relativistic neutrinos have masses in the baryon mass range (∼⃒ 0.9 to 1 GeV/c2), while ground states comprising two neutrinos have masses in the meson mass range (∼⃒ 0.4 to 0.8 GeV/c2). It is also found that the rest mass values of quarks are in good agreement with the heaviest neutrino mass value of 0.05 eV/c2 and that the mass of W± bosons (∼⃒ 81 GeV/c2) corresponds to the mass of a rotating gravitationally confined e± — ve pair. A generalized expression is also derived for the gravitational potential energy of such relativistic Bohr-type structures.

  18. Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress

    Science.gov (United States)

    Tamarkin-Ben-Harush, Ana; Vasseur, Jean-Jacques; Debart, Françoise; Ulitsky, Igor; Dikstein, Rivka

    2017-01-01

    Transcription start-site (TSS) selection and alternative promoter (AP) usage contribute to gene expression complexity but little is known about their impact on translation. Here we performed TSS mapping of the translatome following energy stress. Assessing the contribution of cap-proximal TSS nucleotides, we found dramatic effect on translation only upon stress. As eIF4E levels were reduced, we determined its binding to capped-RNAs with different initiating nucleotides and found the lowest affinity to 5'cytidine in correlation with the translational stress-response. In addition, the number of differentially translated APs was elevated following stress. These include novel glucose starvation-induced downstream transcripts for the translation regulators eIF4A and Pabp, which are also translationally-induced despite general translational inhibition. The resultant eIF4A protein is N-terminally truncated and acts as eIF4A inhibitor. The induced Pabp isoform has shorter 5'UTR removing an auto-inhibitory element. Our findings uncovered several levels of coordination of transcription and translation responses to energy stress. DOI: http://dx.doi.org/10.7554/eLife.21907.001 PMID:28177284

  19. Can DFT and ab initio methods adequately describe binding energies in strongly interacting C6X6⋯C2Xn π-π complexes?

    Science.gov (United States)

    Vamhindi, Berthelot Saïd Duvalier Ramlina; Karton, Amir

    2017-08-01

    We calculate the CCSD(T)/CBS complexation energies of C6X6⋯C2Xn complexes (X = F, Cl; n = 2, 4) by means of the W1-F12 and CCSD(T)/MP2(CBS) procedures. These complexes involve π-π stacking, charge-transfer, and van der Waals interactions and their complexation energies range between 11.1 (C6F6⋯C2F2) and 34.0 (C6Cl6⋯C2Cl4) kJ mol-1. We use our best CCSD(T)/CBS data to assess the performance of DFT, double-hybrid DFT (DHDFT), and standard/composite ab initio methods. The G4 and G4(MP2) composite methods show relatively poor performance with root-mean-square deviations (RMSDs) of 8.7 and 6.3 kJ mol-1, respectively. With the main exception of the Minnesota functionals, DFT functionals without a dispersion correction do not predict binding in these complexes. Most of the conventional DFT procedures attain RMSDs above the 'chemical accuracy' threshold. The best performing functionals with RMSDs ≤2.0 kJ mol-1 are: B3LYP-D3, PW6B95-D3, LC-ωPBE-D3, PWPB95-D3, B2GP-PLYP-D3, and B2-PLYP-D3.

  20. The effect of dielectric constant on binding energy and impurity self-polarization in a GaAs-Ga1- x Al x As spherical quantum dot

    Science.gov (United States)

    Mese, A. I.; Cicek, E.; Erdogan, I.; Akankan, O.; Akbas, H.

    2017-03-01

    The ground state, 1s, and the excited state, 2p, energies of a hydrogenic impurity in a GaAs-Ga1- x Al x As spherical quantum dot, are computed as a function of the donor positions. We study how the impurity self-polarization depends on the location of the impurity and the dielectric constant. The excited state anomalous impurity self-polarization in the quantum dot is found to be present in the absence of any external influence and strongly depends on the impurity position and the radius of the dot. Therefore, the excited state anomalous impurity self-polarization can give information about the impurity position in the system. Also, the variation of E_{b1s} and E_{b2p} with the dielectric constant can be utilized as a tool for finding out the correct dielectric constant of the dot material by measuring the 1s or 2p state binding energy for a fixed dot radius and a fixed impurity position.

  1. Excitation energy transfer and charge separation are affected in Arabidopsis thaliana mutants lacking light-harvesting chlorophyll a/b binding protein Lhcb3.

    Science.gov (United States)

    Adamiec, Małgorzata; Gibasiewicz, Krzysztof; Luciński, Robert; Giera, Wojciech; Chełminiak, Przemysław; Szewczyk, Sebastian; Sipińska, Weronika; van Grondelle, Rienk; Jackowski, Grzegorz

    2015-12-01

    The composition of LHCII trimers as well as excitation energy transfer and charge separation in grana cores of Arabidopsis thaliana mutant lacking chlorophyll a/b binding protein Lhcb3 have been investigated and compared to those in wild-type plants. In grana cores of lhcb3 plants we observed increased amounts of Lhcb1 and Lhcb2 apoproteins per PSII core. The additional copies of Lhcb1 and Lhcb2 are expected to substitute for Lhcb3 in LHCII trimers M as well as in the LHCII "extra" pool, which was found to be modestly enlarged as a result of the absence of Lhcb3. Time-resolved fluorescence measurements reveal a deceleration of the fast phase of excitation dynamics in grana cores of the mutant by ~15 ps, whereas the average fluorescence lifetime is not significantly altered. Monte Carlo modeling predicts a slowing down of the mean hopping time and an increased stabilization of the primary charge separation in the mutant. Thus our data imply that absence of apoprotein Lhcb3 results in detectable differences in excitation energy transfer and charge separation.

  2. Energy

    CERN Document Server

    Foland, Andrew Dean

    2007-01-01

    Energy is the central concept of physics. Unable to be created or destroyed but transformable from one form to another, energy ultimately determines what is and isn''t possible in our universe. This book gives readers an appreciation for the limits of energy and the quantities of energy in the world around them. This fascinating book explores the major forms of energy: kinetic, potential, electrical, chemical, thermal, and nuclear.

  3. Insight into herbicide resistance of W574L mutant Arabidopsis thaliana acetohydroxyacid synthase:molecular dynamics simulations and binding free energy calculations

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Acetohydroxyacid synthase(AHAS) is the target enzyme of several classes of herbicides,such as sulfonylureas and imidazolinones.Now many mutant AHASs with herbicide resistance have emerged along with extensive use of herbicides,therefore it is imperative to understand the detailed interaction mechanism and resistance mechanism so as to develop new potent inhibitors for wild-type or resistant AHAS.With the aid of available crystal structures of the Arabidopsis thaliana(At) AHAS-inhibitor complex,molecular dynamics(MD) simulations were used to investigate the interaction and resistance mechanism directly and dynamically at the atomic level.Nanosecond-level MD simulations were performed on six systems consisting of wild-type or W574L mutant AtAHAS in the complex with three sulfonylurea inhibitors,separately,and binding free energy was calculated for each system using the MM-GBSA method.Comprehensive analyses from structural and energetic aspects confirmed the importance of residue W574,and also indicated that W574L mutation might alert the structural charactersistic of the substrate access channel and decrease the binding affinity of inhibitors,which cooperatively weaken the effective channel-blocked effect and finally result in weaker inhibitory effect of inhibitor and corresponding herbicide resistance of W574L mutant.To our knowledge,it is the first report about MD simulations study on the AHAS-related system,which will pave the way to study the interactions between herbicides and wild-type or mutant AHAS dynamically,and decipher the resistance mechanism at the atomic level for better designing new potent anti-resistance herbicides.

  4. Fluorescence Resonance Energy Transfer-based Structural Analysis of the Dihydropyridine Receptor α1S Subunit Reveals Conformational Differences Induced by Binding of the β1a Subunit*

    Science.gov (United States)

    Mahalingam, Mohana; Perez, Claudio F.; Fessenden, James D.

    2016-01-01

    The skeletal muscle dihydropyridine receptor α1S subunit plays a key role in skeletal muscle excitation-contraction coupling by sensing membrane voltage changes and then triggering intracellular calcium release. The cytoplasmic loops connecting four homologous α1S structural domains have diverse functions, but their structural arrangement is poorly understood. Here, we used a novel FRET-based method to characterize the relative proximity of these intracellular loops in α1S subunits expressed in intact cells. In dysgenic myotubes, energy transfer was observed from an N-terminal-fused YFP to a FRET acceptor, ReAsH (resorufin arsenical hairpin binder), targeted to each α1S intracellular loop, with the highest FRET efficiencies measured to the α1S II-III loop and C-terminal tail. However, in HEK-293T cells, FRET efficiencies from the α1S N terminus to the II-III and III-IV loops and the C-terminal tail were significantly lower, thus suggesting that these loop structures are influenced by the cellular microenvironment. The addition of the β1a dihydropyridine receptor subunit enhanced FRET to the II-III loop, thus indicating that β1a binding directly affects II-III loop conformation. This specific structural change required the C-terminal 36 amino acids of β1a, which are essential to support EC coupling. Direct FRET measurements between α1S and β1a confirmed that both wild type and truncated β1a bind similarly to α1S. These results provide new insights into the role of muscle-specific proteins on the structural arrangement of α1S intracellular loops and point to a new conformational effect of the β1a subunit in supporting skeletal muscle excitation-contraction coupling. PMID:27129199

  5. Fluorescence Resonance Energy Transfer-based Structural Analysis of the Dihydropyridine Receptor α1S Subunit Reveals Conformational Differences Induced by Binding of the β1a Subunit.

    Science.gov (United States)

    Mahalingam, Mohana; Perez, Claudio F; Fessenden, James D

    2016-06-24

    The skeletal muscle dihydropyridine receptor α1S subunit plays a key role in skeletal muscle excitation-contraction coupling by sensing membrane voltage changes and then triggering intracellular calcium release. The cytoplasmic loops connecting four homologous α1S structural domains have diverse functions, but their structural arrangement is poorly understood. Here, we used a novel FRET-based method to characterize the relative proximity of these intracellular loops in α1S subunits expressed in intact cells. In dysgenic myotubes, energy transfer was observed from an N-terminal-fused YFP to a FRET acceptor, ReAsH (resorufin arsenical hairpin binder), targeted to each α1S intracellular loop, with the highest FRET efficiencies measured to the α1S II-III loop and C-terminal tail. However, in HEK-293T cells, FRET efficiencies from the α1S N terminus to the II-III and III-IV loops and the C-terminal tail were significantly lower, thus suggesting that these loop structures are influenced by the cellular microenvironment. The addition of the β1a dihydropyridine receptor subunit enhanced FRET to the II-III loop, thus indicating that β1a binding directly affects II-III loop conformation. This specific structural change required the C-terminal 36 amino acids of β1a, which are essential to support EC coupling. Direct FRET measurements between α1S and β1a confirmed that both wild type and truncated β1a bind similarly to α1S These results provide new insights into the role of muscle-specific proteins on the structural arrangement of α1S intracellular loops and point to a new conformational effect of the β1a subunit in supporting skeletal muscle excitation-contraction coupling. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Identifying the Interaction of Vancomycin With Novel pH-Responsive Lipids as Antibacterial Biomaterials Via Accelerated Molecular Dynamics and Binding Free Energy Calculations.

    Science.gov (United States)

    Ahmed, Shaimaa; Vepuri, Suresh B; Jadhav, Mahantesh; Kalhapure, Rahul S; Govender, Thirumala

    2017-03-09

    Nano-drug delivery systems have proven to be an efficient formulation tool to overcome the challenges with current antibiotics therapy and resistance. A series of pH-responsive lipid molecules were designed and synthesized for future liposomal formulation as a nano-drug delivery system for vancomycin at the infection site. The structures of these lipids differ from each other in respect of hydrocarbon tails: Lipid1, 2, 3 and 4 have stearic, oleic, linoleic, and linolenic acid hydrocarbon chains, respectively. The impact of variation in the hydrocarbon chain in the lipid structure on drug encapsulation and release profile, as well as mode of drug interaction, was investigated using molecular modeling analyses. A wide range of computational tools, including accelerated molecular dynamics, normal molecular dynamics, binding free energy calculations and principle component analysis, were applied to provide comprehensive insight into the interaction landscape between vancomycin and the designed lipid molecules. Interestingly, both MM-GBSA and MM-PBSA binding affinity calculations using normal molecular dynamics and accelerated molecular dynamics trajectories showed a very consistent trend, where the order of binding affinity towards vancomycin was lipid4 > lipid1 > lipid2 > lipid3. From both normal molecular dynamics and accelerated molecular dynamics, the interaction of lipid3 with vancomycin is demonstrated to be the weakest (∆Gbinding = -2.17 and -11.57, for normal molecular dynamics and accelerated molecular dynamics, respectively) when compared to other complexes. We believe that the degree of unsaturation of the hydrocarbon chain in the lipid molecules may impact on the overall conformational behavior, interaction mode and encapsulation (wrapping) of the lipid molecules around the vancomycin molecule. This thorough computational analysis prior to the experimental investigation is a valuable approach to guide for predicting the encapsulation

  7. Microtremor measurements in the northern coast of İzmir Bay, Turkey to evaluate site-specific characteristics and fundamental periods by H/ V spectral ratio method

    Science.gov (United States)

    Eskişar, TuǦBA; Özyalin, Şenol; KuruoǦLU, Mehmet; Yilmaz, H. Recep

    2013-02-01

    Seventy-two microtremor measurements were conducted in the northern coast of İzmir Bay. The dataset has been processed using the horizontal-to-vertical spectral ratio. The fundamental period contour map obtained showed that the fundamental period at rock sites of the northern coast of İzmir Bay was between 0.15 and 0.35 s. However, the fundamental period increased towards the western direction where thick soft sediments exist, the fundamental period varied between 0.5 and 2.0 s. A soil classification map of the area was prepared based on the data estimated from SPT- N values of 25 boreholes. It is seen that major portion of the study area, including the shore line of the northern coast had SPT- N values lower than 15. The fundamental periods obtained by H/ V spectral ratio method and the periods derived from shear wave velocity data available in 11 of 25 boreholes were well-correlated. Fundamental period map obtained from H/ V spectral ratio method illustrated the characteristics of weak soil conditions and the presence of bedrock level under thick alluvial soils. Finally, microtremor investigations have proved to be an effective tool for assessment of local soil conditions in case of thick soft sediments in the northern coast of İzmir Bay.

  8. Microtremor measurements in the northern coast of İzmir Bay, Turkey to evaluate site-specific characteristics and fundamental periods by H/V spectral ratio method

    Indian Academy of Sciences (India)

    Tuğba Eskişar; Şenol Özyalin; Mehmet Kuruoğlu; H Recep Yilmaz

    2013-02-01

    Seventy-two microtremor measurements were conducted in the northern coast of İzmir Bay. The dataset has been processed using the horizontal-to-vertical spectral ratio. The fundamental period contour map obtained showed that the fundamental period at rock sites of the northern coast of İzmir Bay was between 0.15 and 0.35 s. However, the fundamental period increased towards the western direction where thick soft sediments exist, the fundamental period varied between 0.5 and 2.0 s. A soil classification map of the area was prepared based on the data estimated from SPT- values of 25 boreholes. It is seen that major portion of the study area, including the shore line of the northern coast had SPT- values lower than 15. The fundamental periods obtained by H/V spectral ratio method and the periods derived from shear wave velocity data available in 11 of 25 boreholes were well-correlated. Fundamental period map obtained from H/V spectral ratio method illustrated the characteristics of weak soil conditions and the presence of bedrock level under thick alluvial soils. Finally, microtremor investigations have proved to be an effective tool for assessment of local soil conditions in case of thick soft sediments in the northern coast of İzmir Bay.

  9. Soil characterization in urban areas of the Bajo Segura Basin (Southeast Spain) using H/V, F-K and ESAC methods

    Science.gov (United States)

    Rosa-Cintas, S.; Galiana-Merino, J. J.; Molina-Palacios, S.; Rosa-Herranz, J.; García-Fernández, M.; Jiménez, M. J.

    2011-11-01

    Bajo Segura Basin, placed in the south of Alicante province (southeast Spain), is a region of moderate seismicity, which presents frequent seismic episodes. This region, as the rest of south-eastern part of Spain, is growing both economically and demographically. Hence, the presence of soft soils in a seismic region where many towns and villages are placed shows the importance of an adequate characterization of the site effects study in this area. The present work investigates the use of noise measurements for soil characterization by the application of H/V method and array techniques: extended spatial autocorrelation (ESAC) and frequency-wave number (F-K) in three urban areas of the Bajo Segura Basin. The application of these methods will help us to estimate the resonance frequencies, as well as shear-wave velocity profiles, having a better understanding of the sediment depth and site effects phenomena at the studied places. The estimated velocity profiles are used to model the fundamental mode Rayleigh wave ellipticity curves and the S-wave site transfer functions. Finally, the correlation between this curves and the experimental H/V analysis has allowed us a better assessment of the site response in the studied areas.

  10. Theoretical and experimental study of the excitonic binding energy in GaAs/AlGaAs single and coupled double quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Lopes, E.M., E-mail: eldermantovani@yahoo.com.br [Departamento de Física, Química e Biologia, Universidade Estadual Paulista, C. P. 266, Presidente Prudente, São Paulo 17700-000 (Brazil); César, D.F. [Departamento de Física, Universidade Federal de São Carlos, C. P. 676, São Carlos, São Paulo (Brazil); Franchello, F.; Duarte, J.L.; Dias, I.F.L.; Laureto, E. [Departamento de Física, Universidade Estadual de Londrina, C. P. 6001, Londrina, Paraná (Brazil); Elias, D.C.; Pereira, M.V.M.; Guimarães, P.S.S. [Departamento de Física, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, C. P. 702, Belo Horizonte, Minas Gerais (Brazil); Quivy, A.A. [Laboratório de Novos Materiais Semicondutores, Instituto de Física, Universidade de São Paulo, C. P. 66318, São Paulo (Brazil)

    2013-12-15

    This paper discusses the theoretical and experimental results obtained for the excitonic binding energy (E{sub b}) in a set of single and coupled double quantum wells (SQWs and CDQWs) of GaAs/AlGaAs with different Al concentrations (Al%) and inter-well barrier thicknesses. To obtain the theoretical E{sub b} the method proposed by Mathieu, Lefebvre and Christol (MLC) was used, which is based on the idea of fractional-dimension space, together with the approach proposed by Zhao et al., which extends the MLC method for application in CDQWs. Through magnetophotoluminescence (MPL) measurements performed at 4 K with magnetic fields ranging from 0 T to 12 T, the diamagnetic shift curves were plotted and adjusted using two expressions: one appropriate to fit the curve in the range of low intensity fields and another for the range of high intensity fields, providing the experimental E{sub b} values. The effects of increasing the Al% and the inter-well barrier thickness on E{sub b} are discussed. The E{sub b} reduction when going from the SQW to the CDQW with 5 Å inter-well barrier is clearly observed experimentally for 35% Al concentration and this trend can be noticed even for concentrations as low as 25% and 15%, although the E{sub b} variations in these latter cases are within the error bars. As the Zhao's approach is unable to describe this effect, the wave functions and the probability densities for electrons and holes were calculated, allowing us to explain this effect as being due to a decrease in the spatial superposition of the wave functions caused by the thin inter-well barrier. -- Highlights: • Magnetophotoluminescence results from coupled double quantum wells are reported. • Theoretical and experimental values for excitonic binding energy (E{sub b}) are obtained. • The effects of increasing the inter-well barrier height and thickness on E{sub b} are discussed. • An E{sub b} reduction is observed when going from zero to the 5 Å inter-well barrier

  11. Energy

    CERN Document Server

    Robertson, William C

    2002-01-01

    Confounded by kinetic energy? Suspect that teaching about simple machines isn t really so simple? Exasperated by electricity? If you fear the study of energy is beyond you, this entertaining book will do more than introduce you to the topic. It will help you actually understand it. At the book s heart are easy-to-grasp explanations of energy basics work, kinetic energy, potential energy, and the transformation of energy and energy as it relates to simple machines, heat energy, temperature, and heat transfer. Irreverent author Bill Robertson suggests activities that bring the basic concepts of energy to life with common household objects. Each chapter ends with a summary and an applications section that uses practical examples such as roller coasters and home heating systems to explain energy transformations and convection cells. The final chapter brings together key concepts in an easy-to-grasp explanation of how electricity is generated. Energy is the second book in the Stop Faking It! series published by NS...

  12. The hydrostatic pressure and temperature effects on hydrogenic impurity binding energies in lattice matched InP/In0.53Ga0.47As/InP square quantum well

    Science.gov (United States)

    Başer, P.; Elagoz, S.

    2017-02-01

    The on-center shallow-donor impurity binding energy in lattice matched InP/In0.53Ga0.47As square quantum well structure have been theoretically investigated using effective mass and variational techniques. The effects of hydrostatic pressure, temperature and well width has been calculated and the results are discussed.

  13. The effects of polaronic mass and conduction band non-parabolicity on a donor binding energy under the simultaneous effect of pressure and temperature basing on the numerical FEM in a spherical quantum dot

    Science.gov (United States)

    Sali, A.; Kharbach, J.; Rezzouk, A.; Ouazzani Jamil, M.

    2017-04-01

    Basing on the numerical Finite Element Method (FEM), we have investigated the influences of polaronic mass and conduction band non-parabolicity on the binding energy of the ground state of an on-center hydrogenic donor impurity in a spherical GaAs / Ga1 - x AlxAs quantum dot structure. The calculations have been made with a realistic potential barrier height in the framework of the effective mass approximation including the combined effect of hydrostatic pressure and temperature. The donor binding energy is computed as a function of dot size, Al concentration x , hydrostatic pressure and temperature both in the absence and presence of polaronic mass and conduction band non-parabolicity effects. We have taken into account the electronic effective mass, dielectric constant, and conduction band offset between the dot and barriers varying with pressure and temperature. It has been found that the binding energy is strongly affected by the effect of polaronic mass and conduction band non-parabolicity for narrow quantum dot and large Al concentration x. The results show again that the donor binding energy increases linearly with the pressure in direct gap regime and its variation is larger for narrower dots only and drops slightly with the temperature. A good agreement is obtained with the existing literature values.

  14. Thermodynamics of fragment binding.

    Science.gov (United States)

    Ferenczy, György G; Keserű, György M

    2012-04-23

    The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.

  15. Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: importance of mutation-induced structural change.

    Science.gov (United States)

    Anzaki, Satoshi; Watanabe, Chiduru; Fukuzawa, Kaori; Mochizuki, Yuji; Tanaka, Shigenori

    2014-09-01

    On the basis of available molecular structures registered in Protein Data Bank, we have theoretically carried out the interaction energy analysis for the complexes of influenza virus hemagglutinin (HA) proteins and sialosaccharide receptor analogs of host cells. Employing the fragment molecular orbital method for quantum-chemical calculations, the differences in magnitude and pattern of the interactions between the amino acid residues of avian-type (H7N3) or human-type (H7N9) HA and each saccharide part of avian or human receptor were studied in order to elucidate the molecular mechanism of avian-to-human infectious transmission of influenza virus. We have thus confirmed quantitatively that the mutations from the avian HA to the human HA significantly strengthened the binding affinity of human HA to human receptor, while retaining the affinity to avian receptor. In addition to direct effects regarding the changes of interactions between the altered residues and the receptors, we have also found the importance of indirect effects in which structural changes caused by the mutations play vital roles to modify the intermolecular interactions. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Breaking the bottleneck: Use of molecular tailoring approach for the estimation of binding energies at MP2/CBS limit for large water clusters

    Science.gov (United States)

    Singh, Gurmeet; Nandi, Apurba; Gadre, Shridhar R.

    2016-03-01

    A pragmatic method based on the molecular tailoring approach (MTA) for estimating the complete basis set (CBS) limit at Møller-Plesset second order perturbation (MP2) theory accurately for large molecular clusters with limited computational resources is developed. It is applied to water clusters, (H2O)n (n = 7, 8, 10, 16, 17, and 25) optimized employing aug-cc-pVDZ (aVDZ) basis-set. Binding energies (BEs) of these clusters are estimated at the MP2/aug-cc-pVNZ (aVNZ) [N = T, Q, and 5 (whenever possible)] levels of theory employing grafted MTA (GMTA) methodology and are found to lie within 0.2 kcal/mol of the corresponding full calculation MP2 BE, wherever available. The results are extrapolated to CBS limit using a three point formula. The GMTA-MP2 calculations are feasible on off-the-shelf hardware and show around 50%-65% saving of computational time. The methodology has a potential for application to molecular clusters containing ˜100 atoms.

  17. Performance of the TPSS Functional on Predicting Core Level Binding Energies of Main Group Elements Containing Molecules: A Good Choice for Molecules Adsorbed on Metal Surfaces.

    Science.gov (United States)

    Pueyo Bellafont, Noèlia; Viñes, Francesc; Illas, Francesc

    2016-01-12

    Here we explored the performance of Hartree-Fock (HF), Perdew-Burke-Ernzerhof (PBE), and Tao-Perdew-Staroverov-Scuseria (TPSS) functionals in predicting core level 1s binding energies (BEs) and BE shifts (ΔBEs) for a large set of 68 molecules containing a wide variety of functional groups for main group elements B → F and considering up to 185 core levels. A statistical analysis comparing with X-ray photoelectron spectroscopy (XPS) experiments shows that BEs estimations are very accurate, TPSS exhibiting the best performance. Considering ΔBEs, the three methods yield very similar and excellent results, with mean absolute deviations of ∼0.25 eV. When considering relativistic effects, BEs deviations drop approaching experimental values. So, the largest mean percentage deviation is of 0.25% only. Linear trends among experimental and estimated values have been found, gaining offsets with respect to ideality. By adding relativistic effects to offsets, HF and TPSS methods underestimate experimental values by solely 0.11 and 0.05 eV, respectively, well within XPS chemical precision. TPSS is posed as an excellent choice for the characterization, by XPS, of molecules on metal solid substrates, given its suitability in describing metal substrates bonds and atomic and/or molecular orbitals.

  18. Application of the H/V and SPAC Method to Estimate a 3D Shear Wave Velocity Model, in the City of Coatzacoalcos, Veracruz.

    Science.gov (United States)

    Morales, L. E. A. P.; Aguirre, J.; Vazquez Rosas, R.; Suarez, G.; Contreras Ruiz-Esparza, M. G.; Farraz, I.

    2014-12-01

    Methods that use seismic noise or microtremors have become very useful tools worldwide due to its low costs, the relative simplicity in collecting data, the fact that these are non-invasive methods hence there is no need to alter or even perforate the study site, and also these methods require a relatively simple analysis procedure. Nevertheless the geological structures estimated by this methods are assumed to be parallel, isotropic and homogeneous layers. Consequently precision of the estimated structure is lower than that from conventional seismic methods. In the light of these facts this study aimed towards searching a new way to interpret the results obtained from seismic noise methods. In this study, seven triangular SPAC (Aki, 1957) arrays were performed in the city of Coatzacoalcos, Veracruz, varying in sizes from 10 to 100 meters. From the autocorrelation between the stations of each array, a Rayleigh wave phase velocity dispersion curve was calculated. Such dispersion curve was used to obtain a S wave parallel layers velocity (VS) structure for the study site. Subsequently the horizontal to vertical ratio of the spectrum of microtremors H/V (Nogoshi and Igarashi, 1971; Nakamura, 1989, 2000) was calculated for each vertex of the SPAC triangular arrays, and from the H/V spectrum the fundamental frequency was estimated for each vertex. By using the H/V spectral ratio curves interpreted as a proxy to the Rayleigh wave ellipticity curve, a series of VS structures were inverted for each vertex of the SPAC array. Lastly each VS structure was employed to calculate a 3D velocity model, in which the exploration depth was approximately 100 meters, and had a velocity range in between 206 (m/s) to 920 (m/s). The 3D model revealed a thinning of the low velocity layers. This proved to be in good agreement with the variation of the fundamental frequencies observed at each vertex. With the previous kind of analysis a preliminary model can be obtained as a first

  19. Core-level spectra and binding energies of transition metal nitrides by non-destructive x-ray photoelectron spectroscopy through capping layers

    Science.gov (United States)

    Greczynski, G.; Primetzhofer, D.; Lu, J.; Hultman, L.

    2017-02-01

    We present the first measurements of x-ray photoelectron spectroscopy (XPS) core level binding energies (BE:s) for the widely-applicable group IVb-VIb polycrystalline transition metal nitrides (TMN's) TiN, VN, CrN, ZrN, NbN, MoN, HfN, TaN, and WN as well as AlN and SiN, which are common components in the TMN-based alloy systems. Nitride thin film samples were grown at 400 °C by reactive dc magnetron sputtering from elemental targets in Ar/N2 atmosphere. For XPS measurements, layers are either (i) Ar+ ion-etched to remove surface oxides resulting from the air exposure during sample transfer from the growth chamber into the XPS system, or (ii) in situ capped with a few nm thick Cr or W overlayers in the deposition system prior to air-exposure and loading into the XPS instrument. Film elemental composition and phase content is thoroughly characterized with time-of-flight elastic recoil detection analysis (ToF-E ERDA), Rutherford backscattering spectrometry (RBS), and x-ray diffraction. High energy resolution core level XPS spectra acquired with monochromatic Al Kα radiation on the ISO-calibrated instrument reveal that even mild etching conditions result in the formation of a nitrogen-deficient surface layer that substantially affects the extracted binding energy values. These spectra-modifying effects of Ar+ ion bombardment increase with increasing the metal atom mass due to an increasing nitrogen-to-metal sputter yield ratio. The superior quality of the XPS spectra obtained in a non-destructive way from capped TMN films is evident from that numerous metal peaks, including Ti 2p, V 2p, Zr 3d, and Hf 4f, exhibit pronounced satellite features, in agreement with previously published spectra from layers grown and analyzed in situ. In addition, the N/metal concentration ratios are found to be 25-90% higher than those obtained from the corresponding ion-etched surfaces, and in most cases agree very well with the RBS and ToF-E ERDA values. The N 1 s BE:s extracted from

  20. Using thermodynamic integration MD simulation to compute relative protein-ligand binding free energy of a GSK3β kinase inhibitor and its analogs.

    Science.gov (United States)

    Lee, Hsing-Chou; Hsu, Wen-Chi; Liu, An-Lun; Hsu, Chia-Jen; Sun, Ying-Chieh

    2014-06-01

    Thermodynamic integration molecular dynamics simulation was used to investigate how TI-MD simulation preforms in reproducing relative protein-ligand binding free energy of a pair of analogous GSK3β kinase inhibitors of available experimental data (see Fig. 1), and to predict the affinity for other analogs. The computation for the pair gave a ΔΔG of 1.0 kcal/mol, which was in reasonably good agreement with the experimental value of -0.1 kcal/mol. The error bar was estimated at 0.5 kcal/mol. Subsequently, we employed the same protocol to proceed with simulations to find analogous inhibitors with a stronger affinity. Four analogs with a substitution at one site inside the binding pocket were the first to be tried, but no significant enhancement in affinity was found. Subsequent simulations for another 7 analogs was focused on substitutions at the benzene ring of another site, which gave two analogs (analogs 9 and 10) with ΔΔG values of -0.6 and -0.8 kcal/mol, respectively. Both analogs had a OH group at the meta position and another OH group at the ortho position at the other side of the benzene ring, as shown in Table 3. To explore further, another 4 analogs with this characteristic were investigated. Three analogs with ΔΔG values of -2.2, -1.7 and -1.2 kcal/mol, respectively, were found. Hydrogen bond analysis suggested that the additional hydrogen bonds of the added OH groups with Gln185 and/or Asn64, which did not appear in the reference inhibitor or as an analog with one substitution only in the examined cases, were the main contributors to an enhanced affinity. A prediction for better inhibitors should interest experimentalists of enzyme and/or cell assays. Analysis of the interactions between GSK3β kinase and the investigated analogs will be useful in the design of GSK3β kinase inhibitors for compounds of this class. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Evaluation of local site effect in the western side of the Suez Canal area by applying H/V and MASW techniques

    Science.gov (United States)

    Mohamed, Emad K.; Shokry, M. M. F.; Hassoup, Awad; Helal, A. M. A.

    2016-11-01

    The soft sediments are one of the most important factors responsible for the amplification of the seismic ground motion in an area of study. Three components, single-station microtremor measurements were performed at 61 sites along the Suez Canal to estimate the fundamental frequencies of the soil and corresponding H/V amplitude ratios by using the horizontal-to-vertical spectral ratio (HVSR) method. We have applied the investigations of the shear wave velocity for supplementing the existing seismic microzonation of the Suez Canal. The multichannel analysis of surface wave (MASW) tests were done along the Suez Canal in the three cities, Suez, Ismailia, and Port Said using 24 channels digital engineering seismograph with 4.5 Hz geophones from September 2014 to January 2015 to get the shear wave velocity VS30. The SeisImager/SW software was used for analyzing the data, and 1D-shear wave velocity model have achieved for each site. The HVSR curves show that the fundamental frequency values are ranging from 0.57 to 1.08 Hz, and H/V amplitude ratios are ranging from 4.05 to 6.46. The average values of VS30 are (548, 301), (241, 319), (194, 110, 238) for Suez, Ismailia, and Port Said respectively. The average of shear wave velocity up to 30 m depth is estimated and used for site classification based on the National Earthquake Hazard Reduction Program (NEHRP) classification. The majority of the sites was classified as Class D (stiff soil) except one site at Port Said city is classified as Class E (soft soils), and another site in the Suez city is classified as Class C (hard rock).

  2. He-He-Ba三原子体系弱束缚态计算∗%Calculations of the binding energies of weakly b ound He-He-Ba molecules

    Institute of Scientific and Technical Information of China (English)

    勾庆东; 李勇

    2015-01-01

    The three-body Schrödinger equation is approximately solved in the hyperspherical coordinates and the binding energies of the three-body weakly bound systems are calculated with the purpose to find if He-He-Ba trimers could exist. Using the special feature of the B-spline function like the flexible and highly localized properties, hypersphercial potentials are obtained by modifying the knots distribution of the B-spline basis of different weakly bound three-atom systems. Employing the best empirical interaction potentials between each pair of particles, we obtain that in the ground state binding energies of the weakly bound typical three-atom systems, the bindings of the molecules, 4He-4He-138Ba, 4He-3He-138Ba and 3He-3He-138Ba are possible. The binding energies of these systems are shown in the order of 1 Kelvin, each system could support only one bound state. These weakly bound molecules can exist only in a very cold environment. To get insight into the geometry of the molecules, the features of the channel functions associated with the hyperspherical potential curves of each system are investigated.

  3. 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.

  4. Follicle-stimulating hormone encapsulation in the cholesterol-modified chitosan nanoparticles via molecular dynamics simulations and binding free energy calculations.

    Science.gov (United States)

    Yahyaei, Mohammad; Mehrnejad, Faramarz; Naderi-Manesh, Hossein; Rezayan, Ali Hossein

    2017-09-30

    Follicle-stimulating hormone (FSH) is widely applied in the modern ovarian stimulation techniques. However, it must be administered daily because of its short half-life. Recently, the cholesterol (CS) modified chitosan (CTS) nanogels have attracted significant interest as promising controlled release protein delivery because of their ability to minimize the aggregation and irreversible denaturation of proteins. Herein, we report a molecular dynamics (MD) simulation investigation on the molecular mechanisms of FSH encapsulation in the CS-CTS nanogels. The MD simulations have been performed using the GROMACS software for up to 200ns simulation time. Furthermore, the binding free energy has been calculated by the molecular mechanics [MM] with Poisson-Boltzmann [PB] and surface area solvation (MM/PBSA) method by using the g_mmpbsa tool. Our findings suggest that the main driving force of the formation of the CS-CTS nanogels is the hydrophobic interactions between the CS-CS moieties in water. The results have also indicated that the CS-CTS nanogel formation can occur through the hydrogen bonding in addition to the hydrophobic interactions. The obtained data demonstrate that the FSH encapsulation into the CS-CTS nanogels is a gradual process driven by the hydrophobic interactions between the hydrophobic patch of FSH and the hydrophobic nanodomains of the nanogel. Our results also reveal that except in the hydrophobic patch region, the flexibility of FSH was reduced in the presence of the nanogel. This study provides the elucidation of the nanogel-FSH interactions at the molecular level and presents new perspective for the ideal design and applications of the CS-CTS nanogel in protein delivery. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Energy

    Science.gov (United States)

    2003-01-01

    Canada, Britain, and Spain. We found that the energy industry is not in crisis ; however, U.S. government policies, laws, dollars, and even public...CEIMAT (Centro de Investagaciones Energeticas , Medioambeintales y Tecnologicas) Research and development Page 3 of 28ENERGY 8/10/04http://www.ndu.edu...meet an emerging national crisis (war), emergency (natural disaster), or major impact event (Y2K). Certain resources are generally critical to the

  6. Atomistic tight-binding theory of excitonic splitting energies in CdX(X = Se, S and Te)/ZnS core/shell nanocrystals

    Science.gov (United States)

    Sukkabot, Worasak; Pinsook, Udomsilp

    2017-01-01

    Using the atomistic tight-binding theory (TB) and a configuration interaction description (CI), we numerically compute the excitonic splitting of CdX(X = Se, S and Te)/ZnS core/shell nanocrystals with the objective to explain how types of the core materials and growth shell thickness can provide the detailed manipulation of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting, beneficial for the active application of quantum information. To analyze the splitting of the excitonic states, the optical band gaps, ground-state wave function overlaps and atomistic electron-hole interactions tend to be numerically demonstrated. Based on the atomistic computations, the single-particle and excitonic gaps are mainly reduced with the increasing ZnS shell thickness owing to the quantum confinement. In the range of the higher to lower energies, the order of the single-particle gaps is CdSe/ZnS, CdS/ZnS and CdTe/ZnS core/shell nanocrystals, while one of the excitonic gaps is CdS/ZnS, CdSe/ZnS and CdTe/ZnS core/shell nanocrystals because of the atomistic electron-hole interaction. The strongest electron-hole interactions are mainly observed in CdSe/ZnS core/shell nanocrystals. In addition, the computational results underline that the energies of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting are generally reduced with the increasing ZnS growth shell thickness as described by the trend of the electron-hole exchange interaction. The high-to-low splitting of the excitonic states is demonstrated in CdSe/ZnS, CdTe/ZnS and CdS/ZnS core/shell nanocrystals because of the fashion in the electron-hole exchange interaction and overlaps of the electron-hole wave functions. As the resulting calculations, it is expected that CdS/ZnS core/shell nanocrystals are the best candidates to be the source of entangled photons. Finally, the comprehensive information on the excitonic splitting can enable the use of suitable core

  7. 3D model of Campo de Dalías basement from H/V spectral ratio of ambient seismic noise

    Science.gov (United States)

    García-Jerez, Antonio; Seivane, Helena; Luzón, Francisco; Navarro, Manuel; Molina, Luis; Aranda, Carolina; Piña-Flores, José; Navarro, Francisco; Sánchez-Martos, Francisco; Vidal, Francisco; Posadas, Antonio M.; Sánchez-Sesma, Francisco J.

    2017-04-01

    Campo de Dalías is a large coastal plain in the southeastern mountain front of the Betic Cordillera (SE of the Iberian Peninsula), being one of the most seismically active regions of Spain. This area has a population of about 213.000 inhabitants, with a high growth rate during the last decades due to the development of intensive agricultural activities. Seismic risk assessment and hydrogeological issues are major topics of interest for this area, relaying on the knowledge of the geophysical properties of the basin. A passive seismic survey has been conducted throughout the basin. We have recorded ambient noise at 340 sites located approximately on the vertexes of a 1000 x 1000 m square grid, as well as around a set of deep boreholes reaching the Triassic basement. These broad-band records, of at least 45 minutes long each, have been analyzed by using the horizontal-to-vertical spectral ratio method (H/V). The spectral analysis shows clear H/V peaks with periods ranging from 0.3 s to 4 s, approximately, associated to relevant contrasts in S-wave velocity (Vs) at depth. Simulations based on the diffuse field approach (Sánchez-Sesma et al. 2011) show that long periods are explained by the effect of several hundred meters of soft sedimentary rocks (mainly Miocene marls). Well-developed high-frequency secondary peaks have been found in some specific zones (e.g. N of Roquetas de Mar town). Then, fundamental frequencies and basement depths at borehole sites have been fitted by means of a power law, which can be applied down to 900 - 970m. Larger depths are estimated by extrapolation. This relationship has been used to map the basement (main Vs contrast) throughout the plain. The prospected basement model describes well the main structural features of this smoothly folded region, namely, the El Ejido Synform and the Guardias Viejas Antiform, with ENE-WSW-trend. These features are shifted toward the south in comparison with Pedrera et al. (2015). The homogeneous

  8. The effect of gap in n(k, ρ) on the single-particle properties of nucleons and the ground-state binding energy of closed-shell nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Mariji, H. [University of Coimbra, Centro de Fisica Computacional, Department of Physics, Coimbra (Portugal)

    2016-04-15

    The present work evaluates the effect of gap in the density-dependent one-body momentum distribution, n(k, ρ), at the Fermi surface on the calculation of the single-particle properties of nucleons, i.e., the momentum- and density-dependent single-particle potential and the nucleon effective mass, and also on the calculation of the ground-state binding energy of the selected closed-shell nuclei, i.e., {sup 16}O, {sup 40}Ca, and {sup 56}Ni. In order to do this, n(k, ρ) is constructed by use of the calculations of the lowest-order constrained variational method for the symmetric nuclear matter with the Av{sub 18} potential up to J{sub max} = 2 and 5. It is shown that the gap in n(k, ρ) at the Fermi surface has no significant effect on the calculation of single-particle properties in the case of J{sub max} = 5. In the relevant evaluation of the ground-state binding energy of selected nuclei, it is seen that the binding energy of {sup 16}O, improved by including n(k, ρ), is closer to the experimental data, contrary to {sup 40}Ca and {sup 56}Ni. (orig.)

  9. The effects of the electric and intense laser field on the binding energies of donor impurity states (1s and 2p±) and optical absorption between the related states in an asymmetric parabolic quantum well

    Science.gov (United States)

    Kasapoglu, E.; Sakiroglu, S.; Sökmen, I.; Restrepo, R. L.; Mora-Ramos, M. E.; Duque, C. A.

    2016-10-01

    We have calculated the effects of electric and intense laser fields on the binding energies of the ground and some excited states of conduction electrons coupled to shallow donor impurities as well as the total optical absorption coefficient for transitions between 1s and 2p± electron-impurity states in a asymmetric parabolic GaAs/Ga1-x AlxAs quantum well. The binding energies were obtained using the effective-mass approximation within a variational scheme. Total absorption coefficient (linear and nonlinear absorption coefficient) for the transitions between any two impurity states were calculated from first- and third-order dielectric susceptibilities derived within a perturbation expansion for the density matrix formalism. Our results show that the effects of the electric field, intense laser field, and the impurity location on the binding energy of 1s-impurity state are more pronounced compared with other impurity states. If the well center is changed to be Lc0), the effective well width decreases (increases), and thus we can obtain the red or blue shift in the resonant peak position of the absorption coefficient by changing the intensities of the electric and non-resonant intense laser field as well as dimensions of the well and impurity positions.

  10. IgH-V(D)J NGS-MRD measurement pre- and early post-allotransplant defines very low- and very high-risk ALL patients.

    Science.gov (United States)

    Pulsipher, Michael A; Carlson, Chris; Langholz, Bryan; Wall, Donna A; Schultz, Kirk R; Bunin, Nancy; Kirsch, Ilan; Gastier-Foster, Julie M; Borowitz, Michael; Desmarais, Cindy; Williamson, David; Kalos, Michael; Grupp, Stephan A

    2015-05-28

    Positive detection of minimal residual disease (MRD) by multichannel flow cytometry (MFC) prior to hematopoietic cell transplantation (HCT) of patients with acute lymphoblastic leukemia (ALL) identifies patients at high risk for relapse, but many pre-HCT MFC-MRD negative patients also relapse, and the predictive power MFC-MRD early post-HCT is poor. To test whether the increased sensitivity of next-generation sequencing (NGS)-MRD better identifies pre- and post-HCT relapse risk, we performed immunoglobulin heavy chain (IgH) variable, diversity, and joining (V[D]J) DNA sequences J NGS-MRD on 56 patients with B-cell ALL enrolled in Children's Oncology Group trial ASCT0431. NGS-MRD predicted relapse and survival more accurately than MFC-MRD (P NGS-MRD detection was better at predicting relapse than MFC-MRD (P NGS-MRD positive relapse rate, 67%; P = .004). Any post-HCT NGS positivity resulted in an increase in relapse risk by multivariate analysis (hazard ratio, 7.7; P = .05). Absence of detectable IgH-V(D)J NGS-MRD pre-HCT defines good-risk patients potentially eligible for less intense treatment approaches. Post-HCT NGS-MRD is highly predictive of relapse and survival, suggesting a role for this technique in defining patients early who would be eligible for post-HCT interventions. The trial was registered at www.clinicaltrials.gov as #NCT00382109.

  11. Localization-enhanced biexciton binding in semiconductors

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher

    1999-01-01

    The influence of excitonic localization on the binding energy of biexcitons is investigated for quasi-three-dimensional and quasi-two-dimensional AlxGa1-xAs structures. An increase of the biexciton binding energy is observed for localization energies comparable to or larger than the free biexcito...

  12. REEVALUATION OF EXISTING GROUND STRUCTURE MODEL GAINED THROUGH MICROTREMOR ARRAY METHOD BY USING FUNDAMENTAL PROPERTIES OF MODEL SURVEIED THROUGH H/V SPECTRUM - ON GROUND STRUCTURE OF FUKUI PLAIN -

    Science.gov (United States)

    Yasui, Yuzuru; Hashimoto, Yuichi; Noguchi, Tatsuya; Kagawa, Takao

    In order to reduce discrepancies between ground models based on the microtremor array observation in Fukui Plain and models by the H/V survey method and gravity analysis, the existing array ground models were reevaluated. The representative of the dispersion curves was selected so as to fit a theoretical fundamental mode dispersion curve of the H/V ground model. By using the method of selection, a reasonable reevaluation became possible. As a result the correspondences among the three models were much improved as a whole, but in the edge site of the Plain the differences against the gravity model are not reduced.

  13. Infinite-basis calculations of binding energies for the hydrogen bonded and stacked tetramers of formic acid and formamide and their use for validation of hybrid DFT and ab initio methods.

    Science.gov (United States)

    Zhao, Yan; Truhlar, Donald G

    2005-08-04

    Benchmark stabilization energies for planar H-bonded and stacked structures of formic acid tetramers and formamide tetramers were determined as the sum of the infinite basis set limit of MP2 energies and a CCSD(T) correction term evaluated with the 6-31G*(0.25) basis set. The infinite basis (IB) set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and separate extrapolation of the Hartree-Fock and correlation energies with new IB parameters for augmented basis sets determined here. Final stabilization energies (kcal/mol) for the tetramer studied are in the range of 4.6 to approximately 6.7 kcal/mol and they were used as reference data to test 14 density functionals. Among the tested DFT methods, PWB6K gives the best performance with an average error equal to only 30% of the average binding energy. In contrast, the popular B3LYP functional has an average error of 85%. We recommend the PWB6K method for exploring the potential energy surfaces of organic complexes and clusters and supramolecular assemblies.

  14. 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)

    LuXin

    2001-01-01

    [1]Onganer, Y., Saglam, M., Turut, A. et al., High barrier metallic polymer p-type silicon Schottky diodes, Solid State Electron, 1996, 39: 677.[2]Lonergan, M. C., A tunable diode based on an inorganic semiconductor vertical bar conjugated polymer interface, Science,1997, 278: 2103.[3]Wolkow, R. A., Moffatt, D. J., The frustrated motion of benzene on the surface of Si(l11), J. Chem. Phys., 1995,103: 10696.[4]MacPherson, C. D., Leung, K. T., Electron-induced chemistry of pyridine on Si(l 11)7x7 An LEED and TDS study,Surf. Sci., 1995, 324: 202.[5]MacPherson, C. D., Hu, D. Q., Leung, K. T., Room-temperature adsorption of thiophene and related 5-membered cyclicolefins on Si( 111)7x7 by thermal-desorption spectrometry, Surf. Sci., 1992, 276:156.[6]Cao, Y.. Wang, Z., Deng, J. F. et al., Evidence for dangling bond mediated dimerization of furan on the silicon (111 )-(7x7) surface, Angew Chem. Int. Ed., 2000, 39: 2740-2743.[7]Cao, Y., Yong, K. S., Wang, Z. Q. et al., Dry thienylation of the silicon (111)-(7x7) surface, J. Am. Chem. Soc., 2000, 112:1812.[8]Taguchi, Y., Fujisawa, M., Takaoka, T. et al., Adsorbed state of benzene on the Si(100) surface-thermal-desorption and electron-energy loss spectroscopy studies, J. Chem. Phys., 1991,95: 6870.[9]Lopinski, G. P., Fortier, T M., Moffatt, D. J. et al., Multiple bonding geometries and binding state conversion of benzene/Si(100), J. Vac. Sci. Technol., 1998, Al6: 1037.[10]Ellison, M. D., Hamers, R. J., Reactions of substituted aromatic hydrocarbons with the Si(001) surface, J. Vac. Sci.Technol., 2000, Al8: 1965.[11]Qiao, M. H., Cao, Y., Deng, J. F. et al, Formation of covalent Si-N linkages on pyrrole functionalized Si(100)-(2×l),Chem. Phys. Lett., 2000, 325: 508.[12]Konecny, R., Doren, D. J., Cycloaddition reactions of unsaturated hydrocarbons on the Si(100)-(2×1) surface: theoretical predictions, Surf. Sci., 1998, 417: 169.[13]Birkenheuer, U., Gutdeutsch, U., Rosch, N

  15. Threshold collision-induced dissociation of hydrated magnesium: experimental and theoretical investigation of the binding energies for Mg(2+)(H2O)x complexes (x=2-10).

    Science.gov (United States)

    Carl, Damon R; Armentrout, Peter B

    2013-03-18

    The sequential bond energies of Mg(2+)(H2O)x complexes, in which x=2-10, are measured by threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer. From an electrospray ionization source that produces an initial distribution of Mg(2+)(H2O)x complexes in which x=7-10, complexes down to x=3 are formed by using an in-source fragmentation technique. Complexes smaller than Mg(2+)(H2O)3 cannot be formed in this source because charge separation into MgOH(+)(H2O) and H3O(+) is a lower-energy pathway than simple water loss from Mg(2+)(H2O)3. The kinetic energy dependent cross sections for dissociation of Mg(2+)(H2O)x complexes, in which x=3-10, are examined over a wide energy range to monitor all dissociation products and are modeled to obtain 0 and 298 K binding energies. Analysis of both primary and secondary water molecule losses from each sized complex provides thermochemistry for the sequential hydration energies of Mg(2+) for x=2-10 and the first experimental values for x=2-4. Additionally, the thermodynamic onsets leading to the charge-separation products from Mg(2+)(H2O)3 and Mg(2+)(H2O)4 are determined for the first time. Our experimental results for x=3-7 agree well with quantum chemical calculations performed here and previously calculated binding enthalpies, as well as previous measurements for x=6. The present values for x=7-10 are slightly lower than previous experimental results and theory, but within experimental uncertainties.

  16. 铜微团簇结构及结合能的计算机模拟%Computer Simulation of the Structure and Binding Energy of Cu Micro-clusters

    Institute of Scientific and Technical Information of China (English)

    马兴科; 吕清正

    2011-01-01

    Copper cluster has many fantastic properties and is particularly interesting for their potential use in many processes like catalysis,nanotechnology and new electronic materials.Researches on the structures and binding energies of these clusters play significant roles in discussing their properties and applications.In this paper,through the study of the structures and binding energies of Cu micro-clusters(Cun(n=2,…,10)) under their stable state using the Gaussian03,based on the Density Functional Theory(DFT) and Relativistic Effective Core Potential(RECP) we find the binding energies of Cun(n=2,…,10) will increase with the increase of the value of n with rare exceptions.%铜团簇具有奇异的性质,在催化、纳米技术和大规模集成电路制造中有巨大的应用潜力.采用相对论有效原子实势模型(RECP),在密度泛函方法(DFT)下,使用Gaussian软件,研究了铜微团簇Cun(n=2,…,10)在稳态下的结构和结合能,得到了Cun(n=2,…1,0)的结合能和基态结构,发现随着n的增大,Cun(n=2,…,10)平均结合能会逐步微幅增加(极少数个体例外).

  17. Skeletal muscle metabolic characteristics before and after energy restriction in human obesity: fibre type, enzymatic beta-oxidative capacity and fatty acid-binding protein content.

    NARCIS (Netherlands)

    Kempen, K.P.G.; Saris, W.H.M.; Kuipers, H.; Glatz, J.F.; van der Vusse, G.J.

    1998-01-01

    University of Maastricht, Maastricht, The Netherlands. BACKGROUND: Skeletal muscle has the ability to adapt as result of dietary, hormonal or pharmacological interventions affecting energy metabolism. The aim of the present study was to investigate the effects of energy restriction on skeletal muscl

  18. Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis.

    Science.gov (United States)

    Zúñiga, Matías A; Alderete, Joel B; Jaña, Gonzalo A; Jiménez, Verónica A

    2017-07-01

    Peloruside A (PLA) and Laulimalide (LAU) are novel microtubule-stabilizing agents with promising properties against different cancer types. These ligands share a non-taxoid binding site at the outer surface of β-tubulin and promote microtubule stabilization by bridging two adjacent αβ-tubulin dimers from parallel protofilaments. Recent site-directed mutagenesis experiments confirmed the existence of a unique β-tubulin site mutation (Gln293Met) that specifically increased the activity of PLA and caused resistance to LAU, without affecting the stability of microtubules in the absence of the ligands. In this work, fully atomistic molecular dynamics simulations were carried out to examine the PLA and LAU association with native and mutated αβ-tubulin in the search for structural and energetic evidence to explain the role of Gln293Met mutation on determining the activity of these ligands. Our results revealed that Gln293Met mutation induced the loss of relevant LAU-tubulin contacts but exerted negligible changes in the interaction networks responsible for PLA-tubulin association. Binding free energy calculations (MM/GBSA and MM/PBSA), and weak interaction analysis (aNCI) predicted an increased affinity for PLA, and a weakened association for LAU after mutation, thus suggesting that Gln293Met mutation exerts its action by a modulation of drug-tubulin interactions. These results are valuable to increase understanding about PLA and LAU activity and to assist the future design of novel agents targeting the PLA/LAU binding pocket.

  19. Implications of a matter-radius measurement for the binding energy of, and existence of excited Efimov states in, Carbon-22

    CERN Document Server

    Acharya, B; Phillips, D R

    2013-01-01

    We study Borromean 2n-halo nuclei using effective field theory. We compute the universal scaling function that relates the mean-square matter radius of the 2n halo to dimensionless ratios of two- and three-body energies. We use the experimental value of the rms matter radius of 22C measured by Tanaka et al. to put constraints on its 2n separation energy and the 20C-n virtual energy. We also explore the consequences of these constraints for the existence of excited Efimov states in this nucleus. We find that, for 22C to have an rms matter radius within 1-sigma of the experimental value, the two-neutron separation energy of 22C needs to be below 100 keV. Consequently, this three-body halo system can have an excited Efimov state only if the 20C-n system has a resonance within 1 keV of the scattering threshold.

  20. Hydrostatic pressure effects on the {gamma}-X conduction band mixing and the binding energy of a donor impurity in GaAs-Ga{sub 1-x}Al{sub x}As quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Duque, C.A. [Instituto de Fisica, Universidad de Antioquia, AA 1226, Medellin (Colombia); Lopez, S.Y. [Facultad de Educacion, Universidad de Antioquia, AA 1226, Medellin (Colombia); Mora-Ramos, M.E. [Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Av. Universidad 1001, C.P. 62210, Cuernavaca (Mexico)

    2007-06-15

    Mixing between {gamma} and X valleys of the conduction band in GaAs-Ga{sub 1-x}Al{sub x}As quantum wells is investigated taken into account the effect of applied hydrostatic pressure. This effect is introduced via the pressure-dependent values of the corresponding energy gaps and the main band parameters. The mixing is considered along the lines of a phenomenological model. Variation of the confined ground state in the well as a function of the pressure is reported. The dependencies of the variationally calculated binding energy of a donor impurity with the hydrostatic pressure and well width are also presented. It is shown that the inclusion of the {gamma}-X mixing explains the non-linear behavior in the photoluminescence peak of confined exciton states that has been observed for pressures above 20 kbar. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  1. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    Energy Technology Data Exchange (ETDEWEB)

    Rocklin, Gabriel J. [Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550 (United States); Mobley, David L. [Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148 (United States); Dill, Ken A. [Laufer Center for Physical and Quantitative Biology, 5252 Stony Brook University, Stony Brook, New York 11794-0001 (United States); Hünenberger, Philippe H., E-mail: phil@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich (Switzerland)

    2013-11-14

    The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol{sup −1}) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non

  2. Potential performance analysis and future trend prediction of electric vehicle with V2G/V2H/V2B capability

    Directory of Open Access Journals (Sweden)

    Dalong Guo

    2016-03-01

    Full Text Available Due to the intermittent nature, renewable energy sources (RES has brought new challenges on load balancing and energy dispatching to the Smart Grid. Potentially served as distributed energy storage, Electric Vehicle’s (EV battery can be used as a way to help mitigate the pressure of fluctuation brought by RES and reinforce the stability of power systems. This paper gives a comprehensive review of the current situation of EV technology and mainly emphasizing three EV discharging operations which are Vehicle to Grid (V2G, Vehicle to Home (V2H, and Vehicle to Building (V2B, respectively. When needed, EV’s battery can discharge and send its surplus energy back to power grid, residential homes, or buildings. Based on our data analysis, we argue that V2G with the largest transmission power losses is potentially less efficient compared with the other two modes. We show that the residential users have the incentive to schedule the charging, V2G, and V2H according to the real-time price (RTP and the market sell-back price. In addition, we discuss some challenges and potential risks resulting from EVs’ fast growth. Finally we propose some suggestions on future power systems and also argue that some incentives or rewards need to be provided to motivate EV owners to behave in the best interests of the overall power systems.

  3. Nature of the high-binding-energy dip in the low-temperature photoemission spectra of Bi sub 2 Sr sub 2 CaCu sub 2 O sub 8+. delta

    Energy Technology Data Exchange (ETDEWEB)

    Dessau, D.S.; Shen, Z.; Wells, B.O.; King, D.M.; Spicer, W.E. (Stanford Electronics Laboratory, Stanford University, Stanford, California 94305 (United States)); Arko, A.J. (Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)); Lombardo, L.W.; Mitzi, D.B.; Kapitulnik, A. (Department of Applied Physics, Stanford University, Stanford, California 94305 (United States))

    1992-03-01

    At the transition to superconductivity, an anomalous high-binding-energy ({approx}{minus}90 meV) dip appears in the low-temperature photoemission spectra taken along the {Gamma}-{ital {bar M}} high-symmetry direction of Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}}. This paper details experiments which further characterize the energy and {bold k}-space dependence of this dip structure. The dip occurs over a wide portion of the {Gamma}-{ital {bar M}} zone diagonal (110), yet shows minimal energy dispersion. In the spectra taken along the {Gamma}-{ital X} zone edge (100), the dip is very weak or not present. We show that these results imply that the dip is not an artifact dependent on the experiment or special features of the band structure and therefore is an intrinsic feature of the superconducting state of Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}}. The behavior of the normal-state bands along {Gamma}-{ital {bar M}} in relation to the local-density-approximation prediction of a Bi-O-based electron pocket'' is also discussed, with our data explained most naturally if the Bi-O band remains above the Fermi level for all {bold k}.

  4. Positive binding energy of a biexciton confined in a localization center formed in a single InxGa1-xN/GaN quantum disk

    OpenAIRE

    Bardoux, R.; Kaneta, A.; Funato, M.; Kawakami, Y.; Kikuchi, A; Kishino, K.

    2009-01-01

    We report microphotoluminescence spectroscopy performed on individual and ensemble InGaN/GaN quantum disks (Q-disks). The typical spectrum of a single Q-disk exhibited the contribution of localization centers (LCs) formed in the InGaN active layer of the Q-disks, characterized by sharp lines appearing on the low energy side of the spectra. In addition, a broader emission peak identified as the luminescence of the quasi-two-dimensional (2D) InGaN active layer surrounding the LCs appears system...

  5. DFT study of NH{sub 3} adsorption on the (5,0), (8,0), (5,5) and (6,6) single-walled carbon nanotubes. Calculated binding energies, NMR and NQR parameters

    Energy Technology Data Exchange (ETDEWEB)

    Shirvani, Bahram B.; Beheshtian, Javad; Esrafili, Mehdi D. [Department of Chemistry, Tarbiat Modares University, P.O. Box: 14115-175, Tehran (Iran, Islamic Republic of); Hadipour, Nasser L., E-mail: hadipour@modares.ac.i [Department of Chemistry, Tarbiat Modares University, P.O. Box: 14115-175, Tehran (Iran, Islamic Republic of)

    2010-03-15

    Behavior of a single NH{sub 3} molecule adsorbed on external surface of H-capped (5,5), (6,6), (5,0), and (8,0) single-walled carbon nanotubes (SWCNTs) is studied via DFT calculations. Binding energies clearly exhibit adsorption dependence on tube diameter. {sup 13}C, {sup 15}N and {sup 1}H chemical shielding tensors are calculated at the B3LYP level using GIAO method. NMR calculations reveal that {sup 13}C chemical shielding of (8,0) is more sensitive to NH{sub 3} adsorption compared to (5,5), (6,6) and (5,0) tubes. {sup 15}N and {sup 1}H chemical shielding correlate noticeably with diameter of the nanotubes. {sup 14}N and {sup 2}H nuclear quadrupole coupling constants, C{sub Q}, and asymmetry parameter, eta, reveal the remarkable effect of NH{sub 3} adsorption on electronic structure of the SWCNTs.

  6. Molecular evolution and binding free energy analysis on substrates of KPC carbapenemases%KPC型碳青霉烯酶分子进化及与底物结合自由能分析

    Institute of Scientific and Technical Information of China (English)

    糜祖煌; 翁幸鐾; 秦玲

    2010-01-01

    目的 分析KPC-2、KPC-5和KPC-10型碳青霉烯酶的分子进化及与10种β-内酰胺类药物的结合自由能.方法 用MEGA 4.1软件中的Minimum Evolution法分析KPC-2、KPC-5和KPC-10型碳青霉烯酶的分子进化,用ArgusLab 4.1软件中的Dock模块作这3种酶与10种β-内酰胺类药物的分子对接,并计算酶与底物的结合自由能(△G).结果 有碳青霉烯酶活性的A类β-内酰胺酶在同一簇且保守性较好,无碳青霉烯酶活性的普通A类β-内酰胺酶则在另一簇.KPC-2、KPC-5和KPC-10型碳青霉烯酶与碳青霉烯类药物结合自由能均下降,且降幅居前,它们的结合自由能比第三代头孢类抗生素更低.结合自由能较高的为氨曲南和克拉维酸.结论 KPC型碳青霉烯酶对碳青霉烯类药物的催化能力高于对第三代头孢类抗生素的催化能力,对氨曲南和克拉维酸的催化活性最低.%Objective To analyze molecular evolution and binding free energies in substrates of KPC-2,KPC-5 and KPC-10 carbapenemases.Methods Minimum Evolution method in MEGA 4.1 was used to analyze molecular evolution of KPC-2,KPC-5 and KPC-10 carbapenemases,Dock module in ArgusLab 4.1 was used to perform molecular docking of these 3 carbapenemases to 10 kinds of β-lactams substrates,and calculate binding free energies(△G).Results Ambler Class A β-lactamases with carbapenemase activities were grouped in the same cluster and had good conservation,while ordinary Ambler Class A β-lactamases without carbapenemase activities were groupod in the other cluster.Binding free energies of KPC-2,KPC-5 and KPC-10 carbapenemases were lower to carbapenem antibiotics than the thirdgeneration cephalosporins,while binding free energies to aztreonam and clavulanic acid were of comparatively higher levels.Conclusion Catalytic activities of KPC to carbapenem antibiotics are higher than those to the third-generation cephalosporins,but the activities to aztreonam and clavulanic acid are low.

  7. Energies; Energies

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-07-01

    In the framework of the National Debate on the energies in a context of a sustainable development some associations for the environment organized a debate on the nuclear interest facing the renewable energies. The first part presents the nuclear energy as a possible solution to fight against the greenhouse effect and the associated problem of the wastes management. The second part gives information on the solar energy and the possibilities of heat and electric power production. A presentation of the FEE (French wind power association) on the situation and the development of the wind power in France, is also provided. (A.L.B.)

  8. Experimental and theoretical study of the structures and binding energies of eugenol (H2O)n, n=0-2

    Science.gov (United States)

    Longarte, Asier; Unamuno, Iñigo; Fernández, José A.; Castaño, Fernando; Redondo, Carolina

    2004-07-01

    Eugenol (4-Allyl-2-methoxyphenol), a phenol-derivative with an intramolecular -OH⋯OCH3 hydrogen bond (H bond), has been studied in a supersonic expansion using a number of complementary laser spectroscopic techniques. The mass-resolved excitation spectrum of eugenol and its water complexes are reported for the first time. The most intense set of bands on the resonantly enhanced multiphoton ionization (REMPI) spectrum of eugenol originate in a conformer whose S1←S0 transition is at 35 202 cm-1 and the ionization threshold at (I0←S0) 62 544±150 cm-1 (7.755±0.019 eV). In addition, two low intensity features redshifted with respect to the 000 transition have been identified as due to a second, less stable conformer. Ab initio calculations show that the potential energy landscape depicts at least three minima associated with one folded and two extended conformers, one of which is the most stable. Clusters of eugenol/water were prepared in a supersonic expansion by seeding eugenol and water in noble gas He and examined by two-color REMPI (R2PI) and IR-UV double resonance spectroscopies. Only one single isomer was observed for both 1:1 and 1:2 complexes, in contrast with the several stable conformers provided by the computations. The dissociation energies of the 1:1 and 1:2 complexes have been determined by the fragmentation threshold method and the results compared with those from ab initio calculations conducted at the B3LYP and MP2 levels with a variety of basis sets.

  9. Research of characteristics of medium response and H/V spectrum of surface wave on microtremor%微动面波的介质响应和H/V谱特征研究

    Institute of Scientific and Technical Information of China (English)

    杨奎; 梁北援; 刘澜波; 孙春岩

    2012-01-01

    At present, the main research method of surface wave on microtremor is the correlation analysis for the Rayleigh wave of surface wave. To be fully effective use of surface wave information and improve recognition accuracy,the principle of H/V spectrum of surface wave on microtremor is used in this paper. The medium response and H/V spectrum are obtained by computation given models, and the characteristics of medium response factor (MRF) and H/V spectrum of Rayleigh wave and Love wave are analyzed. The analysis results show the correspondence between MRF of surface wave on microtremor and formation interfaces of models. By comparing the H/V spectrum, the coherence of the main frequency of the Rayleigh wave and Love wave is found,and the use of love wave enhances the H/V spectrum. It is also pointed out that the problem to be solved of the H/V spectrum method in high frequency application field. Because this method uses surface wave information in microtremor without any special source,it is much more economic, faster and more widely applicable, and it will probably be a new kind of geological respecting methods with good application prospect.%目前,微动面波信息研究的主要方法是对面波中的Rayleigh波成分进行相关性分析.为了充分有效的利用面波信息和提高识别的准确度,本文基于微动面波H/V谱的基本原理,通过对给定模型的数值计算,得到了微动面波的介质响应曲线和H/V谱,分析了面波中Rayleigh波和Love波多模式波的介质响应和H/V谱特征.结果表明微动面波的介质响应特征与地层界面具有一定的对应关系,且在H/V谱中Rayleigh波和Love波的主频具有一致性,Love波的利用对H/V谱具有增强作用,文中也指出了H/V谱法在高频应用领域中有待进一步解决的问题.由于该方法使用的是地微动噪声中的面波信息,不需要专门的震源,因此具有经济快捷、应用范围广泛等优点,将可能成为一种新的有很

  10. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  11. ADC-57型头孢菌素酶分子进化及与底物结合自由能分析%Molecular evolution and binding free energy analysis of substrates of cephalosporinase ADC-57

    Institute of Scientific and Technical Information of China (English)

    周军; 王玉月; 张秋娣

    2012-01-01

    Objective To analyze molecular evolution and binding free energies of cephalosporinase ADC-57.Methods Minimum Evolution method in MEGA 5.0 was used to analyze molecular evolution of cephalosporinase ADC-57 and other 19 kinds of beta-lactamases.Tertiary structure of ADC-57 was predicted by homology modeling referring to tertiary structure of CMY-2.The molecular docking of ADC-57 to 11kinds of beta-lactams substrates was performed using DOCK module in ArgusLab 4.1and the binding free energies (△G) was calculated.Results ADC-57,CMY-2,DHA-1,ADC-7,ADC-56 were all belong to class C beta-lactamase,and molecular evolution between ADC-57 and ADC-56 was closest.The top three antibiotics with declining binding free energy of beta-lactams were ertapenem,cefoxitin and ceftazidine,while the last two were clavulanic acid and aztreonam.Conclusions Catalytic activities of cephalosporinase ADC-57 to ertapenem,cefoxitin and ceftazidine are high,while to clavulanic acid and aztreonam are low. Hydrolytic activities of enzyme to beta-lactams (substrates) can be analyzed by molecular docking.%目的 分析ADC-57型头孢菌素酶分子进化及其对各种底物的结合自由能.方法 用MEGA 5.0软件中的最小进化法分析ADC-57和其他19种β-内酰胺酶的分子进化,参照同类酶CMY-2型酶作同源建模获得ADC67型头孢菌素酶分子的3D结构,并用ArgusLab 4.1软件中的DOCK模块作ADC-57型头孢菌素酶与11种β-内酰胺类药物底物的分子对接,最后计算酶与底物的结合自由能值(△G).结果 ADC-57与CMY-2、DHA-1、ADC-7、ADC-56归属为C类β-内酰胺酶,均为头孢菌素酶,且与ADC-56关系最为密切.ADC-57与β-内酰胺类药物结合自由能下降居前3位的为厄他培南、头孢西丁和头孢他啶,结合自由能下降排在后2位的为克拉维酸和氨曲南.结论 ADC-57型头孢菌素酶对厄他培南、头孢西丁和头孢他啶的催化能力高,而对克拉维酸和氨曲南的催化能力低.分子对接

  12. An RNA motif that binds ATP

    Science.gov (United States)

    Sassanfar, M.; Szostak, J. W.

    1993-01-01

    RNAs that contain specific high-affinity binding sites for small molecule ligands immobilized on a solid support are present at a frequency of roughly one in 10(10)-10(11) in pools of random sequence RNA molecules. Here we describe a new in vitro selection procedure designed to ensure the isolation of RNAs that bind the ligand of interest in solution as well as on a solid support. We have used this method to isolate a remarkably small RNA motif that binds ATP, a substrate in numerous biological reactions and the universal biological high-energy intermediate. The selected ATP-binding RNAs contain a consensus sequence, embedded in a common secondary structure. The binding properties of ATP analogues and modified RNAs show that the binding interaction is characterized by a large number of close contacts between the ATP and RNA, and by a change in the conformation of the RNA.

  13. A model for positron binding to polar molecules

    CERN Document Server

    Gribakin, G F

    2015-01-01

    A model for positron binding to polar molecules is considered by combining the dipole potential outside the molecule with a strongly repulsive core of a given radius. Using existing experimental data on binding energies leads to unphysically small core radii for all of the molecules studied. This suggests that electron-positron correlations neglected in the simple model play a large role in determining the binding energy. We account for these by including polarization potential via perturbation theory. The improved model enables reliable predictions of binding energies to be made for a range of polar organic molecules and hydrogen cyanide, whose binding energy is known from accurate quantum chemistry calculations. The model explains the linear dependence of the binding energies on the polarizability inferred from the experimental data [Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 235203].

  14. Is there a link between selectivity and binding thermodynamics profiles?

    Science.gov (United States)

    Tarcsay, Ákos; Keserű, György M

    2015-01-01

    Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding.

  15. Membrane binding domains

    OpenAIRE

    Hurley, James H.

    2006-01-01

    Eukaryotic signaling and trafficking proteins are rich in modular domains that bind cell membranes. These binding events are tightly regulated in space and time. The structural, biochemical, and biophysical mechanisms for targeting have been worked out for many families of membrane binding domains. This review takes a comparative view of seven major classes of membrane binding domains, the C1, C2, PH, FYVE, PX, ENTH, and BAR domains. These domains use a combination of specific headgroup inter...

  16. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  17. Mediaeval manuscript bindings

    Directory of Open Access Journals (Sweden)

    Jedert Vodopivec

    1999-01-01

    Full Text Available The present article represents an excerpt from the final chapters of the research study titled "The development of structures in mediaeval manuscript bindings - interdependence with conservatory methods". In it, aims, methods of work, archive and library materials used and directions for conservatory methods are presented. Besides, the research study includes also a historcial overview of book bindings, detailed analysis of separate structural elements in Slovenian mediaeval bindings, comprehensive presentation of separate structures, the techniques of binding and materials of the preserved mediaeval bindings in Slovenian public archives and libraries, terminological dictionary of specific professional terms related to binding as a segment of a book, and a catalogue of all analysed bindings, containing a survey of ajI detectable data, sketches,graphite prints and photographs.

  18. Binding capacity: cooperativity and buffering in biopolymers.

    Science.gov (United States)

    Di Cera, E; Gill, S J; Wyman, J

    1988-01-01

    The group of linkage potentials resulting from the energy of a physicochemical system expressed per mol of a reference component, say a polyfunctional macromolecule, leads to the concept of binding capacity. This concept applies equally to both chemical and physical ligands and opens the way to consideration of higher-order linkage relationships. It provides a means of exploring the consequences of thermodynamic stability on generalized binding phenomena in biopolymers. PMID:3422436

  19. Theoretical studies of binding of mannose-binding protein to monosaccharides

    Science.gov (United States)

    Aida-Hyugaji, Sachiko; Takano, Keiko; Takada, Toshikazu; Hosoya, Haruo; Kojima, Naoya; Mizuochi, Tsuguo; Inoue, Yasushi

    2004-11-01

    Binding properties of mannose-binding protein (MBP) to monosaccharides are discussed based on ab initio molecular orbital calculations for cluster models constructed. The calculated binding energies indicate that MBP has an affinity for N-acetyl- D-glucosamine, D-mannose, L-fucose, and D-glucose rather than D-galactose and N-acetyl- D-galactosamine, which is consistent with the biochemical experimental results. Electrostatic potential surfaces at the binding site of four monosaccharides having binding properties matched well with that of MBP. A vacant frontier orbital was found to be localized around the binding site of MBP, suggesting that MBP-monosaccharide interaction may occur through electrostatic and orbital interactions.

  20. Ureaplasma urealyticum binds mannose-binding lectin.

    Science.gov (United States)

    Benstein, Barbara D; Ourth, Donald D; Crouse, Dennis T; Shanklin, D Radford

    2004-10-01

    Mannose-binding C-type lectin (MBL) is an important component of innate immunity in mammals. Mannose-binding lectin (MBL), an acute phase protein, acts as an opsonin for phagocytosis and also activates the mannan-binding lectin complement pathway. It may play a particularly significant role during infancy before adequate specific protection can be provided by the adaptive immune system. Ureaplasma urealyticum has been linked to several diseases including pneumonia and chronic lung disease (CLD) in premature infants. We therefore investigated the ability of U. urealyticum to bind MBL. A guinea pig IgG anti-rabbit-MBL antiserum was produced. An immunoblot (dot-blot) assay done on nitrocellulose membrane determined that the anti-MBL antibody had specificity against both rabbit and human MBL. Pure cultures of U. urealyticum, serotype 3, were used to make slide preparations. The slides containing the organisms were then incubated with nonimmune rabbit serum containing MBL. Ureaplasma was shown to bind rabbit MBL with an immunocytochemical assay using the guinea pig IgG anti-rabbit MBL antiserum. Horseradish peroxidase (HRP)-labeled anti-guinea pig IgG was used to localize the reaction. The anti-MBL antiserum was also used in an immunocytochemical assay to localize U. urealyticum in histological sections of lungs from mice specifically infected with this organism. The same method also indicated binding of MBL by ureaplasma in human lung tissue obtained at autopsy from culture positive infants. Our results demonstrate that ureaplasma has the capacity to bind MBL. The absence of MBL may play a role in the predisposition of diseases related to this organism.

  1. Ligand binding mechanics of maltose binding protein.

    Science.gov (United States)

    Bertz, Morten; Rief, Matthias

    2009-11-13

    In the past decade, single-molecule force spectroscopy has provided new insights into the key interactions stabilizing folded proteins. A few recent studies probing the effects of ligand binding on mechanical protein stability have come to quite different conclusions. While some proteins seem to be stabilized considerably by a bound ligand, others appear to be unaffected. Since force acts as a vector in space, it is conceivable that mechanical stabilization by ligand binding is dependent on the direction of force application. In this study, we vary the direction of the force to investigate the effect of ligand binding on the stability of maltose binding protein (MBP). MBP consists of two lobes connected by a hinge region that move from an open to a closed conformation when the ligand maltose binds. Previous mechanical experiments, where load was applied to the N and C termini, have demonstrated that MBP is built up of four building blocks (unfoldons) that sequentially detach from the folded structure. In this study, we design the pulling direction so that force application moves the two MBP lobes apart along the hinge axis. Mechanical unfolding in this geometry proceeds via an intermediate state whose boundaries coincide with previously reported MBP unfoldons. We find that in contrast to N-C-terminal pulling experiments, the mechanical stability of MBP is increased by ligand binding when load is applied to the two lobes and force breaks the protein-ligand interactions directly. Contour length measurements indicate that MBP is forced into an open conformation before unfolding even if ligand is bound. Using mutagenesis experiments, we demonstrate that the mechanical stabilization effect is due to only a few key interactions of the protein with its ligand. This work illustrates how varying the direction of the applied force allows revealing important details about the ligand binding mechanics of a large protein.

  2. Influence of different liquid-drop-based bindings on lighter mass fragments and entropy production

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Rohit; Shivani; Gautam, Sakshi [Panjab University, Department of Physics, Chandigarh (India)

    2016-04-15

    We study the production of lighter fragments and associated phenomena within the Quantum Molecular Dynamics (QMD) model. The Minimum Spanning Tree (MST) method is used to identify the pre-clusters. The final stable fragments were identified by imposing binding energy criteria on the fragments formed using the MST method. The effect of different binding energy criteria was investigated by employing various liquid-drop-based binding energy formulae. Though light clusters show significant effect of different binding energies, their associated phenomenon, i.e. entropy production is insensitive towards different binding energy criteria. (orig.)

  3. Protein Binding Pocket Dynamics.

    Science.gov (United States)

    Stank, Antonia; Kokh, Daria B; Fuller, Jonathan C; Wade, Rebecca C

    2016-05-17

    The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five

  4. Isothermal titration calorimetry: general formalism using binding polynomials.

    Science.gov (United States)

    Freire, Ernesto; Schön, Arne; Velazquez-Campoy, Adrian

    2009-01-01

    The theory of the binding polynomial constitutes a very powerful formalism by which many experimental biological systems involving ligand binding can be analyzed under a unified framework. The analysis of isothermal titration calorimetry (ITC) data for systems possessing more than one binding site has been cumbersome because it required the user to develop a binding model to fit the data. Furthermore, in many instances, different binding models give rise to identical binding isotherms, making it impossible to discriminate binding mechanisms using binding data alone. One of the main advantages of the binding polynomials is that experimental data can be analyzed by employing a general model-free methodology that provides essential information about the system behavior (e.g., whether there exists binding cooperativity, whether the cooperativity is positive or negative, and the magnitude of the cooperative energy). Data analysis utilizing binding polynomials yields a set of binding association constants and enthalpy values that conserve their validity after the correct model has been determined. In fact, once the correct model is validated, the binding polynomial parameters can be immediately translated into the model specific constants. In this chapter, we describe the general binding polynomial formalism and provide specific theoretical and experimental examples of its application to isothermal titration calorimetry.

  5. Python bindings for libcloudph++

    OpenAIRE

    Jarecka, Dorota; Arabas, Sylwester; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python ...

  6. DNS & Bind Cookbook

    CERN Document Server

    Liu, Cricket

    2011-01-01

    The DNS & BIND Cookbook presents solutions to the many problems faced by network administrators responsible for a name server. Following O'Reilly's popular problem-and-solution cookbook format, this title is an indispensable companion to DNS & BIND, 4th Edition, the definitive guide to the critical task of name server administration. The cookbook contains dozens of code recipes showing solutions to everyday problems, ranging from simple questions, like, "How do I get BIND?" to more advanced topics like providing name service for IPv6 addresses. It's full of BIND configuration files that yo

  7. Python bindings for libcloudph++

    CERN Document Server

    Jarecka, Dorota; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python bindings to access libcloudph++ from Fortran is presented.

  8. On Binding Domains

    NARCIS (Netherlands)

    Everaert, M.B.H.

    2005-01-01

    In this paper I want to explore reasons for replacing Binding Theory based on the anaphor-pronoun dichotomy by a Binding Theory allowing more domains restricting/defining anaphoric dependencies. This will, thus, have consequences for the partitioning of anaphoric elements, presupposing more types of

  9. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  10. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  11. Asymmetry of calmodulin revealed by peptide binding.

    Science.gov (United States)

    Leclerc, E; Leclerc, L; Marden, M C

    1993-03-01

    The binding of amphiphilic peptides to calmodulin has been studied using fluorescence energy transfer techniques. Calmodulin has no tryptophan residues but possesses two tyrosines (at positions 99 and 138) in the C-terminal half of the protein. The peptides have a single tryptophan which serves as energy acceptor for the protein tyrosine fluorescence. For the binding of mastoparan or peptide Baa17, with a tryptophan at position 3, the observed quenching of the tyrosine fluorescence of over a factor of 2 corresponds to an average tyrosine-trytophan distance of less than 14 Å. These results indicate that the peptides binds preferentially with the tryptophan in the C-terminal half of the protein.

  12. SHBG (Sex Hormone Binding Globulin)

    Science.gov (United States)

    ... as: Testosterone-estrogen Binding Globulin; TeBG Formal name: Sex Hormone Binding Globulin Related tests: Testosterone , Free Testosterone, ... I should know? How is it used? The sex hormone binding globulin (SHBG) test may be used ...

  13. The Elastic Continuum Limit of the Tight Binding Model

    Institute of Scientific and Technical Information of China (English)

    Weinan E; Jianfeng LU

    2007-01-01

    The authors consider the simplest quantum mechanics model of solids, the tight binding model, and prove that in the continuum limit, the energy of tight binding model converges to that of the continuum elasticity model obtained using Cauchy-Born rule. Thet echnique in this paper is based mainly on spectral perturbation theory for large matrices.

  14. Computational search for aflatoxin binding proteins

    Science.gov (United States)

    Wang, Ying; Liu, Jinfeng; Zhang, Lujia; He, Xiao; Zhang, John Z. H.

    2017-10-01

    Aflatoxin is one of the mycotoxins that contaminate various food products. Among various aflatoxin types (B1, B2, G1, G2 and M1), aflatoxin B1 is the most important and the most toxic one. In this study, through computational screening, we found that several proteins may bind specifically with different type of aflatoxins. Combination of theoretical methods including target fishing, molecular docking, molecular dynamics (MD) simulation, MM/PBSA calculation were utilized to search for new aflatoxin B1 binding proteins. A recently developed method for calculating entropic contribution to binding free energy called interaction entropy (IE) was employed to compute the binding free energy between the protein and aflatoxin B1. Through comprehensive comparison, three proteins, namely, trihydroxynaphthalene reductase, GSK-3b, and Pim-1 were eventually selected as potent aflatoxin B1 binding proteins. GSK-3b and Pim-1 are drug targets of cancers or neurological diseases. GSK-3b is the strongest binder for aflatoxin B1.

  15. Study of the influence of chemical binding on resonant absorption and scattering of neutrons; Etude de l'influence des liaisons chimiques sur l'absorption et la diffusion des neutrons aux energies de resonance

    Energy Technology Data Exchange (ETDEWEB)

    Naberejnev, D.G. [Aix-Marseille-1 Univ., 13 - Marseille (France)

    1999-02-01

    At present time the problem of taking into account of the crystalline binding in the heavy nuclei resonance range is not correctly treated in nuclear data processing codes. The present work deals separately with resonant absorption and scattering of neutrons. The influence of crystalline binding is considered for both types of reactions in the harmonic crystal frame work. The harmonic crystal model is applied to the study of resonant absorption cross sections to show the inconsistency of the free gas model widely in use in reactor neutronics. The errors due to the use of the latter were found to be non negligible. These errors should be corrected by introducing a more elaborated harmonic crystal model in codes for resonances analysis and on the nuclear data processing stage. Currently the influence of crystalline binding on transfer cross section in the resonance domain is taken into account in a naive manner using the model of the free nucleus at rest in the laboratory system. In this work I present a formalism (Uncoupled Phonon Approximation) which permits to consider in more detail the crystalline structure of the nuclear fuel. This formalism shows new features in comparison with the static model. (author)

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

    Science.gov (United States)

    Miliordos, Evangelos; Xantheas, Sotiris S

    2015-06-21

    We report MP2 and Coupled Cluster Singles, Doubles, and perturbative Triples [CCSD(T)] binding energies with basis sets up to pentuple zeta quality for the (H2O)m=2-6,8 water clusters. Our best CCSD(T)/Complete Basis Set (CBS) estimates are -4.99 ± 0.04 kcal/mol (dimer), -15.8 ± 0.1 kcal/mol (trimer), -27.4 ± 0.1 kcal/mol (tetramer), -35.9 ± 0.3 kcal/mol (pentamer), -46.2 ± 0.3 kcal/mol (prism hexamer), -45.9 ± 0.3 kcal/mol (cage hexamer), -45.4 ± 0.3 kcal/mol (book hexamer), -44.3 ± 0.3 kcal/mol (ring hexamer), -73.0 ± 0.5 kcal/mol (D2d octamer), and -72.9 ± 0.5 kcal/mol (S4 octamer). We have found that the percentage of both the uncorrected (De) and basis set superposition error-corrected (De (CP)) binding energies recovered with respect to the CBS limit falls into a narrow range on either sides of the CBS limit for each basis set for all clusters. In addition, this range decreases upon increasing the basis set. Relatively accurate estimates (within set) or the "12, 12" (for the AVTZ, AVQZ, and AV5Z sets) mixing ratio between De and De (CP). These mixing rations are determined via a least-mean-squares approach from a dataset that encompasses clusters of various sizes. Based on those findings, we propose an accurate and efficient computational protocol that can be presently used to estimate accurate binding energies of water clusters containing up to 30 molecules (for CCSD(T)) and up to 100 molecules (for MP2).

  17. Tension-induced binding of semiflexible biopolymers

    CERN Document Server

    Benetatos, Panayotis; Zippelius, Annette

    2014-01-01

    We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with a sequence of inter-chain binding sites regularly spaced along the contours. Reversible cross-links attach and detach at the sites with an affinity controlled by a chemical potential. In a mean-field approach, we calculate the free energy of the system and find the emergence of a free-energy barrier which controls the reversible (un)binding. The tension affects the conformational entropy of the chains which competes with the binding energy of the cross-links. This competition gives rise to a sudden increase in the fraction of bound sites as the tension increases. We show that this transition is related to the cross-over between weak and strong localization of a directed polymer in a pinning potential. The cross-over to the strongly bound state can be interpreted as a mechan...

  18. A statistical mechanics handbook for protein-ligand binding simulation.

    Science.gov (United States)

    Rocchia, Walter; Bonella, Sara

    2013-01-01

    In this work, the fundamental elements of statistical mechanics underlying the simulation of the protein-ligand binding process, such as statistical ensembles and the concept of microscopic estimators of macroscopic observables and free energy, are summarized in a self consistent fashion. Particular attention is then devoted to the introduction of some mathematical tools that are used in atomistic simulations aimed at estimating binding affinities and free energy profiles, and to the illustration of the origins of the difficulties encountered in this endeavor.

  19. CARBOHYDRATE-CONTAINING COMPOUNDS WHICH BIND TO CARBOHYDRATE BINDING RECEPTORS

    DEFF Research Database (Denmark)

    1995-01-01

    Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases.......Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases....

  20. Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin.

    Science.gov (United States)

    Zhang, Zhisen; Santos, Andrew P; Zhou, Qing; Liang, Lijun; Wang, Qi; Wu, Tao; Franzen, Stefan

    2016-04-01

    The binding free energy of 4-bromophenol (4-BP), an inhibitor that binds in the internal binding site in dehaloperoxidase-hemoglobin (DHP) was calculated using Molecular Dynamics (MD) methods combined with pulling or umbrella sampling. The effects of systematic changes in the pulling speed, pulling force constant and restraint force constant on the calculated potential of mean force (PMF) are presented in this study. The PMFs calculated using steered molecular dynamics (SMD) were validated by umbrella sampling (US) in the strongly restrained regime. A series of restraint force constants ranging from 1000 down to 5 kJ/(mol nm(2)) were used in SMD simulations. This range was validated using US, however noting that weaker restraints give rise to a broader sampling of configurations. This comparison was further tested by a pulling simulation conducted without any restraints, which was observed to have a value closest to the experimentally measured free energy for binding of 4-BP to DHP based on ultraviolet-visible (UV-vis) and resonance Raman spectroscopies. The protein-inhibitor system is well suited for fundamental study of free energy calculations because the DHP protein is relatively small and the inhibitor is quite rigid. Simulation configuration structures are compared to the X-ray crystallography structures of the binding site of 4-BP in the distal pocket above the heme.

  1. Relating the shape of protein binding sites to binding affinity profiles: is there an association?

    Directory of Open Access Journals (Sweden)

    Bitter István

    2010-10-01

    Full Text Available Abstract Background Various pattern-based methods exist that use in vitro or in silico affinity profiles for classification and functional examination of proteins. Nevertheless, the connection between the protein affinity profiles and the structural characteristics of the binding sites is still unclear. Our aim was to investigate the association between virtual drug screening results (calculated binding free energy values and the geometry of protein binding sites. Molecular Affinity Fingerprints (MAFs were determined for 154 proteins based on their molecular docking energy results for 1,255 FDA-approved drugs. Protein binding site geometries were characterized by 420 PocketPicker descriptors. The basic underlying component structure of MAFs and binding site geometries, respectively, were examined by principal component analysis; association between principal components extracted from these two sets of variables was then investigated by canonical correlation and redundancy analyses. Results PCA analysis of the MAF variables provided 30 factors which explained 71.4% of the total variance of the energy values while 13 factors were obtained from the PocketPicker descriptors which cumulatively explained 94.1% of the total variance. Canonical correlation analysis resulted in 3 statistically significant canonical factor pairs with correlation values of 0.87, 0.84 and 0.77, respectively. Redundancy analysis indicated that PocketPicker descriptor factors explain 6.9% of the variance of the MAF factor set while MAF factors explain 15.9% of the total variance of PocketPicker descriptor factors. Based on the salient structures of the factor pairs, we identified a clear-cut association between the shape and bulkiness of the drug molecules and the protein binding site descriptors. Conclusions This is the first study to investigate complex multivariate associations between affinity profiles and the geometric properties of protein binding sites. We found that

  2. Defining Starch Binding by Glucan Phosphatases

    DEFF Research Database (Denmark)

    Auger, Kyle; Raththagala, Madushi; Wilkens, Casper;

    2015-01-01

    Starch is a vital energy molecule in plants that has a wide variety of uses in industry, such as feedstock for biomaterial processing and biofuel production. Plants employ a three enzyme cyclic process utilizing kinases, amylases, and phosphatases to degrade starch in a diurnal manner. Starch...... is comprised of the branched glucan amylopectin and the more linear glucan amylose. Our lab has determined the first structures of these glucan phosphatases and we have defined their enzymatic action. Despite this progress, we lacked a means to quickly and efficiently quantify starch binding to glucan...... phosphatases. The main objective of this study was to quantify the binding affinity of different enzymes that are involved in this cyclic process. We established a protocol to quickly, reproducibly, and quantitatively measure the binding of the enzymes to glucans utilizing Affinity Gel Electrophoresis (AGE...

  3. Terms of Binding

    NARCIS (Netherlands)

    Sevcenco, A.

    2006-01-01

    The present dissertation aimed at achieving two goals. First, it constitutes an attempt to widen the search for phenomena that bear relevance to the idea that binding has a syntactic residue and is not, therefore, an exclusively semantic matter. Second, it tried to provide the technical means to acc

  4. Cellulose binding domain proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  5. MD-2 binds cholesterol.

    Science.gov (United States)

    Choi, Soo-Ho; Kim, Jungsu; Gonen, Ayelet; Viriyakosol, Suganya; Miller, Yury I

    2016-02-19

    Cholesterol is a structural component of cellular membranes, which is transported from liver to peripheral cells in the form of cholesterol esters (CE), residing in the hydrophobic core of low-density lipoprotein. Oxidized CE (OxCE) is often found in plasma and in atherosclerotic lesions of subjects with cardiovascular disease. Our earlier studies have demonstrated that OxCE activates inflammatory responses in macrophages via toll-like receptor-4 (TLR4). Here we demonstrate that cholesterol binds to myeloid differentiation-2 (MD-2), a TLR4 ancillary molecule, which is a binding receptor for bacterial lipopolysaccharide (LPS) and is indispensable for LPS-induced TLR4 dimerization and signaling. Cholesterol binding to MD-2 was competed by LPS and by OxCE-modified BSA. Furthermore, soluble MD-2 in human plasma and MD-2 in mouse atherosclerotic lesions carried cholesterol, the finding supporting the biological significance of MD-2 cholesterol binding. These results help understand the molecular basis of TLR4 activation by OxCE and mechanisms of chronic inflammation in atherosclerosis.

  6. Binding and Bulgarian

    NARCIS (Netherlands)

    Schürcks-Grozeva, Lilia Lubomirova

    2003-01-01

    In haar proefschrift analyseert Lilia Schürcks de anaforische verschijnselen in de Bulgaarse taal. Het gaat dan om wederkerende aspecten, uitgedrukt bij woorden als ‘zich’ en ‘elkaar’. De situatie in het Bulgaars blijkt moeilijk in te passen in de klassieke Binding Theory van Noam Chomsky. Bron: RUG

  7. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  8. Chiral morphology of calcite through selective binding of amino acids

    Science.gov (United States)

    Orme, Christine

    2002-03-01

    Many living organisms contain biominerals and composites with finely tuned properties, reflecting a remarkable level of control over the nucleation, growth and shape of the constituent crystals. Peptides and proteins play an important role in achieving this control. Using in situ AFM we find that site-specific binding of amino acid residues to surface steps changes the step-edge free energies, giving rise to direction-specific binding energies unique to individual amino acid enantiomers and leading to chiral modifications that propagate from atomic length scales to macroscopic length scales. Molecular modeling studies support an energetic basis for the differences in binding. Our results emphasize that the mechanism under-lying crystal modification through organic molecules is best understood by considering both stereochemical recognition as well as the effects of binding on the interfacial energies of the growing crystal.

  9. Megalin binds and mediates cellular internalization of folate binding protein

    DEFF Research Database (Denmark)

    Birn, Henrik; Zhai, Xiaoyue; Holm, Jan

    2005-01-01

    Folate is an essential vitamin involved in a number of biological processes. High affinity folate binding proteins (FBPs) exist both as glycosylphosphatidylinositol-linked, membrane associated folate binding proteins and as soluble FBPs in plasma and some secretory fluids such as milk, saliva...... to bind and mediate cellular uptake of FBP. Surface plasmon resonance analysis shows binding of bovine and human milk FBP to immobilized megalin, but not to low density lipoprotein receptor related protein. Binding of (125)I-labeled folate binding protein (FBP) to sections of kidney proximal tubule, known...

  10. Essential mechanisms in the triton binding

    Energy Technology Data Exchange (ETDEWEB)

    Brandenburg, R.A.; Chulick, G.S.; Machleidt, R.; Picklesimer, A.; Thaler, R.M.

    1988-03-01

    The recent successful prediction of the triton binding energy, E/sub t/, with the static Bonn potential is examined. Modified versions of the potential are introduced to isolate separately the effects of the deuteron D-state admixture and the /sup 1/S/sub 0/ scattering length on E/sub t/. Within this model study we find a monotonic relation between E/sub t/ and the /sup 1/S/sub 0/ scattering length and a strict linear dependence of E/sub t/ on the D-state admixture, in accordance with general well-known trends and earlier separable-potential model studies. The mechanism through which the weaker tensor force (lower D-state admixture) leads to a stronger binding of the triton is investigated by the introduction and study of effective energy-dependent central potentials

  11. Different thermodynamic signatures for DNA minor groove binding with changes in salt concentration and temperature.

    Science.gov (United States)

    Wang, Shuo; Kumar, Arvind; Aston, Karl; Nguyen, Binh; Bashkin, James K; Boykin, David W; Wilson, W David

    2013-10-04

    The effects of salt concentration and temperature on the thermodynamics of DNA minor groove binding have quite different signatures: binding enthalpy is salt concentration independent but temperature dependent. Conversely, binding free energy is salt dependent but essentially temperature independent through enthalpy-entropy compensation.

  12. Different Thermodynamic Signatures for DNA Minor Groove Binding with Changes in Salt Concentration and Temperature

    OpenAIRE

    2013-01-01

    The effects of salt concentration and temperature on the thermodynamics of DNA minor groove binding have quite different signatures: binding enthalpy is salt concentration independent but temperature dependent. Conversely, binding free energy is salt dependent but essentially temperature independent through enthalpy-entropy compensation.

  13. Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase

    Science.gov (United States)

    Tran, Diem-Trang T.; Le, Ly T.; Truong, Thanh N.

    2013-08-01

    Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called "pathway docking" in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.

  14. Ethylene binding to Au/Cu alloy nanoparticles

    Science.gov (United States)

    Gammage, Michael D.; Stauffer, Shannon; Henkelman, Graeme; Becker, Michael F.; Keto, John W.; Kovar, Desiderio

    2016-11-01

    Weak chemisorption of ethylene has been shown to be an important characteristic in the use of metals for the separation of ethylene from ethane. Previously, density functional theory (DFT) has been used to predict the binding energies of various metals and alloys, with Ag having the lowest chemisorption energy amongst the metals and alloys studied. Here Au/Cu alloys are investigated by a combination of DFT calculations and experimental measurements. It is inferred from experiments that the binding energy between a Au/Cu alloy and ethylene is lower than to either of the pure metals, and DFT calculations confirm that this is the case when Au segregates to the particle surface. Implications of this work suggest that it may be possible to further tune the binding energy with ethylene by compositional and morphological control of films produced from Au-surface segregated alloys.

  15. Correlation between catalytic activity of supported gold catalysts for carbon monoxide oxidation and metal-oxygen binding energy of the support metal oxides%负载金催化剂上CO氧化反应活性与金属氧化物载体中金属-氧结合能之间的关系

    Institute of Scientific and Technical Information of China (English)

    Takashi Fujita; Masanori Horikawa; Takashi Takei; Toru Murayama; Masatake Haruta

    2016-01-01

    The effect of a wide variety of metal oxide (MOx) supports has been discussed for CO oxidation on nanoparticulate gold catalysts. By using typical co‐precipitation and deposition–precipitation methods and under identical calcination conditions, supported gold catalysts were prepared on a wide variety of MOx supports, and the temperature for 50%conversion was measured to qualita‐tively evaluate the catalytic activities of these simple MOx and supported Au catalysts. Furthermore, the difference in these temperatures for the simple MOx compared to the supported Au catalysts is plotted against the metal–oxygen binding energies of the support MOx. A clear volcano‐like correla‐tion between the temperature difference and the metal–oxygen binding energies is observed. This correlation suggests that the use of MOx with appropriate metal–oxygen binding energies (300–500 kJ/atom O) greatly improves the catalytic activity of MOx by the deposition of Au NPs.%讨论了金属氧化物载体(MOx)对其负载纳米金催化剂(Au/MOx)上CO氧化反应的影响。采用典型的共沉淀法和沉积-沉淀法在完全相同的焙烧条件下制备了一系列MOx负载金催化剂,以CO氧化转化50%时的反应温度(T1/2)定量评价了MOx载体和Au/MOx催化剂的催化活性。进一步将MOx载体与相应Au/MOx催化剂的T1/2值之差对MOx载体的金属-氧结合能做曲线进行关联,发现二者呈明显的火山型关系。这一结果表明,采用具有适当金属-氧结合能(300–500 atom O)的MOx可大大提高沉积于其上的Au纳米颗粒的催化活性。

  16. Binding Principles A and B

    Institute of Scientific and Technical Information of China (English)

    陈源

    2014-01-01

    This paper focuses on the discussion of how Binding Principle A and Binding Principe B help with the interpretation of reference in English and Chinese. They are supposedly universal across languages.

  17. Carboplatin binding to histidine

    Energy Technology Data Exchange (ETDEWEB)

    Tanley, Simon W. M. [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom); Diederichs, Kay [University of Konstanz, D-78457 Konstanz (Germany); Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Levy, Colin [University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Schreurs, Antoine M. M. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Helliwell, John R., E-mail: john.helliwell@manchester.ac.uk [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom)

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  18. Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

    Directory of Open Access Journals (Sweden)

    Huiying Zhao

    Full Text Available As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions. A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC of 0.77 with high precision (94% and high sensitivity (65%. We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA] is available as an on-line server at http://sparks-lab.org.

  19. Roles of multiple surface sites, long substrate binding clefts, and carbohydrate binding modules in the action of amylolytic enzymes on polysaccharide substrates

    DEFF Research Database (Denmark)

    Nielsen, Morten Munch; Seo, E.S.; Dilokpimol, Adiphol

    2008-01-01

    with a characteristic subsite binding energy profile around the catalytic site. Furthermore, several amylolytic enzymes that facilitate attack on the natural substrate, i.e. the endosperm starch granules, have secondary sugar binding sites either situated on the surface of the protein domain or structural unit...... that contains the catalytic site or belonging to a separate starch binding domain. The role of surface sites in the function of barley alpha-amylase 1 has been investigated by using mutational analysis in conjunction with carbohydrate binding analyses and crystallography. The ability to bind starch depends...

  20. Highly selective ligand binding by Methylophilus methylotrophus cytochrome c''.

    Science.gov (United States)

    Quintas, Pedro O; Catarino, Teresa; Todorovic, Smilja; Turner, David L

    2011-06-28

    Cytochrome c'' (cyt c'') from Methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. Despite cyt c'' having an axial site available for binding small ligands, we show here that only NO binds readily to the ferrous cyt c''. Binding of CO, as well as CN(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. Standard free energies for the binding of NO and CO reveal high selectivity of the ferrous cyt c'' for NO, indicating its putative physiological role. In this work, we characterize in detail the kinetics of NO binding and the structural features of the Fe(2+)-NO adduct by stopped-flow and resonance Raman spectroscopy, respectively.